1w1p › Citations

Structure-based exploration of cyclic dipeptide chitinase inhibitors.

Houston DR, Synstad B, Eijsink VG, Stark MJ, Eggleston IM, van Aalten DM
J Med Chem 47 5713-20 (2004)
Related entries: 1w1t, 1w1v, 1w1y

Cited: 63 times
EuropePMC logo PMID: 15509170

Abstract

Family 18 chitinases play an essential role in a range of pathogens and pests. Several inhibitors are known, including the potent inhibitors argadin and allosamidin, and the structures of these in complex with chitinases have been elucidated. Recent structural analysis has revealed that CI-4 [cyclo-(L-Arg-D-Pro)] inhibits family 18 chitinases by mimicking the structure of the proposed reaction intermediate. Here we report the high-resolution structures of four new CI-4 derivatives, cyclo-(L-Arg-L-Pro), cyclo-(Gly-L-Pro), cyclo-(L-His-L-Pro), and cyclo-(L-Tyr-L-Pro), in complex with a family 18 chitinase. In addition, details of enzyme inhibition and in vivo activity against Saccharomyces cerevisiae are presented. The structures reveal that the common cyclo-(Gly-Pro) substructure is sufficient for binding, allowing modification of the side chain of the nonproline residue. This suggests that design of cyclic dipeptides with a view to increasing inhibition of family 18 chitinases should be possible through relatively accessible chemistry. The derivatives presented here in complex with chitinase B from Serratia marcescens provide further insight into the mechanism of inhibition of chitinases by cyclic dipeptides as well as providing a new scaffold for chitinase inhibitor design.

Articles - 1w1p mentioned but not cited (11)

  1. Fpocket: an open source platform for ligand pocket detection. Le Guilloux V, Schmidtke P, Tuffery P. BMC Bioinformatics 10 168 (2009)
  2. CB-Dock: a web server for cavity detection-guided protein-ligand blind docking. Liu Y, Grimm M, Dai WT, Hou MC, Xiao ZX, Cao Y. Acta Pharmacol Sin 41 138-144 (2020)
  3. Variability in docking success rates due to dataset preparation. Corbeil CR, Williams CI, Labute P. J Comput Aided Mol Des 26 775-786 (2012)
  4. Docking and scoring with ICM: the benchmarking results and strategies for improvement. Neves MA, Totrov M, Abagyan R. J Comput Aided Mol Des 26 675-686 (2012)
  5. BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Lee HS, Zhang Y. Proteins 80 93-110 (2012)
  6. AutoSite: an automated approach for pseudo-ligands prediction-from ligand-binding sites identification to predicting key ligand atoms. Ravindranath PA, Sanner MF. Bioinformatics 32 3142-3149 (2016)
  7. Automating crystallographic structure solution and refinement of protein-ligand complexes. Echols N, Moriarty NW, Klei HE, Afonine PV, Bunkóczi G, Headd JJ, McCoy AJ, Oeffner RD, Read RJ, Terwilliger TC, Adams PD. Acta Crystallogr D Biol Crystallogr 70 144-154 (2014)
  8. S4MPLE--Sampler for Multiple Protein-Ligand Entities: Methodology and Rigid-Site Docking Benchmarking. Hoffer L, Chira C, Marcou G, Varnek A, Horvath D. Molecules 20 8997-9028 (2015)
  9. High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure. Borbulevych O, Martin RI, Westerhoff LM. Acta Crystallogr D Struct Biol 74 1063-1077 (2018)
  10. Drought Exposed Burkholderia seminalis JRBHU6 Exhibits Antimicrobial Potential Through Pyrazine-1,4-Dione Derivatives Targeting Multiple Bacterial and Fungal Proteins. Prasad JK, Pandey P, Anand R, Raghuwanshi R. Front Microbiol 12 633036 (2021)
  11. A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions. Gu L, Li B, Ming D. BMC Bioinformatics 23 456 (2022)


Reviews citing this publication (6)

  1. Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics. Koopmanschap G, Ruijter E, Orru RV. Beilstein J Org Chem 10 544-598 (2014)
  2. Natural product family 18 chitinase inhibitors. Andersen OA, Dixon MJ, Eggleston IM, van Aalten DM. Nat Prod Rep 22 563-579 (2005)
  3. 2,5-diketopiperazines in food and beverages: Taste and bioactivity. Borthwick AD, Da Costa NC. Crit Rev Food Sci Nutr 57 718-742 (2017)
  4. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Biomolecules 11 1515 (2021)
  5. Microwave-Assisted Synthesis of Bioactive Six-Membered Heterocycles and Their Fused Analogues. Driowya M, Saber A, Marzag H, Demange L, Benhida R, Bougrin K. Molecules 21 492 (2016)
  6. Chitinases: Therapeutic Scaffolds for Allergy and Inflammation. Madan K, Madan M, Sharma S, Paliwal S. Recent Pat Inflamm Allergy Drug Discov 14 46-57 (2020)

Articles citing this publication (46)

  1. Recent developments in asymmetric multicomponent reactions. de Graaff C, Ruijter E, Orru RV. Chem Soc Rev 41 3969-4009 (2012)
  2. Specificity and affinity of natural product cyclopentapeptide inhibitors against A. fumigatus, human, and bacterial chitinases. Rao FV, Houston DR, Boot RG, Aerts JM, Hodkinson M, Adams DJ, Shiomi K, Omura S, van Aalten DM. Chem Biol 12 65-76 (2005)
  3. Methylxanthine drugs are chitinase inhibitors: investigation of inhibition and binding modes. Rao FV, Andersen OA, Vora KA, Demartino JA, van Aalten DM. Chem Biol 12 973-980 (2005)
  4. Hallmarks of processivity in glycoside hydrolases from crystallographic and computational studies of the Serratia marcescens chitinases. Payne CM, Baban J, Horn SJ, Backe PH, Arvai AS, Dalhus B, Bjørås M, Eijsink VG, Sørlie M, Beckham GT, Vaaje-Kolstad G. J Biol Chem 287 36322-36330 (2012)
  5. Cigarette smoking is associated with an altered vaginal tract metabolomic profile. Nelson TM, Borgogna JC, Michalek RD, Roberts DW, Rath JM, Glover ED, Ravel J, Shardell MD, Yeoman CJ, Brotman RM. Sci Rep 8 852 (2018)
  6. Identification of antimicrobial compound, diketopiperazines, from a Bacillus sp. N strain associated with a rhabditid entomopathogenic nematode against major plant pathogenic fungi. Nishanth Kumar S, Mohandas C, Siji JV, Rajasekharan KN, Nambisan B. J Appl Microbiol 113 914-924 (2012)
  7. Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin. Andersen OA, Nathubhai A, Dixon MJ, Eggleston IM, van Aalten DM. Chem Biol 15 295-301 (2008)
  8. Synthesis of peptides and pyrazines from β-amino alcohols through extrusion of H2 catalyzed by ruthenium pincer complexes: ligand-controlled selectivity. Gnanaprakasam B, Balaraman E, Ben-David Y, Milstein D. Angew Chem Int Ed Engl 50 12240-12244 (2011)
  9. A freshwater bacterial strain, Shewanella sp. Lzh-2, isolated from Lake Taihu and its two algicidal active substances, hexahydropyrrolo[1,2-a]pyrazine-1,4-dione and 2, 3-indolinedione. Li Z, Lin S, Liu X, Tan J, Pan J, Yang H. Appl Microbiol Biotechnol 98 4737-4748 (2014)
  10. Crystal structures of Bacillus cereus NCTU2 chitinase complexes with chitooligomers reveal novel substrate binding for catalysis: a chitinase without chitin binding and insertion domains. Hsieh YC, Wu YJ, Chiang TY, Kuo CY, Shrestha KL, Chao CF, Huang YC, Chuankhayan P, Wu WG, Li YK, Chen CJ. J Biol Chem 285 31603-31615 (2010)
  11. Anticancer potential of pyrrole (1, 2, a) pyrazine 1, 4, dione, hexahydro 3-(2-methyl propyl) (PPDHMP) extracted from a new marine bacterium, Staphylococcus sp. strain MB30. Lalitha P, Veena V, Vidhyapriya P, Lakshmi P, Krishna R, Sakthivel N. Apoptosis 21 566-577 (2016)
  12. Asymmetric synthesis of synthetic alkaloids by a tandem biocatalysis/Ugi/Pictet-Spengler-type cyclization sequence. Znabet A, Zonneveld J, Janssen E, De Kanter FJ, Helliwell M, Turner NJ, Ruijter E, Orru RV. Chem Commun (Camb) 46 7706-7708 (2010)
  13. Fully deacetylated chitooligosaccharides act as efficient glycoside hydrolase family 18 chitinase inhibitors. Chen L, Zhou Y, Qu M, Zhao Y, Yang Q. J Biol Chem 289 17932-17940 (2014)
  14. Purification of an antifungal compound, cyclo(l-Pro-d-Leu) for cereals produced by Bacillus cereus subsp. thuringiensis associated with entomopathogenic nematode. Nishanth Kumar S, Mohandas C, Nambisan B. Microbiol Res 168 278-288 (2013)
  15. Antimicrobial and Antibiofilm Activities of the Fungal Metabolites Isolated from the Marine Endophytes Epicoccum nigrum M13 and Alternaria alternata 13A. Qader MM, Hamed AA, Soldatou S, Abdelraof M, Elawady ME, Hassane ASI, Belbahri L, Ebel R, Rateb ME. Mar Drugs 19 232 (2021)
  16. Cyclo(D-Tyr-D-Phe): a new antibacterial, anticancer, and antioxidant cyclic dipeptide from Bacillus sp. N strain associated with a rhabditid entomopathogenic nematode. Nishanth Kumar S, Dileep C, Mohandas C, Nambisan B, Ca J. J Pept Sci 20 173-185 (2014)
  17. Chitinase inhibition by chitobiose and chitotriose thiazolines. Macdonald JM, Tarling CA, Taylor EJ, Dennis RJ, Myers DS, Knapp S, Davies GJ, Withers SG. Angew Chem Int Ed Engl 49 2599-2602 (2010)
  18. Differential aphicidal effects of chitinase inhibitors on the polyphagous homopteran Myzus persicae (Sulzer). Saguez J, Dubois F, Vincent C, Laberche JC, Sangwan-Norreel BS, Giordanengo P. Pest Manag Sci 62 1150-1154 (2006)
  19. Antifungal activity of diketopiperazines and stilbenes against plant pathogenic fungi in vitro. Kumar SN, Nambisan B. Appl Biochem Biotechnol 172 741-754 (2014)
  20. Efficient microwave assisted syntheses of 2,5-diketopiperazines in aqueous media. Pérez-Picaso L, Escalante J, Olivo HF, Rios MY. Molecules 14 2836-2849 (2009)
  21. Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms. Pantoom S, Vetter IR, Prinz H, Suginta W. J Biol Chem 286 24312-24323 (2011)
  22. Purification and identification of two antifungal cyclic dipeptides from Bacillus cereus subsp. thuringiensis associated with a rhabditid entomopathogenic nematode especially against Fusarium oxysporum. Kumar SN, Nambisan B, Mohandas C. J Enzyme Inhib Med Chem 29 190-197 (2014)
  23. Structure elucidation of a new natural diketopiperazine from a Microbispora aerata strain isolated from Livingston Island, Antarctica. Ivanova V, Laatsch H, Kolarova M, Aleksieva K. Nat Prod Res 27 164-170 (2013)
  24. A Small Molecule Coordinates Symbiotic Behaviors in a Host Organ. Zink KE, Ludvik DA, Lazzara PR, Moore TW, Mandel MJ, Sanchez LM. mBio 12 e03637-20 (2021)
  25. Antagonistic Properties of Some Halophilic Thermoactinomycetes Isolated from Superficial Sediment of a Solar Saltern and Production of Cyclic Antimicrobial Peptides by the Novel Isolate Paludifilum halophilum. Frikha Dammak D, Zarai Z, Najah S, Abdennabi R, Belbahri L, Rateb ME, Mejdoub H, Maalej S. Biomed Res Int 2017 1205258 (2017)
  26. One-pot synthesis of diverse DL-configuration dipeptides by a Streptomyces D-stereospecific amidohydrolase. Arima J, Usuki H, Hatanaka T, Mori N. Appl Environ Microbiol 77 8209-8218 (2011)
  27. The aminolysis reaction of streptomyces S9 aminopeptidase promotes the synthesis of diverse prolyl dipeptides. Arima J, Morimoto M, Usuki H, Mori N, Hatanaka T. Appl Environ Microbiol 76 4109-4112 (2010)
  28. Activity and synergistic antimicrobial activity between diketopiperazines against bacteria in vitro. Kumar SN, Siji JV, Nambisan B, Mohandas C. Appl Biochem Biotechnol 168 2285-2296 (2012)
  29. Engineered transaminopeptidase, aminolysin-S for catalysis of peptide bond formation to give linear and cyclic dipeptides by one-pot reaction. Usuki H, Uesugi Y, Arima J, Yamamoto Y, Iwabuchi M, Hatanaka T. Chem Commun (Camb) 46 580-582 (2010)
  30. A new benzotriazole-mediated stereoflexible gateway to hetero-2,5-diketopiperazines. Monbaliu JC, Hansen FK, Beagle LK, Panzner MJ, Steel PJ, Todadze E, Stevens CV, Katritzky AR. Chemistry 18 2632-2638 (2012)
  31. Chemical genetics approach to identify new small molecule modulators of cell growth by phenotypic screening of Saccharomyces cerevisiae strains with a library of morpholine-derived compounds. Trabocchi A, Stefanini I, Morvillo M, Ciofi L, Cavalieri D, Guarna A. Org Biomol Chem 8 5552-5557 (2010)
  32. Purification and synergistic antibacterial activity of arginine derived cyclic dipeptides, from Achromobacter sp. associated with a rhabditid entomopathogenic nematode against major clinically relevant biofilm forming wound bacteria. Deepa I, Kumar SN, Sreerag RS, Nath VS, Mohandas C. Front Microbiol 6 876 (2015)
  33. Total Synthesis of Spirotryprostatins through Organomediated Intramolecular Umpolung Cyclization. Xi YK, Zhang H, Li RX, Kang SY, Li J, Li Y. Chemistry 25 3005-3009 (2019)
  34. Cyclic cis-Locked Phospho-Dipeptides Reduce Entry of AβPP into Amyloidogenic Processing Pathway. Fisher CL, Resnick RJ, De S, Acevedo LA, Lu KP, Schroeder FC, Nicholson LK. J Alzheimers Dis 55 391-410 (2017)
  35. Cyclic dipeptides from rhabditid entomopathogenic nematode-associated Bacillus cereus have antimicrobial activities. Nishanth Kumar S, Nath VS, Pratap Chandran R, Nambisan B. World J Microbiol Biotechnol 30 439-449 (2014)
  36. Traceless synthesis of diketopiperazine fused tetrahydro-β-carbolines on soluble polymer support. Chanda K, Chou CT, Lai JJ, Lin SF, Yellol GS, Sun CM. Mol Divers 15 569-581 (2011)
  37. Bioactive natural products from Pseudonocardia endophytica VUK-10. Mangamuri UK, Muvva V, Poda S, Chitturi B, Yenamandra V. J Genet Eng Biotechnol 14 261-267 (2016)
  38. The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure. Airaghi F, Fiorati A, Lesma G, Musolino M, Sacchetti A, Silvani A. Beilstein J Org Chem 9 147-154 (2013)
  39. A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis. Jitonnom J, Sattayanon C, Kungwan N, Hannongbua S. J Mol Graph Model 56 53-59 (2015)
  40. Antimycobacterial activity of cyclic dipeptides isolated from Bacillus sp. N strain associated with entomopathogenic nematode. Nishanth Kumar S, Mohandas C. Pharm Biol 52 91-96 (2014)
  41. Structural analysis and the effect of cyclo(His-Pro) dipeptide on neurotoxins--a dynamics and density functional theory study. Abiram A, Kolandaivel P. J Mol Model 16 193-202 (2010)
  42. Phage display screening for peptidic chitinase inhibitors. Petter C, Scholz C, Wessner H, Hansen G, Henklein P, Watanabe T, Höhne W. J Mol Recognit 21 401-409 (2008)
  43. Rapid synthesis of new block copolyurethanes derived from L-leucine cyclodipeptide in reusable molten ammonium salts: novel and efficient green media for the synthesis of new hydrolysable and biodegradable copolyurethanes. Rafiemanzelat F, Abdollahi E. Amino Acids 42 2177-2186 (2012)
  44. Synchrotron vacuum ultraviolet (VUV) photo-induced fragmentation of cyclic dipeptides radical cations. Zhang L, Jia L, Zhang L, Guo H, Zhou Z, Weng J, Qi F. Amino Acids 43 279-287 (2012)
  45. Synthesis of spiro-2,6-dioxopiperazine and spiro-2,6-dioxopyrazine scaffolds using amino acids in a three-component reaction to generate potential Sigma-1 (σ1) receptor selective ligands. Uprety R, Váradi A, Allaoa A, Redel-Traub GN, Palmer TC, Feinberg EN, Ferris AC, Pande VS, Pasternak GW, Majumdar S. Eur J Med Chem 164 241-251 (2019)
  46. An economical approach for peptide synthesis via regioselective C-N bond cleavage of lactams. Muramatsu W, Yamamoto H. Chem Sci 13 6309-6315 (2022)


Quick links