6yva Citations

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.

Abstract

The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses3-5. Here we perform biochemical, structural and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.

Reviews - 6yva mentioned but not cited (6)

  1. Structural Characterization of SARS-CoV-2: Where We Are, and Where We Need to Be. Mariano G, Farthing RJ, Lale-Farjat SLM, Bergeron JRC. Front Mol Biosci 7 605236 (2020)
  2. A Comprehensive Review about the Molecular Structure of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Insights into Natural Products against COVID-19. Saied EM, El-Maradny YA, Osman AA, Darwish AMG, Abo Nahas HH, Niedbała G, Piekutowska M, Abdel-Rahman MA, Balbool BA, Abdel-Azeem AM. Pharmaceutics 13 1759 (2021)
  3. Inhibitors of SARS-CoV-2 PLpro. Calleja DJ, Lessene G, Komander D. Front Chem 10 876212 (2022)
  4. An Overview of the Crystallized Structures of the SARS-CoV-2. Ionescu MI. Protein J 39 600-618 (2020)
  5. Genomics insights of SARS-CoV-2 (COVID-19) into target-based drug discovery. Chellapandi P, Saranya S. Med Chem Res 29 1777-1791 (2020)
  6. Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone. Jiang H, Yang P, Zhang J. Front Chem 10 822785 (2022)

Articles - 6yva mentioned but not cited (28)

  1. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I. Nature 587 657-662 (2020)
  2. ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. Liu G, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. Nat Microbiol 6 467-478 (2021)
  3. The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery. Fu Z, Huang B, Tang J, Liu S, Liu M, Ye Y, Liu Z, Xiong Y, Zhu W, Cao D, Li J, Niu X, Zhou H, Zhao YJ, Zhang G, Huang H. Nat Commun 12 488 (2021)
  4. Design of SARS-CoV-2 PLpro Inhibitors for COVID-19 Antiviral Therapy Leveraging Binding Cooperativity. Shen Z, Ratia K, Cooper L, Kong D, Lee H, Kwon Y, Li Y, Alqarni S, Huang F, Dubrovskyi O, Rong L, Thatcher GRJ, Xiong R. J Med Chem 65 2940-2955 (2022)
  5. Development of potent and selective inhibitors targeting the papain-like protease of SARS-CoV-2. Shan H, Liu J, Shen J, Dai J, Xu G, Lu K, Han C, Wang Y, Xu X, Tong Y, Xiang H, Ai Z, Zhuang G, Hu J, Zhang Z, Li Y, Pan L, Tan L. Cell Chem Biol 28 855-865.e9 (2021)
  6. Supporting SARS-CoV-2 Papain-Like Protease Drug Discovery: In silico Methods and Benchmarking. Ibrahim TM, Ismail MI, Bauer MR, Bekhit AA, Boeckler FM. Front Chem 8 592289 (2020)
  7. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz-Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Proteins 90 1054-1080 (2022)
  8. A molecular sensor determines the ubiquitin substrate specificity of SARS-CoV-2 papain-like protease. Patchett S, Lv Z, Rut W, Békés M, Drag M, Olsen SK, Huang TT. Cell Rep 36 109754 (2021)
  9. Repurposing clinically approved drugs for COVID-19 treatment targeting SARS-CoV-2 papain-like protease. Xu Y, Chen K, Pan J, Lei Y, Zhang D, Fang L, Tang J, Chen X, Ma Y, Zheng Y, Zhang B, Zhou Y, Zhan J, Xu W. Int J Biol Macromol 188 137-146 (2021)
  10. SARS-CoV-2 Papain-Like Protease Potential Inhibitors-In Silico Quantitative Assessment. Stasiulewicz A, Maksymiuk AW, Nguyen ML, Bełza B, Sulkowska JI. Int J Mol Sci 22 3957 (2021)
  11. Design and Evaluation of a Novel Peptide-Drug Conjugate Covalently Targeting SARS-CoV-2 Papain-like Protease. Liu N, Zhang Y, Lei Y, Wang R, Zhan M, Liu J, An Y, Zhou Y, Zhan J, Yin F, Li Z. J Med Chem 65 876-884 (2022)
  12. Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study. Ismail MI, Ragab HM, Bekhit AA, Ibrahim TM. Comput Biol Med 131 104295 (2021)
  13. The SARS-CoV-2 SSHHPS Recognized by the Papain-like Protease. Reynolds ND, Aceves NM, Liu JL, Compton JR, Leary DH, Freitas BT, Pegan SD, Doctor KZ, Wu FY, Hu X, Legler PM. ACS Infect Dis 7 1483-1502 (2021)
  14. In silico Exploration of Inhibitors for SARS-CoV-2's Papain-Like Protease. Huynh T, Cornell W, Luan B. Front Chem 8 624163 (2020)
  15. Targeting papain-like protease for broad-spectrum coronavirus inhibition. Yuan S, Gao X, Tang K, Cai JP, Hu M, Luo P, Wen L, Ye ZW, Luo C, Tsang JO, Chan CC, Huang Y, Cao J, Liang R, Qin Z, Qin B, Yin F, Chu H, Jin DY, Sun R, Chan JF, Cui S, Yuen KY. Protein Cell 13 940-953 (2022)
  16. Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Wydorski PM, Osipiuk J, Lanham BT, Tesar C, Endres M, Engle E, Jedrzejczak R, Mullapudi V, Michalska K, Fidelis K, Fushman D, Joachimiak A, Joachimiak LA. Nat Commun 14 2366 (2023)
  17. Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein. Leite WC, Weiss KL, Phillips G, Zhang Q, Qian S, Tsutakawa SE, Coates L, O'Neill H. J Phys Chem Lett 12 5608-5615 (2021)
  18. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Commun Biol 5 805 (2022)
  19. Synthesis, spectroscopy, crystal structure, TGA/DTA study, DFT and molecular docking investigations of (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one. Kalai FE, Çınar EB, Lai CH, Daoui S, Chelfi T, Allali M, Dege N, Karrouchi K, Benchat N. J Mol Struct 1228 129435 (2021)
  20. Ubiquitin variants potently inhibit SARS-CoV-2 PLpro and viral replication via a novel site distal to the protease active site. van Vliet VJE, Huynh N, Palà J, Patel A, Singer A, Slater C, Chung J, van Huizen M, Teyra J, Miersch S, Luu GK, Ye W, Sharma N, Ganaie SS, Russell R, Chen C, Maynard M, Amarasinghe GK, Mark BL, Kikkert M, Sidhu SS. PLoS Pathog 18 e1011065 (2022)
  21. High-throughput screening of SARS-CoV-2 main and papain-like protease inhibitors. Zang Y, Su M, Wang Q, Cheng X, Zhang W, Zhao Y, Chen T, Jiang Y, Shen Q, Du J, Tan Q, Wang P, Gao L, Jin Z, Zhang M, Li C, Zhu Y, Feng B, Tang B, Xie H, Wang MW, Zheng M, Pan X, Yang H, Xu Y, Wu B, Zhang L, Rao Z, Yang X, Jiang H, Xiao G, Zhao Q, Li J. Protein Cell 14 17-27 (2023)
  22. Production of Proteins of the SARS-CoV-2 Proteome for Drug Discovery. Kim C, Mahasenan KV, Bhardwaj A, Wiest O, Chang M, Mobashery S. ACS Omega 6 19983-19994 (2021)
  23. Rapid response to emerging biomedical challenges and threats. Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W. IUCrJ 8 395-407 (2021)
  24. research-article ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease. Liu G, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. bioRxiv 2020.10.26.356048 (2020)
  25. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Chem Sci 14 4681-4696 (2023)
  26. β-catenin ISGylation promotes lipid deposition and apoptosis in ethanol-stimulated liver injury models. Ding Q, Zhang G, Wang Y, Xu L, Wu M, Zhou Y, Xu T, Meng X, Huang C, Zhang L. Redox Rep 27 239-248 (2022)
  27. research-article Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin. Wydorski PM, Osipiuk J, Lanham BT, Tesar C, Endres M, Engle E, Jedrzejczak R, Mullapudi V, Michalska K, Fidelis K, Fushman D, Joachimiak A, Joachimiak LA. bioRxiv 2021.09.15.460543 (2023)
  28. Insights into the ISG15 transfer cascade by the UBE1L activating enzyme. Wallace I, Baek K, Prabu JR, Vollrath R, von Gronau S, Schulman BA, Swatek KN. Nat Commun 14 7970 (2023)


Reviews citing this publication (210)

  1. Structural insights into SARS-CoV-2 proteins. Arya R, Kumari S, Pandey B, Mistry H, Bihani SC, Das A, Prashar V, Gupta GD, Panicker L, Kumar M. J Mol Biol 433 166725 (2021)
  2. Structural biology of SARS-CoV-2 and implications for therapeutic development. Yang H, Rao Z. Nat Rev Microbiol 19 685-700 (2021)
  3. Critical Determinants of Cytokine Storm and Type I Interferon Response in COVID-19 Pathogenesis. Ramasamy S, Subbian S. Clin Microbiol Rev 34 e00299-20 (2021)
  4. Type I and III interferon responses in SARS-CoV-2 infection. Kim YM, Shin EC. Exp Mol Med 53 750-760 (2021)
  5. Innate immune sensing of coronavirus and viral evasion strategies. Kasuga Y, Zhu B, Jang KJ, Yoo JS. Exp Mol Med 53 723-736 (2021)
  6. JAK-STAT Pathway Inhibition and their Implications in COVID-19 Therapy. Satarker S, Tom AA, Shaji RA, Alosious A, Luvis M, Nampoothiri M. Postgrad Med 133 489-507 (2021)
  7. Evolutionary trajectory of SARS-CoV-2 and emerging variants. Singh J, Pandit P, McArthur AG, Banerjee A, Mossman K. Virol J 18 166 (2021)
  8. A Comprehensive Review of Viral Characteristics, Transmission, Pathophysiology, Immune Response, and Management of SARS-CoV-2 and COVID-19 as a Basis for Controlling the Pandemic. Triggle CR, Bansal D, Ding H, Islam MM, Farag EABA, Hadi HA, Sultan AA. Front Immunol 12 631139 (2021)
  9. Structural biology of SARS-CoV-2: open the door for novel therapies. Yan W, Zheng Y, Zeng X, He B, Cheng W. Signal Transduct Target Ther 7 26 (2022)
  10. The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19. Schreiber G. Front Immunol 11 595739 (2020)
  11. Ubiquitination in the regulation of inflammatory cell death and cancer. Cockram PE, Kist M, Prakash S, Chen SH, Wertz IE, Vucic D. Cell Death Differ 28 591-605 (2021)
  12. Natural Products, Alone or in Combination with FDA-Approved Drugs, to Treat COVID-19 and Lung Cancer. Yang L, Wang Z. Biomedicines 9 689 (2021)
  13. A critical overview of computational approaches employed for COVID-19 drug discovery. Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. Chem Soc Rev 50 9121-9151 (2021)
  14. Mitochondria: In the Cross Fire of SARS-CoV-2 and Immunity. Burtscher J, Cappellano G, Omori A, Koshiba T, Millet GP. iScience 23 101631 (2020)
  15. Overview of SARS-CoV-2 genome-encoded proteins. Bai C, Zhong Q, Gao GF. Sci China Life Sci 65 280-294 (2022)
  16. Mechanisms of Antiviral Immune Evasion of SARS-CoV-2. Beyer DK, Forero A. J Mol Biol 434 167265 (2022)
  17. Therapeutic targets and interventional strategies in COVID-19: mechanisms and clinical studies. Zhou YW, Xie Y, Tang LS, Pu D, Zhu YJ, Liu JY, Ma XL. Signal Transduct Target Ther 6 317 (2021)
  18. Role of Host-Mediated Post-Translational Modifications (PTMs) in RNA Virus Pathogenesis. Kumar R, Mehta D, Mishra N, Nayak D, Sunil S. Int J Mol Sci 22 E323 (2020)
  19. Chloroquine and hydroxychloroquine in the treatment of COVID-19: the never-ending story. Gasmi A, Peana M, Noor S, Lysiuk R, Menzel A, Gasmi Benahmed A, Bjørklund G. Appl Microbiol Biotechnol 105 1333-1343 (2021)
  20. Host-pathogen interaction in COVID-19: Pathogenesis, potential therapeutics and vaccination strategies. Varghese PM, Tsolaki AG, Yasmin H, Shastri A, Ferluga J, Vatish M, Madan T, Kishore U. Immunobiology 225 152008 (2020)
  21. An update review of emerging small-molecule therapeutic options for COVID-19. Tian D, Liu Y, Liang C, Xin L, Xie X, Zhang D, Wan M, Li H, Fu X, Liu H, Cao W. Biomed Pharmacother 137 111313 (2021)
  22. Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease. Tan H, Hu Y, Jadhav P, Tan B, Wang J. J Med Chem 65 7561-7580 (2022)
  23. An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19. Gurung AB, Ali MA, Lee J, Farah MA, Al-Anazi KM. Biomed Res Int 2021 8853056 (2021)
  24. Immune evasion of SARS-CoV-2 from interferon antiviral system. Min YQ, Huang M, Sun X, Deng F, Wang H, Ning YJ. Comput Struct Biotechnol J 19 4217-4225 (2021)
  25. Innate Immune Response to SARS-CoV-2 Infection: From Cells to Soluble Mediators. Ricci D, Etna MP, Rizzo F, Sandini S, Severa M, Coccia EM. Int J Mol Sci 22 7017 (2021)
  26. Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19. Wu CR, Yin WC, Jiang Y, Xu HE. Acta Pharmacol Sin 43 3021-3033 (2022)
  27. The Ubiquitin-Proteasome System in Immune Cells. Çetin G, Klafack S, Studencka-Turski M, Krüger E, Ebstein F. Biomolecules 11 60 (2021)
  28. The role of death domain proteins in host response upon SARS-CoV-2 infection: modulation of programmed cell death and translational applications. Ivanisenko NV, Seyrek K, Kolchanov NA, Ivanisenko VA, Lavrik IN. Cell Death Discov 6 101 (2020)
  29. Therapeutic strategies for COVID-19: progress and lessons learned. Li G, Hilgenfeld R, Whitley R, De Clercq E. Nat Rev Drug Discov 22 449-475 (2023)
  30. The Role of Epithelial Damage in the Pulmonary Immune Response. Burgoyne RA, Fisher AJ, Borthwick LA. Cells 10 2763 (2021)
  31. Antagonism of Type I Interferon by Severe Acute Respiratory Syndrome Coronavirus 2. Xia H, Shi PY. J Interferon Cytokine Res 40 543-548 (2020)
  32. Bench-to-bedside: Innovation of small molecule anti-SARS-CoV-2 drugs in China. Yang L, Wang Z. Eur J Med Chem 257 115503 (2023)
  33. EGCG, a Green Tea Catechin, as a Potential Therapeutic Agent for Symptomatic and Asymptomatic SARS-CoV-2 Infection. Chourasia M, Koppula PR, Battu A, Ouseph MM, Singh AK. Molecules 26 1200 (2021)
  34. Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development. Lv Z, Cano KE, Jia L, Drag M, Huang TT, Olsen SK. Front Chem 9 819165 (2021)
  35. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Signal Transduct Target Ther 7 202 (2022)
  36. Interferon induction, evasion, and paradoxical roles during SARS-CoV-2 infection. Chiale C, Greene TT, Zuniga EI. Immunol Rev 309 12-24 (2022)
  37. Metal Complexes as Antiviral Agents for SARS-CoV-2. Karges J, Cohen SM. Chembiochem 22 2600-2607 (2021)
  38. Targeting SARS-CoV-2 viral proteases as a therapeutic strategy to treat COVID-19. Anirudhan V, Lee H, Cheng H, Cooper L, Rong L. J Med Virol 93 2722-2734 (2021)
  39. The battle between host and SARS-CoV-2: Innate immunity and viral evasion strategies. Zhang S, Wang L, Cheng G. Mol Ther 30 1869-1884 (2022)
  40. Type I interferons and SARS-CoV-2: from cells to organisms. Bastard P, Zhang Q, Zhang SY, Jouanguy E, Casanova JL. Curr Opin Immunol 74 172-182 (2022)
  41. An overview of potential inhibitors targeting non-structural proteins 3 (PLpro and Mac1) and 5 (3CLpro/Mpro) of SARS-CoV-2. Yan F, Gao F. Comput Struct Biotechnol J 19 4868-4883 (2021)
  42. Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions. Cascarina SM, Ross ED. J Biol Chem 298 101677 (2022)
  43. Small molecules in the treatment of COVID-19. Lei S, Chen X, Wu J, Duan X, Men K. Signal Transduct Target Ther 7 387 (2022)
  44. The Functional Deubiquitinating Enzymes in Control of Innate Antiviral Immunity. Zong Z, Zhang Z, Wu L, Zhang L, Zhou F. Adv Sci (Weinh) 8 2002484 (2021)
  45. Host cell-intrinsic innate immune recognition of SARS-CoV-2. Madden EA, Diamond MS. Curr Opin Virol 52 30-38 (2022)
  46. Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations. Petushkova AI, Zamyatnin AA. Pharmaceuticals (Basel) 13 E277 (2020)
  47. Antiviral strategies targeting host factors and mechanisms obliging +ssRNA viral pathogens. Mahajan S, Choudhary S, Kumar P, Tomar S. Bioorg Med Chem 46 116356 (2021)
  48. Cell deaths: Involvement in the pathogenesis and intervention therapy of COVID-19. Li X, Zhang Z, Wang Z, Gutiérrez-Castrellón P, Shi H. Signal Transduct Target Ther 7 186 (2022)
  49. Innate immune evasion strategies of SARS-CoV-2. Minkoff JM, tenOever B. Nat Rev Microbiol 21 178-194 (2023)
  50. Natural Products for the Prevention and Control of the COVID-19 Pandemic: Sustainable Bioresources. Singla RK, He X, Chopra H, Tsagkaris C, Shen L, Kamal MA, Shen B. Front Pharmacol 12 758159 (2021)
  51. Transcriptional and Non-Transcriptional Activation, Posttranslational Modifications, and Antiviral Functions of Interferon Regulatory Factor 3 and Viral Antagonism by the SARS-Coronavirus. Glanz A, Chakravarty S, Varghese M, Kottapalli A, Fan S, Chakravarti R, Chattopadhyay S. Viruses 13 575 (2021)
  52. How SARS-CoV-2 (COVID-19) spreads within infected hosts - what we know so far. Sanyal S. Emerg Top Life Sci 4 371-378 (2020)
  53. Interactions between SARS coronavirus 2 papain-like protease and immune system: A potential drug target for the treatment of COVID-19. Mahmoudvand S, Shokri S. Scand J Immunol 94 e13044 (2021)
  54. Sensitivity to Vaccines, Therapeutic Antibodies, and Viral Entry Inhibitors and Advances To Counter the SARS-CoV-2 Omicron Variant. Zhou H, Møhlenberg M, Thakor JC, Tuli HS, Wang P, Assaraf YG, Dhama K, Jiang S. Clin Microbiol Rev 35 e0001422 (2022)
  55. Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Ng TI, Correia I, Seagal J, DeGoey DA, Schrimpf MR, Hardee DJ, Noey EL, Kati WM. Viruses 14 961 (2022)
  56. HERC5 and the ISGylation Pathway: Critical Modulators of the Antiviral Immune Response. Mathieu NA, Paparisto E, Barr SD, Spratt DE. Viruses 13 1102 (2021)
  57. SARS-CoV-2 Immuno-Pathogenesis and Potential for Diverse Vaccines and Therapies: Opportunities and Challenges. McGill AR, Kahlil R, Dutta R, Green R, Howell M, Mohapatra S, Mohapatra SS. Infect Dis Rep 13 102-125 (2021)
  58. An expanded lexicon for the ubiquitin code. Dikic I, Schulman BA. Nat Rev Mol Cell Biol 24 273-287 (2023)
  59. Medicinal chemistry strategies towards the development of effective SARS-CoV-2 inhibitors. Gao S, Huang T, Song L, Xu S, Cheng Y, Cherukupalli S, Kang D, Zhao T, Sun L, Zhang J, Zhan P, Liu X. Acta Pharm Sin B 12 581-599 (2022)
  60. Characterization of SARS-CoV-2 Evasion: Interferon Pathway and Therapeutic Options. Znaidia M, Demeret C, van der Werf S, Komarova AV. Viruses 14 1247 (2022)
  61. Interferon antagonists encoded by SARS-CoV-2 at a glance. Lee JH, Koepke L, Kirchhoff F, Sparrer KMJ. Med Microbiol Immunol 212 125-131 (2023)
  62. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Chem Rev 122 11287-11368 (2022)
  63. Viral Evasion of RIG-I-Like Receptor-Mediated Immunity through Dysregulation of Ubiquitination and ISGylation. Chiang C, Liu G, Gack MU. Viruses 13 182 (2021)
  64. Virus Caused Imbalance of Type I IFN Responses and Inflammation in COVID-19. Zhang J, Zhang J, Zhao C, Zhao W. Front Immunol 12 633769 (2021)
  65. Mega doses of retinol: A possible immunomodulation in Covid-19 illness in resource-limited settings. Midha IK, Kumar N, Kumar A, Madan T. Rev Med Virol 31 1-14 (2021)
  66. Proteomics in the COVID-19 Battlefield: First Semester Check-Up. Grenga L, Armengaud J. Proteomics 21 e2000198 (2021)
  67. The Role of the Host Ubiquitin System in Promoting Replication of Emergent Viruses. Valerdi KM, Hage A, van Tol S, Rajsbaum R, Giraldo MI. Viruses 13 369 (2021)
  68. A Biochemical Perspective of the Nonstructural Proteins (NSPs) and the Spike Protein of SARS CoV-2. Yoshimoto FK. Protein J 40 260-295 (2021)
  69. A structural view of the SARS-CoV-2 virus and its assembly. Hardenbrook NJ, Zhang P. Curr Opin Virol 52 123-134 (2022)
  70. ISGylation in Innate Antiviral Immunity and Pathogen Defense Responses: A Review. Zhang M, Li J, Yan H, Huang J, Wang F, Liu T, Zeng L, Zhou F. Front Cell Dev Biol 9 788410 (2021)
  71. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Razali R, Asis H, Budiman C. Microorganisms 9 2481 (2021)
  72. An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity. Zhang Y, Gargan S, Lu Y, Stevenson NJ. Viruses 13 560 (2021)
  73. Current utilization of interferon alpha for the treatment of coronavirus disease 2019: A comprehensive review. Lu LY, Feng PH, Yu MS, Chen MC, Lin AJ, Chen JL, Yu LH. Cytokine Growth Factor Rev 63 34-43 (2022)
  74. Immunopathology and Immunopathogenesis of COVID-19, what we know and what we should learn. Shahgolzari M, Yavari A, Arjeini Y, Miri SM, Darabi A, Mozaffari Nejad AS, Keshavarz M. Gene Rep 25 101417 (2021)
  75. SARS-CoV-2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion. Quaglia F, Salladini E, Carraro M, Minervini G, Tosatto SCE, Le Mercier P. FEBS J 289 4240-4250 (2022)
  76. Selenium to selenoproteins - role in COVID-19. Tomo S, Saikiran G, Banerjee M, Paul S. EXCLI J 20 781-791 (2021)
  77. Therapeutic Potential of Glycosyl Flavonoids as Anti-Coronaviral Agents. Godinho PIC, Soengas RG, Silva VLM. Pharmaceuticals (Basel) 14 546 (2021)
  78. An Impaired Inflammatory and Innate Immune Response in COVID-19. Park SH. Mol Cells 44 384-391 (2021)
  79. Phyto-pharmacological perspective of Silymarin: A potential prophylactic or therapeutic agent for COVID-19, based on its promising immunomodulatory, anti-coagulant and anti-viral property. Palit P, Mukhopadhyay A, Chattopadhyay D. Phytother Res 35 4246-4257 (2021)
  80. Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research. Praissman JL, Wells L. Mol Cell Proteomics 20 100103 (2021)
  81. SARS-CoV-2 Non-Structural Proteins and Their Roles in Host Immune Evasion. Low ZY, Zabidi NZ, Yip AJW, Puniyamurti A, Chow VTK, Lal SK. Viruses 14 1991 (2022)
  82. SARS-CoV-2-mediated evasion strategies for antiviral interferon pathways. Oh SJ, Shin OS. J Microbiol 60 290-299 (2022)
  83. Therapeutics for COVID-19. Toussi SS, Hammond JL, Gerstenberger BS, Anderson AS. Nat Microbiol 8 771-786 (2023)
  84. Understanding Individual SARS-CoV-2 Proteins for Targeted Drug Development against COVID-19. van de Leemput J, Han Z. Mol Cell Biol 41 e0018521 (2021)
  85. Disorders of ubiquitylation: unchained inflammation. Beck DB, Werner A, Kastner DL, Aksentijevich I. Nat Rev Rheumatol 18 435-447 (2022)
  86. Infection-induced inflammation from specific inborn errors of immunity to COVID-19. Ku CL, Chen IT, Lai MZ. FEBS J 288 5021-5041 (2021)
  87. Post-Translational Modifications of cGAS-STING: A Critical Switch for Immune Regulation. Yu Y, Liu J, Liu C, Liu R, Liu L, Yu Z, Zhuang J, Sun C. Cells 11 3043 (2022)
  88. Reducing SARS-CoV-2 pathological protein activity with small molecules. Pluskota-Karwatka D, Hoffmann M, Barciszewski J. J Pharm Anal 11 383-397 (2021)
  89. Review Devil's tools: SARS-CoV-2 antagonists against innate immunity. Xu D, Biswal M, Neal A, Hai R. Curr Res Virol Sci 2 100013 (2021)
  90. Role of Virally-Encoded Deubiquitinating Enzymes in Regulation of the Virus Life Cycle. Proulx J, Borgmann K, Park IW. Int J Mol Sci 22 4438 (2021)
  91. Viral Proteases as Targets for Coronavirus Disease 2019 Drug Development. Zhu W, Shyr Z, Lo DC, Zheng W. J Pharmacol Exp Ther 378 166-172 (2021)
  92. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Front Immunol 13 834942 (2022)
  93. An update on emerging therapeutics to combat COVID-19. Shah NN, Nabi SU, Rather MA, Kalwar Q, Ali SI, Sheikh WM, Ganai A, Bashir SM. Basic Clin Pharmacol Toxicol 129 104-129 (2021)
  94. Impaired innate antiviral defenses in COVID-19: Causes, consequences and therapeutic opportunities. Galani IE, Andreakos E. Semin Immunol 55 101522 (2021)
  95. Innate lymphoid cells (ILC) in SARS-CoV-2 infection. Kumar A, Cao W, Endrias K, Kuchipudi SV, Mittal SK, Sambhara S. Mol Aspects Med 80 101008 (2021)
  96. Molecular Mechanisms of Possible Action of Phenolic Compounds in COVID-19 Protection and Prevention. Gligorijevic N, Radomirovic M, Nedic O, Stojadinovic M, Khulal U, Stanic-Vucinic D, Cirkovic Velickovic T. Int J Mol Sci 22 12385 (2021)
  97. Protease Inhibition-An Established Strategy to Combat Infectious Diseases. Sojka D, Šnebergerová P, Robbertse L. Int J Mol Sci 22 5762 (2021)
  98. Proteomics Mapping of the ISGylation Landscape in Innate Immunity. Thery F, Eggermont D, Impens F. Front Immunol 12 720765 (2021)
  99. Role of phytoconstituents in the management of COVID-19. Das A, Pandita D, Jain GK, Agarwal P, Grewal AS, Khar RK, Lather V. Chem Biol Interact 341 109449 (2021)
  100. SARS-CoV-2-Morphology, Transmission and Diagnosis during Pandemic, Review with Element of Meta-Analysis. Grudlewska-Buda K, Wiktorczyk-Kapischke N, Wałecka-Zacharska E, Kwiecińska-Piróg J, Buszko K, Leis K, Juszczuk K, Gospodarek-Komkowska E, Skowron K. J Clin Med 10 1962 (2021)
  101. A review on computer-aided chemogenomics and drug repositioning for rational COVID-19 drug discovery. Maghsoudi S, Taghavi Shahraki B, Rameh F, Nazarabi M, Fatahi Y, Akhavan O, Rabiee M, Mostafavi E, Lima EC, Saeb MR, Rabiee N. Chem Biol Drug Des 100 699-721 (2022)
  102. An Update on Innate Immune Responses during SARS-CoV-2 Infection. Zhang Y, Chen S, Jin Y, Ji W, Zhang W, Duan G. Viruses 13 2060 (2021)
  103. DrugDevCovid19: An Atlas of Anti-COVID-19 Compounds Derived by Computer-Aided Drug Design. Liu Y, Gan J, Wang R, Yang X, Xiao Z, Cao Y. Molecules 27 683 (2022)
  104. Host ADP-ribosylation and the SARS-CoV-2 macrodomain. Hoch NC. Biochem Soc Trans 49 1711-1721 (2021)
  105. Mechanistic understanding of innate and adaptive immune responses in SARS-CoV-2 infection. Balkhi MY. Mol Immunol 135 268-275 (2021)
  106. SARS-CoV-2 Papain-Like Protease: Structure, Function and Inhibition. Ullrich S, Nitsche C. Chembiochem 23 e202200327 (2022)
  107. Targeting SARS-CoV-2 papain-like protease in the postvaccine era. Ton AT, Pandey M, Smith JR, Ban F, Fernandez M, Cherkasov A. Trends Pharmacol Sci 43 906-919 (2022)
  108. The effects of SARS-CoV-2 infection on modulating innate immunity and strategies of combating inflammatory response for COVID-19 therapy. Wang Y, Wu M, Li Y, Yuen HH, He ML. J Biomed Sci 29 27 (2022)
  109. A Multidisciplinary Approach to Coronavirus Disease (COVID-19). Gediz Erturk A, Sahin A, Bati Ay E, Pelit E, Bagdatli E, Kulu I, Gul M, Mesci S, Eryilmaz S, Oba Ilter S, Yildirim T. Molecules 26 3526 (2021)
  110. Acriflavine, an Acridine Derivative for Biomedical Application: Current State of the Art. Piorecka K, Kurjata J, Stanczyk WA. J Med Chem 65 11415-11432 (2022)
  111. Drug repurposing against SARS-CoV-2 using computational approaches. Kumar S, Kovalenko S, Bhardwaj S, Sethi A, Gorobets NY, Desenko SM, Poonam, Rathi B. Drug Discov Today 27 2015-2027 (2022)
  112. Host and Viral Zinc-Finger Proteins in COVID-19. Esposito S, D'Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Int J Mol Sci 23 3711 (2022)
  113. Insight into the emerging role of SARS-CoV-2 nonstructural and accessory proteins in modulation of multiple mechanisms of host innate defense. Abdalla AE, Xie J, Junaid K, Younas S, Elsaman T, Abosalif KOA, Alameen AAM, Mahjoob MO, Elamir MYM, Ejaz H. Bosn J Basic Med Sci 21 515-527 (2021)
  114. Precursors of Viral Proteases as Distinct Drug Targets. Majerová T, Novotný P. Viruses 13 1981 (2021)
  115. The deciphering of the immune cells and marker signature in COVID-19 pathogenesis: An update. Jasim SA, Mahdi RS, Bokov DO, Najm MAA, Sobirova GN, Bafoyeva ZO, Taifi A, Alkadir OKA, Mustafa YF, Mirzaei R, Karampoor S. J Med Virol 94 5128-5148 (2022)
  116. Understanding Severe Acute Respiratory Syndrome Coronavirus 2 Replication to Design Efficient Drug Combination Therapies. Ortega JT, Zambrano JL, Jastrzebska B, Liprandi F, Rangel HR, Pujol FH. Intervirology 63 2-9 (2020)
  117. A critical evaluation of risk to reward ratio of quercetin supplementation for COVID-19 and associated comorbid conditions. Pawar A, Russo M, Rani I, Rani I, Goswami K, Russo GL, Pal A. Phytother Res 36 2394-2415 (2022)
  118. Chalcone-amide, a privileged backbone for the design and development of selective SARS-CoV/SARS-CoV-2 papain-like protease inhibitors. Valipour M. Eur J Med Chem 240 114572 (2022)
  119. Functional Contribution and Targeted Migration of Group-2 Innate Lymphoid Cells in Inflammatory Lung Diseases: Being at the Right Place at the Right Time. Wirtz S, Schulz-Kuhnt A, Neurath MF, Atreya I. Front Immunol 12 688879 (2021)
  120. Host Protective Immunity against Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) and the COVID-19 Vaccine-Induced Immunity against SARS-CoV-2 and Its Variants. Noor R. Viruses 14 2541 (2022)
  121. Innate Immunity Evasion Strategies of Highly Pathogenic Coronaviruses: SARS-CoV, MERS-CoV, and SARS-CoV-2. Li JY, Zhou ZJ, Wang Q, He QN, Zhao MY, Qiu Y, Ge XY. Front Microbiol 12 770656 (2021)
  122. Insights into pandemic respiratory viruses: manipulation of the antiviral interferon response by SARS-CoV-2 and influenza A virus. Liu G, Gack MU. Curr Opin Immunol 78 102252 (2022)
  123. Inter-proteomic posttranslational modifications of the SARS-CoV-2 and the host proteins ‒ A new frontier. Mishra S, Bassi G, Nyomba BG. Exp Biol Med (Maywood) 246 749-757 (2021)
  124. Nuclear Medicine in Times of COVID-19: How Radiopharmaceuticals Could Help to Fight the Current and Future Pandemics. Neumaier F, Zlatopolskiy BD, Neumaier B. Pharmaceutics 12 E1247 (2020)
  125. Recent advances in small-molecular therapeutics for COVID-19. Zhong L, Zhao Z, Peng X, Zou J, Yang S. Precis Clin Med 5 pbac024 (2022)
  126. Structural biology in the time of COVID-19: perspectives on methods and milestones. Lynch ML, Snell EH, Bowman SEJ. IUCrJ 8 335-341 (2021)
  127. Structural insights of key enzymes into therapeutic intervention against SARS-CoV-2. Shahid M, Shahzad-Ul-Hussan S. J Struct Biol 213 107690 (2021)
  128. A Review of Extracellular Vesicles in COVID-19 Diagnosis, Treatment, and Prevention. Su P, Wu Y, Xie F, Zheng Q, Chen L, Liu Z, Meng X, Zhou F, Zhang L. Adv Sci (Weinh) 10 e2206095 (2023)
  129. Coronaviral PLpro proteases and the immunomodulatory roles of conjugated versus free Interferon Stimulated Gene product-15 (ISG15). Gold IM, Reis N, Glaser F, Glickman MH. Semin Cell Dev Biol 132 16-26 (2022)
  130. Deciphering Respiratory-Virus-Associated Interferon Signaling in COPD Airway Epithelium. Guo-Parke H, Linden D, Weldon S, Kidney JC, Taggart CC. Medicina (Kaunas) 58 121 (2022)
  131. Imaging and visualizing SARS-CoV-2 in a new era for structural biology. Leigh KE, Modis Y. Interface Focus 11 20210019 (2021)
  132. Molecular Insights of SARS-CoV-2 Antivirals Administration: A Balance between Safety Profiles and Impact on Cardiovascular Phenotypes. Nappi F, Iervolino A, Avtaar Singh SS. Biomedicines 10 437 (2022)
  133. Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. Obeng EM, Fianu I, Danquah MK. Nano Today 46 101580 (2022)
  134. Pharmacotherapeutics of SARS-CoV-2 Infections. Kevadiya BD, Machhi J, Herskovitz J, Oleynikov MD, Blomberg WR, Bajwa N, Soni D, Das S, Hasan M, Patel M, Senan AM, Gorantla S, McMillan J, Edagwa B, Eisenberg R, Gurumurthy CB, Reid SPM, Punyadeera C, Chang L, Gendelman HE. J Neuroimmune Pharmacol 16 12-37 (2021)
  135. Structural insights into SARS-CoV-2 infection and therapeutics development. Sun G, Xue L, He Q, Zhao Y, Xu W, Wang Z. Stem Cell Res 52 102219 (2021)
  136. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O'Brien DP, Pinto-Fernández A. Biomolecules 12 300 (2022)
  137. The Regulatory Network of Cyclic GMP-AMP Synthase-Stimulator of Interferon Genes Pathway in Viral Evasion. Hu T, Pan M, Yin Y, Wang C, Cui Y, Wang Q. Front Microbiol 12 790714 (2021)
  138. The Role of Antibodies in the Treatment of SARS-CoV-2 Virus Infection, and Evaluating Their Contribution to Antibody-Dependent Enhancement of Infection. Farouq MAH, Acevedo R, Ferro VA, Mulheran PA, Al Qaraghuli MM. Int J Mol Sci 23 6078 (2022)
  139. The Role of Deubiquitinases in Virus Replication and Host Innate Immune Response. Zhang Q, Jia Q, Gao W, Zhang W. Front Microbiol 13 839624 (2022)
  140. Therapeutic potential of green tea catechin, (-)-epigallocatechin-3-O-gallate (EGCG) in SARS-CoV-2 infection: Major interactions with host/virus proteases. Dinda B, Dinda S, Dinda M. Phytomed Plus 3 100402 (2023)
  141. Type-I interferons in the immunopathogenesis and treatment of Coronavirus disease 2019. Khorramdelazad H, Kazemi MH, Azimi M, Aghamajidi A, Mehrabadi AZ, Shahba F, Aghamohammadi N, Falak R, Faraji F, Jafari R. Eur J Pharmacol 927 175051 (2022)
  142. Biology and Pathogenesis of SARS-CoV-2: Understandings for Therapeutic Developments against COVID-19. Sharma HN, Latimore COD, Matthews QL. Pathogens 10 1218 (2021)
  143. Biomolecular interactions with nanoparticles: applications for coronavirus disease 2019. Farouq MAH, Al Qaraghuli MM, Kubiak-Ossowska K, Ferro VA, Mulheran PA. Curr Opin Colloid Interface Sci 54 101461 (2021)
  144. Coordinated regulation of interferon and inflammasome signaling pathways by SARS-CoV-2 proteins. Kim NE, Song YJ. J Microbiol 60 300-307 (2022)
  145. Coronaviral Infection and Interferon Response: The Virus-Host Arms Race and COVID-19. Liu Q, Chi S, Dmytruk K, Dmytruk O, Tan S. Viruses 14 1349 (2022)
  146. Luciferase-Based Biosensors in the Era of the COVID-19 Pandemic. Azad T, Janse van Rensburg HJ, Morgan J, Rezaei R, Crupi MJF, Chen R, Ghahremani M, Jamalkhah M, Forbes N, Ilkow C, Bell JC. ACS Nanosci Au 1 15-37 (2021)
  147. Novel antiviral effects of chloroquine, hydroxychloroquine, and green tea catechins against SARS CoV-2 main protease (Mpro) and 3C-like protease for COVID-19 treatment. Shaik FB, Swarnalatha K, Mohan MC, Thomas A, Chikati R, Sandeep G, Maddu N. Clin Nutr Open Sci 42 62-72 (2022)
  148. SARS-CoV-2 and the Nucleus. Chen M, Ma Y, Chang W. Int J Biol Sci 18 4731-4743 (2022)
  149. Significance of Immune Status of SARS-CoV-2 Infected Patients in Determining the Efficacy of Therapeutic Interventions. Saratale GD, Shin HS, Shinde SK, Kim DY, Saratale RG, Kadam AA, Kumar M, Bahkali AH, Syed A, Ghodake GS. J Pers Med 12 349 (2022)
  150. The Evolutionary Dance between Innate Host Antiviral Pathways and SARS-CoV-2. Aliyari SR, Quanquin N, Pernet O, Zhang S, Wang L, Cheng G. Pathogens 11 538 (2022)
  151. The role of multi-omics in the diagnosis of COVID-19 and the prediction of new therapeutic targets. Ma J, Deng Y, Zhang M, Yu J. Virulence 13 1101-1110 (2022)
  152. Through DNA sensors and hidden mitochondrial effects of SARS-CoV-2. Targhetta VP, Amaral MA, Camara NOS. J Venom Anim Toxins Incl Trop Dis 27 e20200183 (2021)
  153. Viral proteases as therapeutic targets. Majerová T, Konvalinka J. Mol Aspects Med 88 101159 (2022)
  154. Accelerating antiviral drug discovery: lessons from COVID-19. von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Nat Rev Drug Discov 22 585-603 (2023)
  155. COVID-19 and the potential of Janus family kinase (JAK) pathway inhibition: A novel treatment strategy. Khaledi M, Sameni F, Yahyazade S, Radandish M, Owlia P, Bagheri N, Afkhami H, Mahjoor M, Esmaelpour Z, Kohansal M, Aghaei F. Front Med (Lausanne) 9 961027 (2022)
  156. COVID-19 signalome: Potential therapeutic interventions. Lundstrom K, Hromić-Jahjefendić A, Bilajac E, Aljabali AAA, Baralić K, Sabri NA, Shehata EM, Raslan M, Raslan SA, Ferreira ACBH, Orlandi L, Serrano-Aroca Á, Uversky VN, Hassan SS, Redwan EM, Azevedo V, Alzahrani KJ, Alsharif KF, Halawani IF, Alzahrani FM, Tambuwala MM, Barh D. Cell Signal 103 110559 (2023)
  157. Computational anti-COVID-19 drug design: progress and challenges. Wang J, Zhang Y, Nie W, Luo Y, Deng L. Brief Bioinform 23 bbab484 (2022)
  158. Control of Innate Immune Activation by Severe Acute Respiratory Syndrome Coronavirus 2 and Other Coronaviruses. Kehrer T, García-Sastre A, Miorin L. J Interferon Cytokine Res 41 205-219 (2021)
  159. Delineating the SARS-CoV-2 Induced Interplay between the Host Immune System and the DNA Damage Response Network. Papanikolaou C, Rapti V, Stellas D, Stefanou DT, Syrigos K, Pavlakis GN, Souliotis VL. Vaccines (Basel) 10 1764 (2022)
  160. Druggable targets and therapeutic development for COVID-19. Duan X, Lacko LA, Chen S. Front Chem 10 963701 (2022)
  161. Dysregulation of Protein S in COVID-19. Sim MMS, Wood JP. Best Pract Res Clin Haematol 35 101376 (2022)
  162. Interferon at the crossroads of SARS-CoV-2 infection and COVID-19 disease. Samuel CE. J Biol Chem 299 104960 (2023)
  163. Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics. Pavan M, Moro S. Int J Mol Sci 24 4401 (2023)
  164. Mechanisms of Viral Degradation of Cellular Signal Transducer and Activator of Transcription 2. Barik S. Int J Mol Sci 23 489 (2022)
  165. Pathogenic Mechanism and Multi-omics Analysis of Oral Manifestations in COVID-19. Hao M, Wang D, Xia Q, Kan S, Chang L, Liu H, Yang Z, Liu W. Front Immunol 13 879792 (2022)
  166. SARS-CoV-2 and the host-immune response. Maison DP, Deng Y, Gerschenson M. Front Immunol 14 1195871 (2023)
  167. Surgical Strikes on Host Defenses: Role of the Viral Protease Activity in Innate Immune Antagonism. Chin CV, Saeed M. Pathogens 11 522 (2022)
  168. The Pathogenic Features of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Possible Mechanisms for Immune Evasion? Wang Z, Zhou M, Fu Z, Zhao L. Front Immunol 12 693579 (2021)
  169. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Mahmoudi S, Dehkordi MM, Asgarshamsi MH. Biophys Chem 288 106824 (2022)
  170. The origins of COVID-19 pandemic: A brief overview. Hao YJ, Wang YL, Wang MY, Zhou L, Shi JY, Cao JM, Wang DP. Transbound Emerg Dis 69 3181-3197 (2022)
  171. Uncovering Novel Viral Innate Immune Evasion Strategies: What Has SARS-CoV-2 Taught Us? Tay DJW, Lew ZZR, Chu JJH, Tan KS. Front Microbiol 13 844447 (2022)
  172. Viral evasion of the interferon response at a glance. Zhu J, Chiang C, Gack MU. J Cell Sci 136 jcs260682 (2023)
  173. A Review of In Silico Research, SARS-CoV-2, and Neurodegeneration: Focus on Papain-Like Protease. Rieder AS, Deniz BF, Netto CA, Wyse ATS. Neurotox Res 40 1553-1569 (2022)
  174. A hypothesis on designing strategy of effective RdRp inhibitors for the treatment of SARS-CoV-2. Chaube U, Patel BD, Bhatt HG. 3 Biotech 13 12 (2023)
  175. A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. Ruchawapol C, Fu WW, Xu HX. Phytomedicine 104 154324 (2022)
  176. Can Probiotics, Particularly Limosilactobacillus fermentum UCO-979C and Lacticaseibacillus rhamnosus UCO-25A, Be Preventive Alternatives against SARS-CoV-2? Valdebenito-Navarrete H, Fuentes-Barrera V, Smith CT, Salas-Burgos A, Zuniga FA, Gomez LA, García-Cancino A. Biology (Basel) 12 384 (2023)
  177. Cellular Deubiquitylating Enzyme: A Regulatory Factor of Antiviral Innate Immunity. Long S, Yang L, Dang W, Xin S, Jiang M, Zhang W, Li J, Wang Y, Zhang S, Lu J. Front Microbiol 12 805223 (2021)
  178. Cellular Sensors and Viral Countermeasures: A Molecular Arms Race between Host and SARS-CoV-2. Sun H, Chan JF, Yuan S. Viruses 15 352 (2023)
  179. Critical Review of Plant-Derived Compounds as Possible Inhibitors of SARS-CoV-2 Proteases: A Comparison with Experimentally Validated Molecules. Guerra Y, Celi D, Cueva P, Perez-Castillo Y, Giampieri F, Alvarez-Suarez JM, Tejera E. ACS Omega 7 44542-44555 (2022)
  180. Deubiquitylating Enzymes in Cancer and Immunity. Ren J, Yu P, Liu S, Li R, Niu X, Chen Y, Zhang Z, Zhou F, Zhang L. Adv Sci (Weinh) 10 e2303807 (2023)
  181. Distinct Molecular Mechanisms Characterizing Pathogenesis of SARS-CoV-2. Lee SJ, Kim YJ, Ahn DG. J Microbiol Biotechnol 32 1073-1085 (2022)
  182. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Front Bioeng Biotechnol 11 1124100 (2023)
  183. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Front Bioeng Biotechnol 10 1052436 (2022)
  184. SARS-CoV-2 Spike-Mediated Entry and Its Regulation by Host Innate Immunity. Yu S, Hu H, Ai Q, Bai R, Ma K, Zhou M, Wang S. Viruses 15 639 (2023)
  185. The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. Kocabaş F, Uslu M. Turk J Biol 45 469-483 (2021)
  186. A review on in silico virtual screening methods in COVID-19 using anticancer drugs and other natural/chemical inhibitors. Sokouti B. Explor Target Antitumor Ther 4 994-1026 (2023)
  187. Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era. Harrison CM, Doster JM, Landwehr EH, Kumar NP, White EJ, Beachboard DC, Stobart CC. Microorganisms 11 445 (2023)
  188. Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective. Sinha A, Sangeet S, Roy S. ACS Omega 8 23283-23304 (2023)
  189. Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Minetti CA, Remeta DP. Life (Basel) 12 1438 (2022)
  190. Harnessing the Power of Venomous Animal-Derived Toxins against COVID-19. Oliveira I, Ferreira I, Jacob B, Cardenas K, Cerni F, Baia-da-Silva D, Arantes E, Monteiro W, Pucca M. Toxins (Basel) 15 159 (2023)
  191. Highlights on molecular targets in the management of COVID-19: Possible role of pharmacogenomics. Thabet RH, Massadeh NA, Badarna OB, Al-Momani OM. J Int Med Res 51 3000605231153764 (2023)
  192. Immunopathological events surrounding IL-6 and IFN-α: A bridge for anti-lupus erythematosus drugs used to treat COVID-19. Zhou B, Li S, Ye J, Liu Y, Hu L, Tang Y, Wu Z, Zhang P. Int Immunopharmacol 101 108254 (2021)
  193. Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2. Yevsieieva LV, Lohachova KO, Kyrychenko A, Kovalenko SM, Ivanov VV, Kalugin ON. RSC Adv 13 35500-35524 (2023)
  194. Mechanisms of impairment of interferon production by SARS-CoV-2. Hoang HD, Naeli P, Alain T, Jafarnejad SM. Biochem Soc Trans 51 1047-1056 (2023)
  195. Metallo-antiviral aspirants: Answer to the upcoming virus outbreak. Mehrotra R, Shukla SN, Gaur P. Eur J Med Chem Rep 8 100104 (2023)
  196. New insights for infection mechanism and potential targets of COVID-19: Three Chinese patent medicines and three Chinese medicine formulas as promising therapeutic approaches. Jia K, Li Y, Liu T, Gu X, Li X. Chin Herb Med 15 157-168 (2023)
  197. Repurposing clinically available drugs and therapies for pathogenic targets to combat SARS-CoV-2. Xue Y, Mei H, Chen Y, Griffin JD, Liu Q, Weisberg E, Yang J. MedComm (2020) 4 e254 (2023)
  198. Role of E3 ubiquitin ligases and deubiquitinating enzymes in SARS-CoV-2 infection. Zhao M, Zhang M, Yang Z, Zhou Z, Huang J, Zhao B. Front Cell Infect Microbiol 13 1217383 (2023)
  199. SARS-CoV-2 Evasion of the Interferon System: Can We Restore Its Effectiveness? Sacchi A, Giannessi F, Sabatini A, Percario ZA, Affabris E. Int J Mol Sci 24 9353 (2023)
  200. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. Cell Mol Immunol (2023)
  201. SARS-CoV-2 biology and host interactions. Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. Nat Rev Microbiol (2024)
  202. SARS-CoV-PLpro-Inhibitoren als mögliche Breitspektrum-Virostatika. Hammerschmidt SJ, Müller P, Schirmeister T. Biospektrum (Heidelb) 27 254-256 (2021)
  203. Significant perspectives on various viral infections targeted antiviral drugs and vaccines including COVID-19 pandemicity. Arumugam GS, Damodharan K, Doble M, Thennarasu S. Mol Biomed 3 21 (2022)
  204. Strategies for the development and approval of COVID-19 vaccines and therapeutics in the post-pandemic period. Ao D, He X, Liu J, Xu L. Signal Transduct Target Ther 8 466 (2023)
  205. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Cell Commun Signal 21 110 (2023)
  206. Targeting SARS-CoV-2 Non-Structural Proteins. Tam D, Lorenzo-Leal AC, Hernández LR, Bach H. Int J Mol Sci 24 13002 (2023)
  207. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Spano D, Catara G. Cells 13 29 (2023)
  208. Ubiquitin-Dependent and Independent Proteasomal Degradation in Host-Pathogen Interactions. Bialek W, Collawn JF, Bartoszewski R. Molecules 28 6740 (2023)
  209. What do we know about the function of SARS-CoV-2 proteins? Justo Arevalo S, Castillo-Chávez A, Uribe Calampa CS, Zapata Sifuentes D, Huallpa CJ, Landa Bianchi G, Garavito-Salini Casas R, Quiñones Aguilar M, Pineda Chavarría R. Front Immunol 14 1249607 (2023)
  210. [Interaction between SARS-CoV-2 and Host Innate Immunity]. Duan XQ, Xie H, Chen LM. Sichuan Da Xue Xue Bao Yi Xue Ban 53 1-6 (2022)

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  1. SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling. Miorin L, Kehrer T, Sanchez-Aparicio MT, Zhang K, Cohen P, Patel RS, Cupic A, Makio T, Mei M, Moreno E, Danziger O, White KM, Rathnasinghe R, Uccellini M, Gao S, Aydillo T, Mena I, Yin X, Martin-Sancho L, Krogan NJ, Chanda SK, Schotsaert M, Wozniak RW, Ren Y, Rosenberg BR, Fontoura BMA, García-Sastre A. Proc Natl Acad Sci U S A 117 28344-28354 (2020)
  2. Mechanism and inhibition of the papain-like protease, PLpro, of SARS-CoV-2. Klemm T, Ebert G, Calleja DJ, Allison CC, Richardson LW, Bernardini JP, Lu BG, Kuchel NW, Grohmann C, Shibata Y, Gan ZY, Cooney JP, Doerflinger M, Au AE, Blackmore TR, van der Heden van Noort GJ, Geurink PP, Ovaa H, Newman J, Riboldi-Tunnicliffe A, Czabotar PE, Mitchell JP, Feltham R, Lechtenberg BC, Lowes KN, Dewson G, Pellegrini M, Lessene G, Komander D. EMBO J 39 e106275 (2020)
  3. Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors. Osipiuk J, Azizi SA, Dvorkin S, Endres M, Jedrzejczak R, Jones KA, Kang S, Kathayat RS, Kim Y, Lisnyak VG, Maki SL, Nicolaescu V, Taylor CA, Tesar C, Zhang YA, Zhou Z, Randall G, Michalska K, Snyder SA, Dickinson BC, Joachimiak A. Nat Commun 12 743 (2021)
  4. SARS-CoV-2 proteases PLpro and 3CLpro cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species. Moustaqil M, Ollivier E, Chiu HP, Van Tol S, Rudolffi-Soto P, Stevens C, Bhumkar A, Hunter DJB, Freiberg AN, Jacques D, Lee B, Sierecki E, Gambin Y. Emerg Microbes Infect 10 178-195 (2021)
  5. SARS-CoV-2 infection of human iPSC-derived cardiac cells reflects cytopathic features in hearts of patients with COVID-19. Perez-Bermejo JA, Kang S, Rockwood SJ, Simoneau CR, Joy DA, Silva AC, Ramadoss GN, Flanigan WR, Fozouni P, Li H, Chen PY, Nakamura K, Whitman JD, Hanson PJ, McManus BM, Ott M, Conklin BR, McDevitt TC. Sci Transl Med 13 eabf7872 (2021)
  6. Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities. Hayn M, Hirschenberger M, Koepke L, Nchioua R, Straub JH, Klute S, Hunszinger V, Zech F, Prelli Bozzo C, Aftab W, Christensen MH, Conzelmann C, Müller JA, Srinivasachar Badarinarayan S, Stürzel CM, Forne I, Stenger S, Conzelmann KK, Münch J, Schmidt FI, Sauter D, Imhof A, Kirchhoff F, Sparrer KMJ. Cell Rep 35 109126 (2021)
  7. Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay. Jang WD, Jeon S, Kim S, Lee SY. Proc Natl Acad Sci U S A 118 e2024302118 (2021)
  8. SARS-CoV-2 nsp12 attenuates type I interferon production by inhibiting IRF3 nuclear translocation. Wang W, Zhou Z, Xiao X, Tian Z, Dong X, Wang C, Li L, Ren L, Lei X, Xiang Z, Wang J. Cell Mol Immunol 18 945-953 (2021)
  9. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Zhang K, Zheludev IN, Hagey RJ, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Wu MT, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D'Souza V, Glenn JS, Chiu W, Das R. Nat Struct Mol Biol 28 747-754 (2021)
  10. RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-κB hyper-activation and inflammation. Wu Y, Ma L, Cai S, Zhuang Z, Zhao Z, Jin S, Xie W, Zhou L, Zhang L, Zhao J, Cui J. Signal Transduct Target Ther 6 167 (2021)
  11. Discovery of SARS-CoV-2 Papain-like Protease Inhibitors through a Combination of High-Throughput Screening and a FlipGFP-Based Reporter Assay. Ma C, Sacco MD, Xia Z, Lambrinidis G, Townsend JA, Hu Y, Meng X, Szeto T, Ba M, Zhang X, Gongora M, Zhang F, Marty MT, Xiang Y, Kolocouris A, Chen Y, Wang J. ACS Cent Sci 7 1245-1260 (2021)
  12. High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors. Zhao Y, Du X, Duan Y, Pan X, Sun Y, You T, Han L, Jin Z, Shang W, Yu J, Guo H, Liu Q, Wu Y, Peng C, Wang J, Zhu C, Yang X, Yang K, Lei Y, Guddat LW, Xu W, Xiao G, Sun L, Zhang L, Rao Z, Yang H. Protein Cell 12 877-888 (2021)
  13. SARS-CoV-2 Nonstructural Protein 1 Inhibits the Interferon Response by Causing Depletion of Key Host Signaling Factors. Kumar A, Ishida R, Strilets T, Cole J, Lopez-Orozco J, Fayad N, Felix-Lopez A, Elaish M, Evseev D, Magor KE, Mahal LK, Nagata LP, Evans DH, Hobman TC. J Virol 95 e0026621 (2021)
  14. SARS-CoV-2 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress the effects of added interferon. Shemesh M, Aktepe TE, Deerain JM, McAuley JL, Audsley MD, David CT, Purcell DFJ, Urin V, Hartmann R, Moseley GW, Mackenzie JM, Schreiber G, Harari D. PLoS Pathog 17 e1009800 (2021)
  15. Differential plasmacytoid dendritic cell phenotype and type I Interferon response in asymptomatic and severe COVID-19 infection. Severa M, Diotti RA, Etna MP, Rizzo F, Fiore S, Ricci D, Iannetta M, Sinigaglia A, Lodi A, Mancini N, Criscuolo E, Clementi M, Andreoni M, Balducci S, Barzon L, Stefanelli P, Clementi N, Coccia EM. PLoS Pathog 17 e1009878 (2021)
  16. SARS-CoV-2 Nsp5 Demonstrates Two Distinct Mechanisms Targeting RIG-I and MAVS To Evade the Innate Immune Response. Liu Y, Qin C, Rao Y, Ngo C, Feng JJ, Zhao J, Zhang S, Wang TY, Carriere J, Savas AC, Zarinfar M, Rice S, Yang H, Yuan W, Camarero JA, Yu J, Chen XS, Zhang C, Feng P. mBio 12 e0233521 (2021)
  17. Altered ISGylation drives aberrant macrophage-dependent immune responses during SARS-CoV-2 infection. Munnur D, Teo Q, Eggermont D, Lee HHY, Thery F, Ho J, van Leur SW, Ng WWS, Siu LYL, Beling A, Ploegh H, Pinto-Fernandez A, Damianou A, Kessler B, Impens F, Mok CKP, Sanyal S. Nat Immunol 22 1416-1427 (2021)
  18. The SARS-CoV-2 Nsp3 macrodomain reverses PARP9/DTX3L-dependent ADP-ribosylation induced by interferon signaling. Russo LC, Tomasin R, Matos IA, Manucci AC, Sowa ST, Dale K, Caldecott KW, Lehtiö L, Schechtman D, Meotti FC, Bruni-Cardoso A, Hoch NC. J Biol Chem 297 101041 (2021)
  19. Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir. Xia Z, Sacco M, Hu Y, Ma C, Meng X, Zhang F, Szeto T, Xiang Y, Chen Y, Wang J. ACS Pharmacol Transl Sci 4 1408-1421 (2021)
  20. Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CLpro substrate degradome. Pablos I, Machado Y, de Jesus HCR, Mohamud Y, Kappelhoff R, Lindskog C, Vlok M, Bell PA, Butler GS, Grin PM, Cao QT, Nguyen JP, Solis N, Abbina S, Rut W, Vederas JC, Szekely L, Szakos A, Drag M, Kizhakkedathu JN, Mossman K, Hirota JA, Jan E, Luo H, Banerjee A, Overall CM. Cell Rep 109892 (2021)
  21. Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir. Lo HS, Hui KPY, Lai HM, He X, Khan KS, Kaur S, Huang J, Li Z, Chan AKN, Cheung HH, Ng KC, Ho JCW, Chen YW, Ma B, Cheung PM, Shin D, Wang K, Lee MH, Selisko B, Eydoux C, Guillemot JC, Canard B, Wu KP, Liang PH, Dikic I, Zuo Z, Chan FKL, Hui DSC, Mok VCT, Wong KB, Mok CKP, Ko H, Aik WS, Chan MCW, Ng WL. ACS Cent Sci 7 792-802 (2021)
  22. Development of humanized tri-specific nanobodies with potent neutralization for SARS-CoV-2. Dong J, Huang B, Wang B, Titong A, Gallolu Kankanamalage S, Jia Z, Wright M, Parthasarathy P, Liu Y. Sci Rep 10 17806 (2020)
  23. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. Int J Biol Sci 17 1547-1554 (2021)
  24. Biochemical characterization of protease activity of Nsp3 from SARS-CoV-2 and its inhibition by nanobodies. Armstrong LA, Lange SM, Dee Cesare V, Matthews SP, Nirujogi RS, Cole I, Hope A, Cunningham F, Toth R, Mukherjee R, Bojkova D, Gruber F, Gray D, Wyatt PG, Cinatl J, Dikic I, Davies P, Kulathu Y. PLoS One 16 e0253364 (2021)
  25. Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics. Oerlemans R, Ruiz-Moreno AJ, Cong Y, Dinesh Kumar N, Velasco-Velazquez MA, Neochoritis CG, Smith J, Reggiori F, Groves MR, Dömling A. RSC Med Chem 12 370-379 (2020)
  26. Potent Anti-SARS-CoV-2 Activity by the Natural Product Gallinamide A and Analogues via Inhibition of Cathepsin L. Ashhurst AS, Tang AH, Fajtová P, Yoon MC, Aggarwal A, Bedding MJ, Stoye A, Beretta L, Pwee D, Drelich A, Skinner D, Li L, Meek TD, McKerrow JH, Hook V, Tseng CT, Larance M, Turville S, Gerwick WH, O'Donoghue AJ, Payne RJ. J Med Chem 65 2956-2970 (2022)
  27. Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. Banerjee A, El-Sayes N, Budylowski P, Jacob RA, Richard D, Maan H, Aguiar JA, Demian WL, Baid K, D'Agostino MR, Ang JC, Murdza T, Tremblay BJ, Afkhami S, Karimzadeh M, Irving AT, Yip L, Ostrowski M, Hirota JA, Kozak R, Capellini TD, Miller MS, Wang B, Mubareka S, McGeer AJ, McArthur AG, Doxey AC, Mossman K. iScience 24 102477 (2021)
  28. A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV2 main protease. Baker JD, Uhrich RL, Kraemer GC, Love JE, Kraemer BC. PLoS One 16 e0245962 (2021)
  29. Famotidine inhibits toll-like receptor 3-mediated inflammatory signaling in SARS-CoV-2 infection. Mukherjee R, Bhattacharya A, Bojkova D, Mehdipour AR, Shin D, Khan KS, Hei-Yin Cheung H, Wong KB, Ng WL, Cinatl J, Geurink PP, van der Heden van Noort GJ, Rajalingam K, Ciesek S, Hummer G, Dikic I. J Biol Chem 297 100925 (2021)
  30. Ginkgolic acid and anacardic acid are specific covalent inhibitors of SARS-CoV-2 cysteine proteases. Chen Z, Cui Q, Cooper L, Zhang P, Lee H, Chen Z, Wang Y, Liu X, Rong L, Du R. Cell Biosci 11 45 (2021)
  31. Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay. Pitsillou E, Liang J, Ververis K, Lim KW, Hung A, Karagiannis TC. Front Chem 8 623971 (2020)
  32. Discovery and Mechanism of SARS-CoV-2 Main Protease Inhibitors. Huff S, Kummetha IR, Tiwari SK, Huante MB, Clark AE, Wang S, Bray W, Smith D, Carlin AF, Endsley M, Rana TM. J Med Chem 65 2866-2879 (2022)
  33. Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs. Stoddard CI, Galloway J, Chu HY, Shipley MM, Sung K, Itell HL, Wolf CR, Logue JK, Magedson A, Garrett ME, Crawford KHD, Laserson U, Matsen FA, Overbaugh J. Cell Rep 35 109164 (2021)
  34. On-target versus off-target effects of drugs inhibiting the replication of SARS-CoV-2. Sauvat A, Ciccosanti F, Colavita F, Di Rienzo M, Castilletti C, Capobianchi MR, Kepp O, Zitvogel L, Fimia GM, Piacentini M, Kroemer G. Cell Death Dis 11 656 (2020)
  35. Pomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor (in vitro): A Promising Source of Novel Antiviral Drugs. Tito A, Colantuono A, Pirone L, Pedone E, Intartaglia D, Giamundo G, Conte I, Vitaglione P, Apone F. Front Chem 9 638187 (2021)
  36. Ring finger protein 213 assembles into a sensor for ISGylated proteins with antimicrobial activity. Thery F, Martina L, Asselman C, Zhang Y, Vessely M, Repo H, Sedeyn K, Moschonas GD, Bredow C, Teo QW, Zhang J, Leandro K, Eggermont D, De Sutter D, Boucher K, Hochepied T, Festjens N, Callewaert N, Saelens X, Dermaut B, Knobeloch KP, Beling A, Sanyal S, Radoshevich L, Eyckerman S, Impens F. Nat Commun 12 5772 (2021)
  37. IL-33 in COVID-19: friend or foe? Liang Y, Ge Y, Sun J. Cell Mol Immunol 18 1602-1604 (2021)
  38. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp3 papain-like protease. Lim CT, Tan KW, Wu M, Ulferts R, Armstrong LA, Ozono E, Drury LS, Milligan JC, Zeisner TU, Zeng J, Weissmann F, Canal B, Bineva-Todd G, Howell M, O'Reilly N, Beale R, Kulathu Y, Labib K, Diffley JFX. Biochem J 478 2517-2531 (2021)
  39. 6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro. Swaim CD, Dwivedi V, Perng YC, Zhao X, Canadeo LA, Harastani HH, Darling TL, Boon ACM, Lenschow DJ, Kulkarni V, Huibregtse JM. iScience 24 103213 (2021)
  40. Identifying structural-functional analogue of GRL0617, the only well-established inhibitor for papain-like protease (PLpro) of SARS-CoV2 from the pool of fungal metabolites using docking and molecular dynamics simulation. Rao P, Patel R, Shukla A, Parmar P, Rawal RM, Saraf M, Goswami D. Mol Divers 26 309-329 (2022)
  41. Organ-specific genome diversity of replication-competent SARS-CoV-2. Van Cleemput J, van Snippenberg W, Lambrechts L, Dendooven A, D'Onofrio V, Couck L, Trypsteen W, Vanrusselt J, Theuns S, Vereecke N, van den Bosch TPP, Lammens M, Driessen A, Achten R, Bracke KR, Van den Broeck W, Von der Thüsen J, Nauwynck H, Van Dorpe J, Gerlo S, Maes P, Cox J, Vandekerckhove L. Nat Commun 12 6612 (2021)
  42. Hepatitis C Virus Protease Inhibitors Show Differential Efficacy and Interactions with Remdesivir for Treatment of SARS-CoV-2 In Vitro. Gammeltoft KA, Zhou Y, Duarte Hernandez CR, Galli A, Offersgaard A, Costa R, Pham LV, Fahnøe U, Feng S, Scheel TKH, Ramirez S, Bukh J, Gottwein JM. Antimicrob Agents Chemother 65 e0268020 (2021)
  43. Histamine receptors and COVID-19. Ennis M, Tiligada K. Inflamm Res 70 67-75 (2021)
  44. Randomized double-blind placebo-controlled proof-of-concept trial of resveratrol for outpatient treatment of mild coronavirus disease (COVID-19). McCreary MR, Schnell PM, Rhoda DA. Sci Rep 12 10978 (2022)
  45. Congress Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit. Hall MD, Anderson JM, Anderson A, Baker D, Bradner J, Brimacombe KR, Campbell EA, Corbett KS, Carter K, Cherry S, Chiang L, Cihlar T, de Wit E, Denison M, Disney M, Fletcher CV, Ford-Scheimer SL, Götte M, Grossman AC, Hayden FG, Hazuda DJ, Lanteri CA, Marston H, Mesecar AD, Moore S, Nwankwo JO, O'Rear J, Painter G, Singh Saikatendu K, Schiffer CA, Sheahan TP, Shi PY, Smyth HD, Sofia MJ, Weetall M, Weller SK, Whitley R, Fauci AS, Austin CP, Collins FS, Conley AJ, Davis MI. J Infect Dis 224 S1-S21 (2021)
  46. Molecular docking of potential SARS-CoV-2 papain-like protease inhibitors. Li D, Luan J, Zhang L. Biochem Biophys Res Commun 538 72-79 (2021)
  47. Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus. Umar HI, Siraj B, Ajayi A, Jimoh TO, Chukwuemeka PO. J Genet Eng Biotechnol 19 16 (2021)
  48. Protease cleavage of RNF20 facilitates coronavirus replication via stabilization of SREBP1. Zhang S, Wang J, Cheng G. Proc Natl Acad Sci U S A 118 e2107108118 (2021)
  49. Acriflavine, a clinically approved drug, inhibits SARS-CoV-2 and other betacoronaviruses. Napolitano V, Dabrowska A, Schorpp K, Mourão A, Barreto-Duran E, Benedyk M, Botwina P, Brandner S, Bostock M, Chykunova Y, Czarna A, Dubin G, Fröhlich T, Hölscher M, Jedrysik M, Matsuda A, Owczarek K, Pachota M, Plettenburg O, Potempa J, Rothenaigner I, Schlauderer F, Slysz K, Szczepanski A, Greve-Isdahl Mohn K, Blomberg B, Sattler M, Hadian K, Popowicz GM, Pyrc K. Cell Chem Biol 29 774-784.e8 (2022)
  50. An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets. Thurakkal L, Singh S, Roy R, Kar P, Sadhukhan S, Porel M. Chem Phys Lett 763 138193 (2021)
  51. Impact of remdesivir according to the pre-admission symptom duration in patients with COVID-19. Garcia-Vidal C, Alonso R, Camon AM, Cardozo C, Albiach L, Agüero D, Marcos MA, Ambrosioni J, Bodro M, Chumbita M, de la Mora L, Garcia-Pouton N, Dueñas G, Hernandez-Meneses M, Inciarte A, Cuesta G, Meira F, Morata L, Puerta-Alcalde P, Herrera S, Tuset M, Castro P, Prieto-Gonzalez S, Almuedo-Riera A, Mensa J, Martínez JA, Sanjuan G, Nicolas JM, Del Rio A, Muñoz J, Vila J, Garcia F, Soriano A, Hospital Clinic of Barcelona COVID-19 Research Group. J Antimicrob Chemother 76 3296-3302 (2021)
  52. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, Zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Front Mol Biosci 8 653148 (2021)
  53. Novel cleavage sites identified in SARS-CoV-2 spike protein reveal mechanism for cathepsin L-facilitated viral infection and treatment strategies. Zhao MM, Zhu Y, Zhang L, Zhong G, Tai L, Liu S, Yin G, Lu J, He Q, Li MJ, Zhao RX, Wang H, Huang W, Fan C, Shuai L, Wen Z, Wang C, He X, Chen Q, Liu B, Xiong X, Bu Z, Wang Y, Sun F, Yang JK. Cell Discov 8 53 (2022)
  54. Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. Han N, Hwang W, Tzelepis K, Schmerer P, Yankova E, MacMahon M, Lei W, M Katritsis N, Liu A, Felgenhauer U, Schuldt A, Harris R, Chapman K, McCaughan F, Weber F, Kouzarides T. Sci Adv 7 eabh3032 (2021)
  55. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp5 main protease. Milligan JC, Zeisner TU, Papageorgiou G, Joshi D, Soudy C, Ulferts R, Wu M, Lim CT, Tan KW, Weissmann F, Canal B, Fujisawa R, Deegan T, Nagaraj H, Bineva-Todd G, Basier C, Curran JF, Howell M, Beale R, Labib K, O'Reilly N, Diffley JFX. Biochem J 478 2499-2515 (2021)
  56. Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay. Pitsillou E, Liang J, Ververis K, Hung A, Karagiannis TC. J Mol Graph Model 104 107851 (2021)
  57. Structure-based phylogeny identifies avoralstat as a TMPRSS2 inhibitor that prevents SARS-CoV-2 infection in mice. Sun YJ, Velez G, Parsons DE, Li K, Ortiz ME, Sharma S, McCray PB, Bassuk AG, Mahajan VB. J Clin Invest 131 147973 (2021)
  58. All hands on deck: SARS-CoV-2 proteins that block early anti-viral interferon responses. Setaro AC, Gaglia MM. Curr Res Virol Sci 2 100015 (2021)
  59. Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study. Nejat R, Sadr AS. In Silico Pharmacol 9 1 (2021)
  60. Computational Determination of Potential Multiprotein Targeting Natural Compounds for Rational Drug Design Against SARS-COV-2. Muhseen ZT, Hameed AR, Al-Hasani HMH, Ahmad S, Li G. Molecules 26 674 (2021)
  61. Generation of a Sleeping Beauty Transposon-Based Cellular System for Rapid and Sensitive Screening for Compounds and Cellular Factors Limiting SARS-CoV-2 Replication. Widera M, Wilhelm A, Toptan T, Raffel JM, Kowarz E, Roesmann F, Grözinger F, Siemund AL, Luciano V, Külp M, Reis J, Bracharz S, Pallas C, Ciesek S, Marschalek R. Front Microbiol 12 701198 (2021)
  62. Identification of phytocompounds from Houttuynia cordata Thunb. as potential inhibitors for SARS-CoV-2 replication proteins through GC-MS/LC-MS characterization, molecular docking and molecular dynamics simulation. Das SK, Mahanta S, Tanti B, Tag H, Hui PK. Mol Divers 26 365-388 (2022)
  63. The SARS-unique domain (SUD) of SARS-CoV and SARS-CoV-2 interacts with human Paip1 to enhance viral RNA translation. Lei J, Ma-Lauer Y, Han Y, Thoms M, Buschauer R, Jores J, Thiel V, Beckmann R, Deng W, Leonhardt H, Hilgenfeld R, von Brunn A. EMBO J 40 e102277 (2021)
  64. Validation and Invalidation of SARS-CoV-2 Papain-like Protease Inhibitors. Ma C, Wang J. ACS Pharmacol Transl Sci 5 102-109 (2022)
  65. Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning. Ong E, Cooke MF, Huffman A, Xiang Z, Wong MU, Wang H, Seetharaman M, Valdez N, He Y. Nucleic Acids Res 49 W671-W678 (2021)
  66. Nanoparticles of ZnO/Berberine complex contract COVID-19 and respiratory co-bacterial infection in addition to elimination of hydroxychloroquine toxicity. Ghareeb DA, Saleh SR, Seadawy MG, Nofal MS, Abdulmalek SA, Hassan SF, Khedr SM, AbdElwahab MG, Sobhy AA, Abdel-Hamid ASA, Yassin AM, Elmoneam AAA, Masoud AA, Kaddah MMY, El-Zahaby SA, Al-Mahallawi AM, El-Gharbawy AM, Zaki A, Seif IK, Kenawy MY, Amin M, Amer K, El Demellawy MA. J Pharm Investig 51 735-757 (2021)
  67. Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening. Manandhar A, Blass BE, Colussi DJ, Almi I, Abou-Gharbia M, Klein ML, Elokely KM. J Chem Inf Model 61 1020-1032 (2021)
  68. In Silico Screening of Semi-Synthesized Compounds as Potential Inhibitors for SARS-CoV-2 Papain-like Protease: Pharmacophoric Features, Molecular Docking, ADMET, Toxicity and DFT Studies. Alesawy MS, Elkaeed EB, Alsfouk AA, Metwaly AM, Eissa IH. Molecules 26 6593 (2021)
  69. Bispecific repurposed medicines targeting the viral and immunological arms of COVID-19. Redhead MA, Owen CD, Brewitz L, Collette AH, Lukacik P, Strain-Damerell C, Robinson SW, Collins PM, Schäfer P, Swindells M, Radoux CJ, Hopkins IN, Fearon D, Douangamath A, von Delft F, Malla TR, Vangeel L, Vercruysse T, Thibaut J, Leyssen P, Nguyen TT, Hull M, Tumber A, Hallett DJ, Schofield CJ, Stuart DI, Hopkins AL, Walsh MA. Sci Rep 11 13208 (2021)
  70. Drug Repurposing for the SARS-CoV-2 Papain-Like Protease. Cho CC, Li SG, Lalonde TJ, Yang KS, Yu G, Qiao Y, Xu S, Ray Liu W. ChemMedChem 17 e202100455 (2022)
  71. Novel mutations in NSP-1 and PLPro of SARS-CoV-2 NIB-1 genome mount for effective therapeutics. Hossain MU, Bhattacharjee A, Emon MTH, Chowdhury ZM, Ahammad I, Mosaib MG, Moniruzzaman M, Rahman MH, Islam MN, Ahmed I, Amin MR, Rashed A, Das KC, Keya CA, Salimullah M, Salimullah M. J Genet Eng Biotechnol 19 52 (2021)
  72. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. Dodero-Rojas E, Onuchic JN, Whitford PC. Elife 10 e70362 (2021)
  73. Non-Toxic Dimeric Peptides Derived from the Bothropstoxin-I Are Potent SARS-CoV-2 and Papain-like Protease Inhibitors. Freire MCLC, Noske GD, Bitencourt NV, Sanches PRS, Santos-Filho NA, Gawriljuk VO, de Souza EP, Nogueira VHR, de Godoy MO, Nakamura AM, Fernandes RS, Godoy AS, Juliano MA, Peres BM, Barbosa CG, Moraes CB, Freitas-Junior LHG, Cilli EM, Guido RVC, Oliva G. Molecules 26 4896 (2021)
  74. Antiviral Activity of Selected Lamiaceae Essential Oils and Their Monoterpenes Against SARS-Cov-2. Ćavar Zeljković S, Schadich E, Džubák P, Hajdúch M, Tarkowski P. Front Pharmacol 13 893634 (2022)
  75. Identification of DAXX as a restriction factor of SARS-CoV-2 through a CRISPR/Cas9 screen. Mac Kain A, Maarifi G, Aicher SM, Arhel N, Baidaliuk A, Munier S, Donati F, Vallet T, Tran QD, Hardy A, Chazal M, Porrot F, OhAinle M, Carlson-Stevermer J, Oki J, Holden K, Zimmer G, Simon-Lorière E, Bruel T, Schwartz O, van der Werf S, Jouvenet N, Nisole S, Vignuzzi M, Roesch F. Nat Commun 13 2442 (2022)
  76. Meticulous assessment of natural compounds from NPASS database for identifying analogue of GRL0617, the only known inhibitor for SARS-CoV2 papain-like protease (PLpro) using rigorous computational workflow. Parmar P, Rao P, Sharma A, Shukla A, Rawal RM, Saraf M, Patel BV, Goswami D. Mol Divers 26 389-407 (2022)
  77. Structure-based drug designing of naphthalene based SARS-CoV PLpro inhibitors for the treatment of COVID-19. Bhati S. Heliyon 6 e05558 (2020)
  78. The African swine fever virus protease pS273R inhibits DNA sensing cGAS-STING pathway by targeting IKKε. Luo J, Zhang J, Ni J, Jiang S, Xia N, Guo Y, Shao Q, Cao Q, Zheng W, Chen N, Zhang Q, Chen H, Chen Q, Zhu H, Meurens F, Zhu J. Virulence 13 740-756 (2022)
  79. Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells. Chen X, Saccon E, Appelberg KS, Mikaeloff F, Rodriguez JE, Vinhas BS, Frisan T, Végvári Á, Mirazimi A, Neogi U, Gupta S. Cell Death Discov 7 114 (2021)
  80. Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2. Kumar V, Parate S, Yoon S, Lee G, Lee KW. Front Microbiol 12 647295 (2021)
  81. Dynamic landscape mapping of humoral immunity to SARS-CoV-2 identifies non-structural protein antibodies associated with the survival of critical COVID-19 patients. Cheng L, Zhang X, Chen Y, Wang D, Zhang D, Yan S, Wang H, Xiao M, Liang T, Li H, Xu M, Hou X, Dai J, Wu X, Li M, Lu M, Wu D, Tian R, Zhao J, Zhang Y, Cao W, Wang J, Yan X, Zhou X, Liu Z, Xu Y, He F, Li Y, Yu X, Zhang S. Signal Transduct Target Ther 6 304 (2021)
  82. A Dual-Color Fluorescent Probe Allows Simultaneous Imaging of Main and Papain-like Proteases of SARS-CoV-2-Infected Cells for Accurate Detection and Rapid Inhibitor Screening. Cheng Y, Borum RM, Clark AE, Jin Z, Moore C, Fajtová P, O'Donoghue AJ, Carlin AF, Jokerst JV. Angew Chem Int Ed Engl 61 e202113617 (2022)
  83. Antiviral cyclic peptides targeting the main protease of SARS-CoV-2. Johansen-Leete J, Ullrich S, Fry SE, Frkic R, Bedding MJ, Aggarwal A, Ashhurst AS, Ekanayake KB, Mahawaththa MC, Sasi VM, Luedtke S, Ford DJ, O'Donoghue AJ, Passioura T, Larance M, Otting G, Turville S, Jackson CJ, Nitsche C, Payne RJ. Chem Sci 13 3826-3836 (2022)
  84. Effect of immunosuppression maintenance in solid organ transplant recipients with COVID-19: Systematic review and meta-analysis. Karruli A, Spiezia S, Boccia F, Gagliardi M, Patauner F, Salemme A, Maiello C, Zampino R, Durante-Mangoni E. Transpl Infect Dis 23 e13595 (2021)
  85. Proteins from SARS-CoV-2 reduce T cell proliferation: A mirror image of sepsis. Avendaño-Ortiz J, Lozano-Rodríguez R, Martín-Quirós A, Maroun-Eid C, Terrón V, Valentín J, Montalbán-Hernández K, Ruiz de la Bastida F, García-Garrido MA, Cubillos-Zapata C, Del Balzo-Castillo Á, Aguirre LA, López-Collazo E. Heliyon 6 e05635 (2020)
  86. iPSC screening for drug repurposing identifies anti-RNA virus agents modulating host cell susceptibility. Imamura K, Sakurai Y, Enami T, Shibukawa R, Nishi Y, Ohta A, Shu T, Kawaguchi J, Okada S, Hoenen T, Yasuda J, Inoue H. FEBS Open Bio 11 1452-1464 (2021)
  87. Aloin isoforms (A and B) selectively inhibits proteolytic and deubiquitinating activity of papain like protease (PLpro) of SARS-CoV-2 in vitro. Lewis DSM, Ho J, Wills S, Kawall A, Sharma A, Chavada K, Ebert MCCJC, Evoli S, Singh A, Rayalam S, Mody V, Taval S. Sci Rep 12 2145 (2022)
  88. Comparative Genomics and Characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern From Amazonas, Brazil. Zimerman RA, Ferrareze PAG, Cadegiani FA, Wambier CG, Fonseca DDN, de Souza AR, Goren A, Rotta LN, Ren Z, Thompson CE. Front Med (Lausanne) 9 806611 (2022)
  89. Computational investigation of benzalacetophenone derivatives against SARS-CoV-2 as potential multi-target bioactive compounds. Khanal P, Patil VS, Bhandare VV, Dwivedi PSR, Shastry CS, Patil BM, Gurav SS, Harish DR, Roy S. Comput Biol Med 146 105668 (2022)
  90. Evolution of SARS-CoV-2 in Spain during the First Two Years of the Pandemic: Circulating Variants, Amino Acid Conservation, and Genetic Variability in Structural, Non-Structural, and Accessory Proteins. Troyano-Hernáez P, Reinosa R, Holguín Á. Int J Mol Sci 23 6394 (2022)
  91. Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication. Vanderwall ER, Barrow KA, Rich LM, Read DF, Trapnell C, Okoloko O, Ziegler SF, Hallstrand TS, White MP, Debley JS. Sci Rep 12 6972 (2022)
  92. Comparative Host Interactomes of the SARS-CoV-2 Nonstructural Protein 3 and Human Coronavirus Homologs. Almasy KM, Davies JP, Plate L. Mol Cell Proteomics 20 100120 (2021)
  93. Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 Mpro. Ngo ST, Nguyen TH, Tung NT, Mai BK. RSC Adv 12 3729-3737 (2022)
  94. Pyronaridine Protects against SARS-CoV-2 Infection in Mouse. Puhl AC, Gomes GF, Damasceno S, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Monakhova N, Riabova O, Lane TR, Makarov V, Veras FP, Batah SS, Fabro AT, Oliva G, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. ACS Infect Dis 8 1147-1160 (2022)
  95. SARS-CoV-2 Spike Antagonizes Innate Antiviral Immunity by Targeting Interferon Regulatory Factor 3. Freitas RS, Crum TF, Parvatiyar K. Front Cell Infect Microbiol 11 789462 (2021)
  96. SARS-CoV-2 nsp5 Exhibits Stronger Catalytic Activity and Interferon Antagonism than Its SARS-CoV Ortholog. Chen J, Li Z, Guo J, Xu S, Zhou J, Chen Q, Tong X, Wang D, Peng G, Fang L, Xiao S. J Virol 96 e0003722 (2022)
  97. Identifying and repurposing antiviral drugs against severe acute respiratory syndrome coronavirus 2 with in silico and in vitro approaches. Watashi K. Biochem Biophys Res Commun 538 137-144 (2021)
  98. Mechanism-based traps enable protease and hydrolase substrate discovery. Tang S, Beattie AT, Kafkova L, Petris G, Huguenin-Dezot N, Fiedler M, Freeman M, Chin JW. Nature 602 701-707 (2022)
  99. Nonstructural protein 7 and 8 complexes of SARS-CoV-2. Zhang C, Li L, He J, Chen C, Su D. Protein Sci 30 873-881 (2021)
  100. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Nat Commun 14 1733 (2023)
  101. SARS-CoV-2 Nsp6 damages Drosophila heart and mouse cardiomyocytes through MGA/MAX complex-mediated increased glycolysis. Zhu JY, Wang G, Huang X, Lee H, Lee JG, Yang P, van de Leemput J, Huang W, Kane MA, Yang P, Han Z. Commun Biol 5 1039 (2022)
  102. In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease. Sanachai K, Mahalapbutr P, Sanghiran Lee V, Rungrotmongkol T, Hannongbua S. J Phys Chem B 125 13644-13656 (2021)
  103. An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population. Cuspoca AF, Díaz LL, Acosta AF, Peñaloza MK, Méndez YR, Clavijo DC, Yosa Reyes J. Vaccines (Basel) 9 581 (2021)
  104. Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns. Mslati H, Gentile F, Perez C, Cherkasov A. J Chem Inf Model 61 3771-3788 (2021)
  105. Drug-Repurposing Screening Identified Tropifexor as a SARS-CoV-2 Papain-like Protease Inhibitor. Ma C, Hu Y, Wang Y, Choza J, Wang J. ACS Infect Dis 8 1022-1030 (2022)
  106. High-Throughput Fluorescent Assay for Inhibitor Screening of Proteases from RNA Viruses. Cihlova B, Huskova A, Böserle J, Nencka R, Boura E, Silhan J. Molecules 26 3792 (2021)
  107. Mesenchymal Stem Cells and Their Extracellular Vesicles: A Potential Game Changer for the COVID-19 Crisis. Kassem DH, Kamal MM. Front Cell Dev Biol 8 587866 (2020)
  108. Natural biflavones are potent inhibitors against SARS-CoV-2 papain-like protease. Li L, Ma L, Hu Y, Li X, Yu M, Shang H, Zou Z. Phytochemistry 193 112984 (2022)
  109. Unraveling the unbinding pathways of SARS-CoV-2 Papain-like proteinase known inhibitors by Supervised Molecular Dynamics simulation. Sohraby F, Aryapour H. PLoS One 16 e0251910 (2021)
  110. Computational screening of potential drugs against COVID-19 disease: the Neuropilin-1 receptor as molecular target. Charoute H, Elkarhat Z, Elkhattabi L, El Fahime E, Oukkache N, Rouba H, Barakat A. Virusdisease 33 23-31 (2022)
  111. Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease. Hajbabaie R, Harper MT, Rahman T. Molecules 26 1134 (2021)
  112. Heterologous Immunity Between SARS-CoV-2 and Pathogenic Bacteria. Eggenhuizen PJ, Ng BH, Chang J, Cheong RMY, Yellapragada A, Wong WY, Ting YT, Monk JA, Gan PY, Holdsworth SR, Ooi JD. Front Immunol 13 821595 (2022)
  113. Mass Spectrometric Assays Reveal Discrepancies in Inhibition Profiles for the SARS-CoV-2 Papain-Like Protease. Brewitz L, Kamps JJAG, Lukacik P, Strain-Damerell C, Zhao Y, Tumber A, Malla TR, Orville AM, Walsh MA, Schofield CJ. ChemMedChem 17 e202200016 (2022)
  114. Polyphenols as alternative treatments of COVID-19. Wu Y, Pegan SD, Crich D, Desrochers E, Starling EB, Hansen MC, Booth C, Nicole Mullininx L, Lou L, Chang KY, Xie ZR. Comput Struct Biotechnol J 19 5371-5380 (2021)
  115. Predicted coronavirus Nsp5 protease cleavage sites in the human proteome. Scott BM, Lacasse V, Blom DG, Tonner PD, Blom NS. BMC Genom Data 23 25 (2022)
  116. Upregulated Proteasome Subunits in COVID-19 Patients: A Link with Hypoxemia, Lymphopenia and Inflammation. Alfaro E, Díaz-García E, García-Tovar S, Zamarrón E, Mangas A, Galera R, López-Collazo E, García-Rio F, Cubillos-Zapata C. Biomolecules 12 442 (2022)
  117. Zinc pyrithione is a potent inhibitor of PLPro and cathepsin L enzymes with ex vivo inhibition of SARS-CoV-2 entry and replication. Kladnik J, Dolinar A, Kljun J, Perea D, Grau-Expósito J, Genescà M, Novinec M, Buzon MJ, Turel I. J Enzyme Inhib Med Chem 37 2158-2168 (2022)
  118. Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine. Brewitz L, Dumjahn L, Zhao Y, Owen CD, Laidlaw SM, Malla TR, Nguyen D, Lukacik P, Salah E, Crawshaw AD, Warren AJ, Trincao J, Strain-Damerell C, Carroll MW, Walsh MA, Schofield CJ. J Med Chem 66 2663-2680 (2023)
  119. An electrochemical biosensor for SARS-CoV-2 detection via its papain-like cysteine protease and the protease inhibitor screening. Liang Q, Huang Y, Wang M, Kuang D, Yang J, Yi Y, Shi H, Li J, Yang J, Li G. Chem Eng J 452 139646 (2023)
  120. Design of modular autoproteolytic gene switches responsive to anti-coronavirus drug candidates. Franko N, Teixeira AP, Xue S, Charpin-El Hamri G, Fussenegger M. Nat Commun 12 6786 (2021)
  121. Evaluation of the anti-SARS-CoV-2 properties of essential oils and aromatic extracts. Strub DJ, Talma M, Strub M, Rut W, Zmudzinski M, Brud W, Neyts J, Vangeel L, Zhang L, Sun X, Lv Z, Nayak D, Olsen SK, Hilgenfeld R, Jochmans D, Drąg M. Sci Rep 12 14230 (2022)
  122. Host E3 ligase HUWE1 attenuates the proapoptotic activity of the MERS-CoV accessory protein ORF3 by promoting its ubiquitin-dependent degradation. Zhou Y, Zheng R, Liu S, Disoma C, Du A, Li S, Chen Z, Dong Z, Zhang Y, Li S, Liu P, Razzaq A, Chen X, Liao Y, Tao S, Liu Y, Xu L, Zhang Q, Peng J, Deng X, Li S, Jiang T, Xia Z. J Biol Chem 298 101584 (2022)
  123. Identification of Cysteine 270 as a Novel Site for Allosteric Modulators of SARS-CoV-2 Papain-Like Protease. Hu H, Wang Q, Su H, Shao Q, Zhao W, Chen G, Li M, Xu Y. Angew Chem Int Ed Engl 61 e202212378 (2022)
  124. Identifying enhancers of innate immune signaling as broad-spectrum antivirals active against emerging viruses. Maarifi G, Martin MF, Zebboudj A, Boulay A, Nouaux P, Fernandez J, Lagisquet J, Garcin D, Gaudin R, Arhel NJ, Nisole S. Cell Chem Biol 29 1113-1125.e6 (2022)
  125. Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses. Shi R, Feng Z, Zhang X. Genomics Proteomics Bioinformatics 19 707-726 (2021)
  126. Mutations in the nonstructural proteins of SARS-CoV-2 may contribute to adverse clinical outcome in patients with COVID-19. Ichikawa T, Torii S, Suzuki H, Takada A, Suzuki S, Nakajima M, Tampo A, Kakinoki Y. Int J Infect Dis 122 123-129 (2022)
  127. SARS-CoV-2 Unrevealed: Ultrastructural and Nanomechanical Analysis. Cardoso-Lima R, Souza PFN, Guedes MIF, Santos-Oliveira R, Rebelo Alencar LM. Langmuir 37 10762-10769 (2021)
  128. A proof-of-concept study on the genomic evolution of Sars-Cov-2 in molnupiravir-treated, paxlovid-treated and drug-naïve patients. Alteri C, Fox V, Scutari R, Burastero GJ, Volpi S, Faltoni M, Fini V, Granaglia A, Esperti S, Gallerani A, Costabile V, Fontana B, Franceschini E, Meschiari M, Campana A, Bernardi S, Villani A, Bernaschi P, Russo C, Guaraldi G, Mussini C, Perno CF. Commun Biol 5 1376 (2022)
  129. Genome-Wide Analysis of the Indispensable Role of Non-structural Proteins in the Replication of SARS-CoV-2. Jin Y, Ouyang M, Yu T, Zhuang J, Wang W, Liu X, Duan F, Guo D, Peng X, Pan JA. Front Microbiol 13 907422 (2022)
  130. Innate immunology in COVID-19-a living review. Part I: viral entry, sensing and evasion. Coveney C, Tellier M, Lu F, Maleki-Toyserkani S, Jones R, Bart VMT, Pring E, Alrubayyi A, Richter FC, Scourfield DO, Rehwinkel J, Rodrigues PRS, Davies LC, Gea-Mallorquí E, Oxford-Cardiff COVID19 Literature Consortium. Oxf Open Immunol 1 iqaa004 (2020)
  131. Molecular docking unveils the potential of andrographolide derivatives against COVID-19: an in silico approach. Veerasamy R, Karunakaran R. J Genet Eng Biotechnol 20 58 (2022)
  132. Profiling COVID-19 Genetic Research: A Data-Driven Study Utilizing Intelligent Bibliometrics. Wu M, Zhang Y, Grosser M, Tipper S, Venter D, Lin H, Lu J. Front Res Metr Anal 6 683212 (2021)
  133. Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation. Patel R, Prajapati J, Rao P, Rawal RM, Saraf M, Goswami D. Mol Divers 26 2189-2209 (2022)
  134. Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, Mpro and PLpro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. Naidoo D, Kar P, Roy A, Mutanda T, Bwapwa J, Sen A, Anandraj A. Molecules 26 5114 (2021)
  135. Structure of the multiple functional domains from coronavirus nonstructural protein 3. Li M, Ye G, Si Y, Shen Z, Liu Z, Shi Y, Xiao S, Fu ZF, Peng G. Emerg Microbes Infect 10 66-80 (2021)
  136. Structure-based lead optimization of peptide-based vinyl methyl ketones as SARS-CoV-2 main protease inhibitors. Previti S, Ettari R, Calcaterra E, Di Maro S, Hammerschmidt SJ, Müller C, Ziebuhr J, Schirmeister T, Cosconati S, Zappalà M. Eur J Med Chem 247 115021 (2023)
  137. The pivotal roles of the host immune response in the fine-tuning the infection and the development of the vaccines for SARS-CoV-2. Alturaiki W, Mubarak A, Al Jurayyan A, Hemida MG. Hum Vaccin Immunother 17 3297-3309 (2021)
  138. In silico analysis of SARS-CoV-2 papain-like protease potential inhibitors. Elseginy SA, Anwar MM. RSC Adv 11 38616-38631 (2021)
  139. Binding of SARS-CoV Covalent Non-Covalent Inhibitors to the SARS-CoV-2 Papain-Like Protease and Ovarian Tumor Domain Deubiquitinases. Sivakumar D, Stein M. Biomolecules 11 802 (2021)
  140. Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics. Abdallah HM, El-Halawany AM, Darwish KM, Algandaby MM, Mohamed GA, Ibrahim SRM, Koshak AE, Elhady SS, Fadil SA, Alqarni AA, Abdel-Naim AB, Elfaky MA. Plants (Basel) 11 1914 (2022)
  141. Celastrol: A lead compound that inhibits SARS-CoV-2 replication, the activity of viral and human cysteine proteases, and virus-induced IL-6 secretion. Fuzo CA, Martins RB, Fraga-Silva TFC, Amstalden MK, Canassa De Leo T, Souza JP, Lima TM, Faccioli LH, Okamoto DN, Juliano MA, França SC, Juliano L, Bonato VLD, Arruda E, Dias-Baruffi M. Drug Dev Res 83 1623-1640 (2022)
  142. In Silico Study towards Repositioning of FDA-Approved Drug Candidates for Anticoronaviral Therapy: Molecular Docking, Molecular Dynamics and Binding Free Energy Calculations. Qayed WS, Ferreira RS, Silva JRA. Molecules 27 5988 (2022)
  143. In search of drugs to alleviate suppression of the host's innate immune responses against SARS-CoV-2 using a molecular modeling approach. Choudhury S, Moulick D, Borah A, Saikia P, Mazumder MK. In Silico Pharmacol 9 26 (2021)
  144. Inhibitor induced conformational changes in SARS-COV-2 papain-like protease. Ferreira GM, Pillaiyar T, Hirata MH, Poso A, Kronenberger T. Sci Rep 12 11585 (2022)
  145. Investigation of small molecule inhibitors of the SARS-CoV-2 papain-like protease by all-atom microsecond modelling, PELE Monte Carlo simulations, and in vitro activity inhibition. Liang JJ, Pitsillou E, Ververis K, Guallar V, Hung A, Karagiannis TC. Chem Phys Lett 788 139294 (2022)
  146. Multi-Design Differential Expression Profiling of COVID-19 Lung Autopsy Specimens Reveals Significantly Deregulated Inflammatory Pathways and SFTPC Impaired Transcription. Fassan M, Collesei A, Angerilli V, Sbaraglia M, Fortarezza F, Pezzuto F, De Gaspari M, Businello G, Moni M, Rizzo S, Traverso G, Colosso V, Taschin E, Lunardi F, Valls AF, Schiavi F, Basso C, Calabrese F, Dei Tos AP. Cells 11 1011 (2022)
  147. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Viruses 13 883 (2021)
  148. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. Bell EW, Schwartz JH, Freddolino PL, Zhang Y. J Mol Biol 434 167530 (2022)
  149. Papain-like protease of SARS-CoV-2 inhibits RLR signaling in a deubiquitination-dependent and deubiquitination-independent manner. Ran XH, Zhu JW, Chen YY, Ni RZ, Mu D. Front Immunol 13 947272 (2022)
  150. Polyphenolic Compounds Isolated from Marine Algae Attenuate the Replication of SARS-CoV-2 in the Host Cell through a Multi-Target Approach of 3CLpro and PLpro. Nagahawatta DP, Liyanage NM, Je JG, Jayawardhana HHACK, Jayawardena TU, Jeong SH, Kwon HJ, Choi CS, Jeon YJ. Mar Drugs 20 786 (2022)
  151. SARS-CoV-2 Infected Pediatric Cerebral Cortical Neurons: Transcriptomic Analysis and Potential Role of Toll-like Receptors in Pathogenesis. Gugliandolo A, Chiricosta L, Calcaterra V, Biasin M, Cappelletti G, Carelli S, Zuccotti G, Avanzini MA, Bramanti P, Pelizzo G, Mazzon E. Int J Mol Sci 22 8059 (2021)
  152. Structure-Based Design of a Dual-Targeted Covalent Inhibitor Against Papain-like and Main Proteases of SARS-CoV-2. Yu W, Zhao Y, Ye H, Wu N, Liao Y, Chen N, Li Z, Wan N, Hao H, Yan H, Xiao Y, Lai M. J Med Chem 65 16252-16267 (2022)
  153. Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. Roy R, Jonniya NA, Poddar S, Sk MF, Kar P. J Chem Inf Model 61 6038-6052 (2021)
  154. Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis. Naderi S, Chen PE, Murall CL, Poujol R, Kraemer S, Pickering BS, Sagan SM, Shapiro BJ. Elife 12 e83685 (2023)
  155. A strategy for evaluating potential antiviral resistance to small molecule drugs and application to SARS-CoV-2. Sargsyan K, Mazmanian K, Lim C. Sci Rep 13 502 (2023)
  156. Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease. Hognon C, Marazzi M, García-Iriepa C. Int J Mol Sci 23 5855 (2022)
  157. Design, synthesis and in silico screening of benzoxazole-thiazolidinone hybrids as potential inhibitors of SARS-CoV-2 proteases. Krishna Cheerala VS, Ghanta P, Neelakantan SC. RSC Adv 11 39328-39342 (2021)
  158. Design, synthesis and docking study of Vortioxetine derivatives as a SARS-CoV-2 main protease inhibitor. Suryavanshi H, Chaudhari RD, Patil V, Majumdar S, Debnath S, Biswas G. Daru 30 139-152 (2022)
  159. Direct Interaction of Coronavirus Nonstructural Protein 3 with Melanoma Differentiation-Associated Gene 5 Modulates Type I Interferon Response during Coronavirus Infection. Sun X, Quan L, Chen R, Liu D. Int J Mol Sci 23 11692 (2022)
  160. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PLpro and Mpro proteases, and nsp14 guanine N7-methyltransferase. Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Sci Rep 13 9161 (2023)
  161. Evaluation of antiviral activity of Carica papaya leaves against SARS-CoV-2 assisted by metabolomic profiling. Adel A, Elnaggar MS, Albohy A, Elrashedy AA, Mostafa A, Kutkat O, Abdelmohsen UR, Al-Sayed E, Rabeh MA. RSC Adv 12 32844-32852 (2022)
  162. Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses. Freitas BT, Ahiadorme DA, Bagul RS, Durie IA, Ghosh S, Hill J, Kramer NE, Murray J, O'Boyle BM, Onobun E, Pirrone MG, Shepard JD, Enos S, Subedi YP, Upadhyaya K, Tripp RA, Cummings BS, Crich D, Pegan SD. ACS Infect Dis 8 596-611 (2022)
  163. Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses. Zhang K, Wang K, Zhang C, Teng X, Li D, Chen M. BMC Cancer 22 687 (2022)
  164. Identification of Natural Products Inhibiting SARS-CoV-2 by Targeting Viral Proteases: A Combined in Silico and in Vitro Approach. Wasilewicz A, Kirchweger B, Bojkova D, Abi Saad MJ, Langeder J, Bütikofer M, Adelsberger S, Grienke U, Cinatl J, Petermann O, Scapozza L, Orts J, Kirchmair J, Rabenau HF, Rollinger JM. J Nat Prod 86 264-275 (2023)
  165. Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules: In silico studies. Pitsillou E, Liang J, Hung A, Karagiannis TC. Chem Phys Lett 771 138468 (2021)
  166. Inhibitors of Deubiquitinating Enzymes Interfere with the SARS-CoV-2 Papain-like Protease and Block Virus Replication In Vitro. Große M, Setz C, Rauch P, Auth J, Morokutti-Kurz M, Temchura V, Schubert U. Viruses 14 1404 (2022)
  167. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Wiley Interdiscip Rev Comput Mol Sci e1622 (2022)
  168. Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, and in vitro Studies. Kulandaisamy R, Kushwaha T, Dalal A, Kumar V, Singh D, Baswal K, Sharma P, Praneeth K, Jorwal P, Kayampeta SR, Sharma T, Maddur S, Kumar M, Kumar S, Polamarasetty A, Singh A, Sehgal D, Gholap SL, Appaiahgari MB, Katika MR, Inampudi KK. Front Microbiol 13 877813 (2022)
  169. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding. Dudouet P, Colson P, Aherfi S, Levasseur A, Beye M, Delerce J, Burel E, Lavrard P, Bader W, Lagier JC, Fournier PE, La Scola B, Raoult D. Sci Rep 12 18721 (2022)
  170. Systematic Exploration of SARS-CoV-2 Adaptation to Vero E6, Vero E6/TMPRSS2, and Calu-3 Cells. Aiewsakun P, Phumiphanjarphak W, Ludowyke N, Purwono PB, Manopwisedjaroen S, Srisaowakarn C, Ekronarongchai S, Suksatu A, Yuvaniyama J, Thitithanyanont A. Genome Biol Evol 15 evad035 (2023)
  171. The main protease of SARS-CoV-2 cleaves histone deacetylases and DCP1A, attenuating the immune defense of the interferon-stimulated genes. Song L, Wang D, Abbas G, Li M, Cui M, Wang J, Lin Z, Zhang XE. J Biol Chem 299 102990 (2023)
  172. A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2. Singh E, Jha RK, Khan RJ, Kumar A, Jain M, Muthukumaran J, Singh AK. Comput Biol Chem 99 107721 (2022)
  173. A robust high-throughput fluorescence polarization assay for rapid screening of SARS-CoV-2 papain-like protease inhibitors. Yan H, Liu Z, Yan G, Liu X, Liu X, Wang Y, Chen Y. Virology 574 18-24 (2022)
  174. An MVA-based vector expressing cell-free ISG15 increases IFN-I production and improves HIV-1-specific CD8 T cell immune responses. Falqui M, Perdiguero B, Coloma R, Albert M, Marcos-Villar L, McGrail JP, Sorzano CÓS, Esteban M, Gómez CE, Guerra S. Front Cell Infect Microbiol 13 1187193 (2023)
  175. An optimized circular polymerase extension reaction-based method for functional analysis of SARS-CoV-2. Liu G, Gack MU. Virol J 20 63 (2023)
  176. Annotating Spike Protein Polymorphic Amino Acids of Variants of SARS-CoV-2, Including Omicron. Mahardika GN, Mahendra NB, Mahardika BK, Suardana IBK, Pharmawati M. Biochem Res Int 2022 2164749 (2022)
  177. Discovery of Potential SARS-CoV-2 Papain-like Protease Natural Inhibitors Employing a Multi-Phase In Silico Approach. Elkaeed EB, Metwaly AM, Alesawy MS, Saleh AM, Alsfouk AA, Eissa IH. Life (Basel) 12 1407 (2022)
  178. Evaluating Stability and Activity of SARS-CoV-2 PLpro for High-throughput Screening of Inhibitors. Arya R, Prashar V, Kumar M. Mol Biotechnol 64 1-8 (2022)
  179. Green and efficient one-pot three-component synthesis of novel drug-like furo[2,3-d]pyrimidines as potential active site inhibitors and putative allosteric hotspots modulators of both SARS-CoV-2 MPro and PLPro. Mousavi H, Zeynizadeh B, Rimaz M. Bioorg Chem 135 106390 (2023)
  180. Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease. Ewert W, Günther S, Miglioli F, Falke S, Reinke PYA, Niebling S, Günther C, Han H, Srinivasan V, Brognaro H, Lieske J, Lorenzen K, Garcia-Alai MM, Betzel C, Carcelli M, Hinrichs W, Rogolino D, Meents A. Front Chem 10 832431 (2022)
  181. Hydrogen bonding penalty used for virtual screening to discover potent inhibitors for Papain-Like cysteine proteases of SARS-CoV-2. Zhao G, Liu X, Wang S, Bai Z, Zhang S, Wang Y, Yu H, Xu X. Chem Biol Drug Des 100 502-514 (2022)
  182. Hydroxytyrosol Recovers SARS-CoV-2-PLpro-Dependent Impairment of Interferon Related Genes in Polarized Human Airway, Intestinal and Liver Epithelial Cells. Crudele A, Smeriglio A, Ingegneri M, Panera N, Bianchi M, Braghini MR, Pastore A, Tocco V, Carsetti R, Zaffina S, Alisi A, Trombetta D. Antioxidants (Basel) 11 1466 (2022)
  183. ILRUN Downregulates ACE2 Expression and Blocks Infection of Human Cells by SARS-CoV-2. Tribolet L, Alexander MR, Brice AM, van Vuren PJ, Rootes CL, Mara K, McDonald M, Bruce KL, Gough TJ, Shi S, Cowled C, Bean AGD, Stewart CR. J Virol 95 e0032721 (2021)
  184. Identification of Human Host Substrates of the SARS-CoV-2 Mpro and PLpro Using Subtiligase N-Terminomics. Luo SY, Moussa EW, Lopez-Orozco J, Felix-Lopez A, Ishida R, Fayad N, Gomez-Cardona E, Wang H, Wilson JA, Kumar A, Hobman TC, Julien O. ACS Infect Dis 9 749-761 (2023)
  185. Identification of bio-active food compounds as potential SARS-CoV-2 PLpro inhibitors-modulators via negative image-based screening and computational simulations. Bhowmick S, AlFaris NA, Zaidan ALTamimi J, ALOthman ZA, Patil PC, Aldayel TS, Wabaidur SM, Saha A. Comput Biol Med 145 105474 (2022)
  186. Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches. Bhowmick S, Saha A, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. J Mol Graph Model 111 108113 (2022)
  187. Integration and Reanalysis of Four RNA-Seq Datasets Including BALF, Nasopharyngeal Swabs, Lung Biopsy, and Mouse Models Reveals Common Immune Features of COVID-19. Alberts R, Chan SC, Meng QF, He S, Rao L, Liu X, Zhang Y. Immune Netw 22 e22 (2022)
  188. Letter Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19. Xiao M, Lu B, Ding R, Liu X, Wu X, Li Y, Liu X, Qiu L, Zhang Z, Xie J, Chen Y, Zhang D, Dong L, Zhang M, Peng J, Yang H, Kudihna T, Xu Y, Li T, Yi C, Zhu L. Sci China Life Sci 65 1473-1476 (2022)
  189. Molecular docking studies of phytochemicals from Terminalia chebula for identification of potential multi-target inhibitors of SARS-CoV-2 proteins. Sarkar A, Agarwal R, Bandyopadhyay B. J Ayurveda Integr Med 13 100557 (2022)
  190. Molecular dynamics simulations, molecular docking, and kinetics study of kaempferol interaction on Jack bean urease: Comparison of extended solvation model. Zolghadr L, Behbehani GR, PakBin B, Hosseini SA, Divsalar A, Gheibi N. Food Sci Nutr 10 3585-3597 (2022)
  191. Parthenolide reveals an allosteric mode to inhibit the deISGylation activity of SARS-CoV‑2 papain-like protease. Zou Z, Shan H, Sun D, Xia L, Shi Y, Wan J, Zhou A, Wu Y, Xu H, Lei H, Xu Z, Wu Y. Acta Biochim Biophys Sin (Shanghai) 54 1133-1139 (2022)
  192. Phospholipids dock SARS-CoV-2 spike protein via hydrophobic interactions: a minimal in-silico study of lecithin nasal spray therapy. Qaisrani MN, Belousov R, Rehman JU, Goliaei EM, Girotto I, Franklin-Mergarejo R, Güell O, Hassanali A, Roldán É. Eur Phys J E Soft Matter 44 132 (2021)
  193. Potential role of marine species-derived bioactive agents in the management of SARS-CoV-2 infection. Asif M, Saleem M, Yaseen HS, Yehya AH, Saadullah M, Zubair HM, Oon CE, Khaniabadi PM, Khalid SH, Khan IU, Mahrukh. Future Microbiol 16 1289-1301 (2021)
  194. Pyrazolone-type compounds: synthesis and in silico assessment of antiviral potential against key viral proteins of SARS-CoV-2. Branković J, Milovanović VM, Simijonović D, Novaković S, Petrović ZD, Trifunović SS, Bogdanović GA, Petrović VP. RSC Adv 12 16054-16070 (2022)
  195. Rilpivirine inhibits SARS-CoV-2 protein targets: A potential multi-target drug. Ameen F, Mamidala E, Davella R, Vallala S. J Infect Public Health 14 1454-1460 (2021)
  196. Tau protein aggregation associated with SARS-CoV-2 main protease. Eberle RJ, Coronado MA, Gering I, Sommerhage S, Korostov K, Stefanski A, Stühler K, Kraemer-Schulien V, Blömeke L, Bannach O, Willbold D. PLoS One 18 e0288138 (2023)
  197. The FDA-approved drug Auranofin has a dual inhibitory effect on SARS-CoV-2 entry and NF-κB signaling. Laplantine E, Chable-Bessia C, Oudin A, Swain J, Soria A, Merida P, Gourdelier M, Mestiri S, Besseghe I, Bremaud E, Neyret A, Lyonnais S, Favard C, Benaroch P, Hubert M, Schwartz O, Guerin M, Danckaert A, Del Nery E, Muriaux D, Weil R. iScience 25 105066 (2022)
  198. The druggable genome: Twenty years later. Radoux CJ, Vianello F, McGreig J, Desai N, Bradley AR. Front Bioinform 2 958378 (2022)
  199. Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography. Smith N, Wilson MA. Crystals (Basel) 12 1671 (2022)
  200. A Method to Monitor Activity of SARS-CoV-2 Nsp3 from Cells. Rainville C, Sterner DE, Suresh K. Methods Mol Biol 2591 269-282 (2023)
  201. Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding. Perlinska AP, Stasiulewicz A, Nguyen ML, Swiderska K, Zmudzinski M, Maksymiuk AW, Drag M, Sulkowska JI. PLoS Comput Biol 18 e1010667 (2022)
  202. article-commentary An all-out assault on SARS-CoV-2 replication. Hay RT. Biochem J 478 2399-2403 (2021)
  203. Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies. Alabbas AB, Alamri MA. Saudi J Biol Sci 29 526-533 (2022)
  204. Association between Mutations in Papain-like Protease (PLpro) of SARS-CoV-2 with COVID-19 Clinical Outcomes. Tan J, Wu Z, Hu P, Gan L, Wang Y, Zhang D. Pathogens 11 1008 (2022)
  205. Crystal structure of the Rubella virus protease reveals a unique papain-like protease fold. Cheong EZK, Quek JP, Xin L, Li C, Chan JY, Liew CW, Mu Y, Zheng J, Luo D. J Biol Chem 298 102250 (2022)
  206. Detection and Quantification of SARS-CoV-2 by Real-Time RT-PCR Assay. Wilhelm A, Pallas C, Marschalek R, Widera M. Methods Mol Biol 2452 75-98 (2022)
  207. Host- and Species-Dependent Quasispecies Divergence of Severe Acute Respiratory Syndrome Coronavirus-2 in Non-human Primate Models. Hwang EH, Chung H, Kim G, Oh H, An YJ, Kang P, Ryu CM, Park JH, Hong J, Koo BS. Front Microbiol 12 694897 (2021)
  208. In Silico Discovery of Small-Molecule Inhibitors Targeting SARS-CoV-2 Main Protease. Gao M, Kang D, Liu N, Liu Y. Molecules 28 5320 (2023)
  209. In Silico and In Vitro Inhibition of SARS-CoV-2 PLpro with Gramicidin D. Protić S, Kaličanin N, Sencanski M, Prodanović O, Milicevic J, Perovic V, Paessler S, Prodanović R, Glisic S. Int J Mol Sci 24 1955 (2023)
  210. In-silico docking studies of selected phytochemicals against papain like protease of SARS-Cov-2. Saranya P, Karunya R, Keerthi Varshini G, Kowsikan K, Prathiksha R. Vegetos 36 188-194 (2023)
  211. Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors. Calleja DJ, Kuchel N, Lu BGC, Birkinshaw RW, Klemm T, Doerflinger M, Cooney JP, Mackiewicz L, Au AE, Yap YQ, Blackmore TR, Katneni K, Crighton E, Newman J, Jarman KE, Call MJ, Lechtenberg BC, Czabotar PE, Pellegrini M, Charman SA, Lowes KN, Mitchell JP, Nachbur U, Lessene G, Komander D. Front Chem 10 861209 (2022)
  212. Local energetic frustration conservation in protein families and superfamilies. Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A. Nat Commun 14 8379 (2023)
  213. Luminescent Assay for the Screening of SARS-CoV-2 MPro Inhibitors. Sondag D, Merx J, Rossing E, Boltje TJ, Löwik DWPM, Nelissen FHT, van Geffen M, van 't Veer C, van Heerde WL, Rutjes FPJT. Chembiochem 23 e202200190 (2022)
  214. Molecular basis for ubiquitin/Fubi cross-reactivity in USP16 and USP36. O'Dea R, Kazi N, Hoffmann-Benito A, Zhao Z, Recknagel S, Wendrich K, Janning P, Gersch M. Nat Chem Biol 19 1394-1405 (2023)
  215. Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19. Mun CS, Hui LY, Sing LC, Karunakaran R, Ravichandran V. Saudi J Biol Sci 29 103458 (2022)
  216. Natural Compound ZINC12899676 Reduces Porcine Epidemic Diarrhea Virus Replication by Inhibiting the Viral NTPase Activity. Wang P, Wang X, Liu X, Sun M, Liang X, Bai J, Jiang P. Front Pharmacol 13 879733 (2022)
  217. Pharmacotherapeutic Potential of Natural Products to Target the SARS-CoV-2 PLpro Using Molecular Screening and Simulation Approaches. Sayaf AM, Ahmad H, Aslam MA, Ghani SA, Bano S, Yousafi Q, Suleman M, Khan A, Yeoh KK, Wei DQ. Appl Biochem Biotechnol 195 6959-6978 (2023)
  218. Rhenium(V) Complexes as Cysteine-Targeting Coordinate Covalent Warheads. Karges J, Cohen SM. J Med Chem 66 3088-3105 (2023)
  219. Seeking antiviral drugs to inhibit SARS-CoV-2 RNA dependent RNA polymerase: A molecular docking analysis. Khater I, Nassar A. PLoS One 17 e0268909 (2022)
  220. Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins. Fukuzawa K, Kato K, Watanabe C, Kawashima Y, Handa Y, Yamamoto A, Watanabe K, Ohyama T, Kamisaka K, Takaya D, Honma T. J Chem Inf Model 61 4594-4612 (2021)
  221. Stability of SARS-CoV-2-Encoded Proteins and Their Antibody Levels Correlate with Interleukin 6 in COVID-19 Patients. Li W, Kitsios GD, Bain W, Wang C, Li T, Fanning KV, Deshpande R, Qin X, Morris A, Lee JS, Zou C. mSystems 7 e0005822 (2022)
  222. Structural and Biochemical Characterization of Porcine Epidemic Diarrhea Virus Papain-Like Protease 2. Chu HF, Cheng SC, Sun CY, Chou CY, Lin TH, Chen WY. J Virol 96 e0137221 (2022)
  223. Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq. Sunshine S, Puschnik AS, Replogle JM, Laurie MT, Liu J, Zha BS, Nuñez JK, Byrum JR, McMorrow AH, Frieman MB, Winkler J, Qiu X, Rosenberg OS, Leonetti MD, Ye CJ, Weissman JS, DeRisi JL, Hein MY. Nat Commun 14 6245 (2023)
  224. Whole-Genome Sequencing of SARS-CoV-2 Infection in a Cluster of Immunocompromised Children in Indonesia. Putri ND, Johar E, Dewi YP, Indrasari ND, Wulandari D, Br Pasaribu MM, Sari TT, Cakti FP, Jasin MR, Tartila T, Yudhaputri FA, Malik SG, Myint KSA. Front Med (Lausanne) 9 835998 (2022)
  225. ZnO-chlorogenic acid nanostructured complex inhibits Covid-19 pathogenesis and increases hydroxychloroquine efficacy. Abomughaid MM, Nofal MS, Ghaleb KI, Seadawy MG, AbdEl-Wahab MG, Hegazy AS, Ghareeb DA. J King Saud Univ Sci 34 102296 (2022)
  226. FHL2 Inhibits SARS-CoV-2 Replication by Enhancing IFN-β Expression through Regulating IRF-3. Xu Z, Tian M, Tan Q, Hao P, Gao Z, Li C, Jin N. Int J Mol Sci 25 353 (2023)
  227. In silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators. Mezhibovsky E, Hoang SH, Szeto S, Roopchand DE. J Biomol Struct Dyn 41 14339-14357 (2023)
  228. In silico study of novel niclosamide derivatives, SARS-CoV-2 nonstructural proteins catalytic residue-targeting small molecules drug candidates. Lawal B, Tsai SK, Wu ATH, Huang HS. Arab J Chem 16 104654 (2023)
  229. In vitro metabolic characterization of the SARS-CoV-2 papain-like protease inhibitors GRL0617 and HY-17542. Cho H, Kim YJ, Chae JW, Meyer MR, Kim SK, Ryu CS. Front Pharmacol 14 1067408 (2023)
  230. A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication. Han H, Gracia AV, Røise JJ, Boike L, Leon K, Schulze-Gahmen U, Stentzel MR, Bajaj T, Chen D, Li IC, He M, Behrouzi K, Khodabakhshi Z, Nomura DK, Mofrad MRK, Kumar GR, Ott M, Murthy N. RSC Adv 13 10636-10641 (2023)
  231. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. J Virol 97 e0059723 (2023)
  232. A new framework for host-pathogen interaction research. Yu H, Li L, Huffman A, Beverley J, Hur J, Merrell E, Huang HH, Wang Y, Liu Y, Ong E, Cheng L, Zeng T, Zhang J, Li P, Liu Z, Wang Z, Zhang X, Ye X, Handelman SK, Sexton J, Eaton K, Higgins G, Omenn GS, Athey B, Smith B, Chen L, He Y. Front Immunol 13 1066733 (2022)
  233. Activity-based Tools for Interrogating Host Biology During Infection. Ramanathan R, Hatzios SK. Isr J Chem 63 e202200095 (2023)
  234. Atlas of interactions between SARS-CoV-2 macromolecules and host proteins. Li G, Tang Z, Fan W, Wang X, Huang L, Jia Y, Wang M, Hu Z, Zhou Y. Cell Insight 2 100068 (2023)
  235. Benchmarked molecular docking integrated molecular dynamics stability analysis for prediction of SARS-CoV-2 papain-like protease inhibition by olive secoiridoids. Thangavel N, Albratty M. J King Saud Univ Sci 35 102402 (2023)
  236. Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach. Alam MM, Hannan SB, Saikat TA, Limon MBH, Topu MR, Rana MJ, Salauddin A, Bosu S, Rahman MZ. Evol Bioinform Online 19 11769343231182258 (2023)
  237. Biobran/MGN-3, an Arabinoxylan Rice Bran, Protects against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): An In Vitro and In Silico Study. Ghoneum M, Abdulmalek S, Fadel HH. Nutrients 15 453 (2023)
  238. Characterization of the Ubiquitin and ISG15 Deconjugase Activity of SARS-CoV-1 and SARS-CoV-2 Papain-Like Protease. Nayak D, Dos Santos Bury P, Drag M, Nijkerk AN, El Oualid F, Olsen SK. Methods Mol Biol 2591 171-188 (2023)
  239. Chemical Synthesis of Non-hydrolyzable Ubiquitin(-Like) Hybrid Chains. Pérez Berrocal DA, van der Heden van Noort GJ, Mulder MPC. Methods Mol Biol 2602 41-49 (2023)
  240. Collective synthesis of aspulvinone and its analogues by vinylogous aldol condensation of substituted tetronic acids with aldehydes. Yu X, Gu X, Zhao Y, Wang F, Sun W, Qi C, Gu L, Zhang Y. RSC Adv 13 4859-4864 (2023)
  241. Computer-aided drug design for the pain-like protease (PLpro) inhibitors against SARS-CoV-2. Gao H, Dai R, Su R. Biomed Pharmacother 159 114247 (2023)
  242. Coronaviral Main Protease Induces LPCAT3 Cleavage and Endoplasmic Reticulum (ER) Stress. Wang J, Zhang M, Ding Y, Lin Y, Xue Y, Wang X, Wang X. Viruses 15 1696 (2023)
  243. Cotton flower metabolites inhibit SARS-CoV-2 main protease. Zhang Y, Li W, Hu Y, Ding T, Zafar MM, Jia X, Zhang L, Ren M, Li F, Wang W. FEBS Open Bio 12 1886-1895 (2022)
  244. Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Afsar M, Liu G, Jia L, Ruben EA, Nayak D, Sayyad Z, Bury PDS, Cano KE, Nayak A, Zhao XR, Shukla A, Sung P, Wasmuth EV, Gack MU, Olsen SK. Nat Commun 14 4786 (2023)
  245. Curcumin partly prevents ISG15 activation via ubiquitin-activating enzyme E1-like protein and decreases ISGylation. Oki N, Yamada S, Tanaka T, Fukui H, Hatakeyama S, Okumura F. Biochem Biophys Res Commun 625 94-101 (2022)
  246. Development of 2-chloroquinoline based heterocyclic frameworks as dual inhibitors of SARS-CoV-2 MPro and PLPro. Kattula B, Reddi B, Jangam A, Naik L, Adimoolam BM, Vavilapalli S, Are S, Thota JR, Jadav SS, Arifuddin M, Addlagatta A. Int J Biol Macromol 242 124772 (2023)
  247. Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19. Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH. Eur J Med Chem 254 115380 (2023)
  248. Docking Studies and Molecular Dynamics Simulations of Potential Inhibitors from the Brown Seaweed Sargassum polycystum (Phaeophyceae) against PLpro of SARS-CoV-2. Tassakka ACMAR, Iskandar IW, Alam JF, Permana AD, Massi MN, Sulfahri, Jompa J, Liao LM. BioTech (Basel) 12 46 (2023)
  249. Effectiveness of famotidine on the risk of poor prognosis in patients with COVID-19: A nationwide cohort study in Korea. Kwon R, Kim HJ, Lee SW, Koyanagi A, Shin JI, Song TJ, Yon DK, Smith L. Heliyon 9 e16171 (2023)
  250. Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease. Duan L, Tang B, Luo S, Xiong D, Wang Q, Xu X, Zhang JZH. Cell Mol Life Sci 80 313 (2023)
  251. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. Guerler A, Baker D, van den Beek M, Gruening B, Bouvier D, Coraor N, Shank SD, Zehr JD, Schatz MC, Nekrutenko A. BMC Bioinformatics 24 263 (2023)
  252. Genetically Encoded Detection of Biosynthetic Protease Inhibitors. Kramer L, Sarkar A, Foderaro T, Markley AL, Lee J, Edstrom H, Sharma S, Gill E, Traylor MJ, Fox JM. ACS Synth Biol 12 83-94 (2023)
  253. ISG15 Is Required for the Dissemination of Vaccinia Virus Extracellular Virions. Bécares M, Albert M, Tárrega C, Coloma R, Falqui M, Luhmann EK, Radoshevich L, Guerra S. Microbiol Spectr 11 e0450822 (2023)
  254. Identification and characterization of aurintricarboxylic acid as a potential inhibitor of SARS-CoV-2 PLpro. Arya R, Prashar V, Kumar M. Int J Biol Macromol 230 123347 (2023)
  255. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. J Enzyme Inhib Med Chem 39 2301772 (2024)
  256. Identification of SARS-CoV-2 PLpro and 3CLpro human proteome substrates using substrate phage display coupled with protein network analysis. Zhao K, Li Y, Guo M, Ma L, Dang B. J Biol Chem 299 104831 (2023)
  257. Immune responses of different COVID-19 vaccination strategies by analyzing single-cell RNA sequencing data from multiple tissues using machine learning methods. Li H, Ma Q, Ren J, Guo W, Feng K, Li Z, Huang T, Cai YD. Front Genet 14 1157305 (2023)
  258. In silico discovery of 3 novel quercetin derivatives against papain-like protease, spike protein, and 3C-like protease of SARS-CoV-2. Bhattacharya K, Bordoloi R, Chanu NR, Kalita R, Sahariah BJ, Bhattacharjee A. J Genet Eng Biotechnol 20 43 (2022)
  259. In silico drug repurposing carvedilol and its metabolites against SARS-CoV-2 infection using molecular docking and molecular dynamic simulation approaches. Zhang C, Liu J, Sui Y, Liu S, Yang M. Sci Rep 13 21404 (2023)
  260. Inhibitory effect of phytochemicals towards SARS-CoV-2 papain like protease (PLpro) proteolytic and deubiquitinase activity. Kawall A, Lewis DSM, Sharma A, Chavada K, Deshmukh R, Rayalam S, Mody V, Taval S. Front Chem 10 1100460 (2022)
  261. Inhibitory efficacy of 2, 4-diacetylphloroglucinol against SARS-COV-2 proteins: in silico study. Kankariya RA, Chaudhari AB, Dandi ND. Biologia (Bratisl) 77 815-828 (2022)
  262. Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease. Chen X, Chen K, Zhang Z, Wei P, Zhang L, Xu Y, Lun Q, Ma Y, Wu F, Zhang Y, Wang Y, Zhao J, Zhou Y, Zhan J, Xu W. ACS Omega 7 48416-48426 (2022)
  263. Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication. Bajaj T, Wehri E, Suryawanshi RK, King E, Pardeshi KS, Behrouzi K, Khodabakhshi Z, Schulze-Gahmen U, Kumar GR, Mofrad MRK, Nomura DK, Ott M, Schaletzky J, Murthy N. RSC Adv 13 17667-17677 (2023)
  264. Molecular Dynamics Simulations to Decipher the Role of Phosphorylation of SARS-CoV-2 Nonstructural Proteins (nsps) in Viral Replication. Alomair L, Mustafa S, Jafri MS, Alharbi W, Aljouie A, Almsned F, Alawad M, Bokhari YA, Rashid M. Viruses 14 2436 (2022)
  265. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. Zhao Z, O'Dea R, Wendrich K, Kazi N, Gersch M. J Am Chem Soc 145 20801-20812 (2023)
  266. Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan. Imai R, Rongduo W, Kaixin L, Borjigin S, Matsumura H, Masuda T, Ozawa T, Oba M, Makino S, Nagai M, Mizutani T. J Vet Med Sci 85 252-265 (2023)
  267. Potential of Interferon Lambda as an Inhibitor of SARS-CoV-2. Oleinik LA, Madonov PG, Pykhtina MB. Mol Biol 57 291-298 (2023)
  268. Preparation and characterization of nanobodies targeting SARS-CoV-2 papain-like protease. Qiao H, Li L, Wang L, Yu H, Hu F, Zhou X, Yang H, Xu J, Meng X, Geng Y, Dai Y. Protein Expr Purif 207 106267 (2023)
  269. Recent computational drug repositioning strategies against SARS-CoV-2. Lu L, Qin J, Chen J, Yu N, Miyano S, Deng Z, Li C. Comput Struct Biotechnol J 20 5713-5728 (2022)
  270. Repurposing 1,2,4-oxadiazoles as SARS-CoV-2 PLpro inhibitors and investigation of their possible viral entry blockade potential. Ayoup MS, ElShafey MM, Abdel-Hamid H, Ghareeb DA, Abu-Serie MM, Heikal LA, Teleb M. Eur J Med Chem 252 115272 (2023)
  271. Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling. D'Anna L, Miclot T, Bignon E, Perricone U, Barone G, Monari A, Terenzi A. Chem Sci 14 11332-11339 (2023)
  272. SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions. Ershov PV, Yablokov EO, Mezentsev YV, Chuev GN, Fedotova MV, Kruchinin SE, Ivanov AS. Biophysics (Oxf) 67 902-912 (2022)
  273. SARS-CoV-2 Papain-like Protease Negatively Regulates the NLRP3 Inflammasome Pathway and Pyroptosis by Reducing the Oligomerization and Ubiquitination of ASC. Meng H, Zhou J, Wang M, Zheng M, Xing Y, Wang Y. Microorganisms 11 2799 (2023)
  274. SARS-CoV-2 papain-like protease plays multiple roles in regulating cellular proteins in the endoplasmic reticulum. Yang M, Mariano J, Su R, Smith CE, Das S, Gill C, Andresson T, Loncarek J, Tsai YC, Weissman AM. J Biol Chem 299 105346 (2023)
  275. Screening, Synthesis and Biochemical Characterization of SARS-CoV-2 Protease Inhibitors. Bagdonas M, Čerepenkaitė K, Mickevičiūtė A, Kananavičiūtė R, Grybaitė B, Anusevičius K, Rukšėnaitė A, Kojis T, Gedgaudas M, Mickevičius V, Matulis D, Zubrienė A, Matulienė J. Int J Mol Sci 24 13491 (2023)
  276. Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe. Li C, Wang T, Liang L, Chu G, Zhang J, He W, Liu L, Li J. Sci China Chem 66 837-844 (2023)
  277. Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease. Wang Q, Chen G, He J, Li J, Xiong M, Su H, Li M, Hu H, Xu Y. Int J Mol Sci 24 8633 (2023)
  278. Synthetic Diubiquitin Fluorogenic Substrates to Study DUBs. Kloet MS, van der Heden van Noort GJ. Methods Mol Biol 2591 17-24 (2023)
  279. The Discovery of Potential SARS-CoV-2 Natural Inhibitors among 4924 African Metabolites Targeting the Papain-like Protease: A Multi-Phase In Silico Approach. Elkaeed EB, Khalifa MM, Alsfouk BA, Alsfouk AA, El-Attar AMM, Eissa IH, Metwaly AM. Metabolites 12 1122 (2022)
  280. The Potential of Eukaryotic Cell-Free Systems as a Rapid Response to Novel Zoonotic Pathogens: Analysis of SARS-CoV-2 Viral Proteins. Ramm F, Dondapati SK, Trinh HA, Wenzel D, Walter RM, Zemella A, Kubick S. Front Bioeng Biotechnol 10 896751 (2022)
  281. The Swiss Light Source and SwissFEL at the Paul Scherrer Institute. Nolting F, Bostedt C, Schietinger T, Braun H. Eur Phys J Plus 138 126 (2023)
  282. The role of IBV PL1pro in virus replication and suppression of host innate immune responses. Liu W, Mu G, Jia Y, Yu M, Zhang S, Wang Z, Fang S. BMC Vet Res 19 270 (2023)
  283. UBR5 Acts as an Antiviral Host Factor against MERS-CoV via Promoting Ubiquitination and Degradation of ORF4b. Zhou Y, Zheng R, Liu D, Liu S, Disoma C, Li S, Liao Y, Chen Z, Du A, Dong Z, Zhang Y, Liu P, Razzaq A, Chen D, Chen X, Zhong X, Liu S, Tao S, Liu Y, Xu L, Deng X, Li J, Jiang T, Zhao J, Li S, Xia Z. J Virol 96 e0074122 (2022)
  284. USP2 inhibition prevents infection with ACE2-dependent coronaviruses in vitro and is protective against SARS-CoV-2 in mice. Dang F, Bai L, Dong J, Hu X, Wang J, Paulo JA, Xiong Y, Liang X, Sun Y, Chen Y, Guo M, Wang X, Huang Z, Inuzuka H, Chen L, Chu C, Liu J, Zhang T, Rezaeian AH, Liu J, Kaniskan HÜ, Zhong B, Zhang J, Letko M, Jin J, Lan K, Wei W. Sci Transl Med 15 eadh7668 (2023)
  285. Vaccine Design by Reverse Vaccinology and Machine Learning. Ong E, He Y. Methods Mol Biol 2414 1-16 (2022)
  286. β-Cyclodextrins as affordable antivirals to treat coronavirus infection. Raïch-Regué D, Tenorio R, Fernández de Castro I, Tarrés-Freixas F, Sachse M, Perez-Zsolt D, Muñoz-Basagoiti J, Fernández-Sánchez SY, Gallemí M, Ortega-González P, Fernández-Oliva A, Gabaldón JA, Nuñez-Delicado E, Casas J, Roca N, Cantero G, Pérez M, Usai C, Lorca-Oró C, Alert JV, Segalés J, Carrillo J, Blanco J, Clotet Sala B, Cerón-Carrasco JP, Izquierdo-Useros N, Risco C. Biomed Pharmacother 164 114997 (2023)


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