Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method

PLoS ONE

Volumn 10, Issue 5, 2015, Pages

  Yoshino, Ryunosuke ^a,b   Yasuo, Nobuaki ^a   Inaoka, Daniel Ken ^c   Hagiwara, Yohsuke ^d   Ohno, Kazuki ^d   Orita, Masaya ^a,d   Inoue, Masayuki ^e   Shiba, Tomoo ^f   Harada, Shigeharu ^f   Honma, Teruki ^c   Balogun, Emmanuel Oluwadare ^c,g   Da Rocha, Josmar Rodrigues ^h   Montanari, Carlos Alberto ^h   Kita, Kiyoshi ^c   Sekijima, Masakazu ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d ASTELLAS PHARMA INC   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

^f KYOTO INSTITUTE OF TECHNOLOGY   (Japan)

^g AHMADU BELLO UNIVERSITY   (Nigeria)

^h UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; DIHYDROOROTATE DEHYDROGENASE; DIHYDROOROTATE DEHYDROGENASE INHIBITOR; FLAVINE MONONUCLEOTIDE; LYSINE; OROTIC ACID DERIVATIVE; OTERACIL; ANTITRYPANOSOMAL AGENT; ENZYME INHIBITOR; OXIDOREDUCTASE; PROTEIN BINDING;

ARTICLE; CHAGAS DISEASE; DRUG DESIGN; DRUG INTERACTION; DRUG STRUCTURE; FRAGMENT MOLECULAR ORBITAL METHOD; HYDROGEN BOND; NONHUMAN; PHARMACOPHORE; TRYPANOSOMA CRUZI; ANTAGONISTS AND INHIBITORS; CHEMISTRY; CONFORMATION; DRUG EFFECTS; ENZYMOLOGY; HUMAN; MOLECULAR MODEL; PARASITOLOGY;

TRYPANOSOMA CRUZI;

CHAGAS DISEASE; DRUG DESIGN; ENZYME INHIBITORS; HUMANS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PROTEIN BINDING; TRYPANOCIDAL AGENTS; TRYPANOSOMA CRUZI;

EID: 84930633582     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0125829     Document Type: Article

References (44)

1. Lockman JW, Hamilton AD. Recent developments in the identification of chemotherapeutics for Chagas disease. Curr Med Chem. 2005; 12: 945-959. PMID: 15853707
2. Schmunis GA, Yadon ZE. Chagas disease: a Latin American health problem becoming a world health problem. Acta Trop. 2010; 115: 14-21. doi: 10.1016/j.actatropica.2009.11.003 PMID: 19932071
3. Roellig DM, Brown EL, Barnabe C, Tibayrenc M, Steurer FJ, Yabsley MJ. Molecular typing of Trypanosoma cruzi isolates. United States. Emerg Infect Dis. 2008; 14: 1123-1125. doi: 10.3201/eid1407.080175 PMID: 18598637
4. Marcet PL, Duffy T, Cardinal MV, Burgos JM, Lauricella MA, Levin MJ, et al. PCR-based screening and lineage identification of Trypanosoma cruzi directly from faecal samples of triatomine bugs from northwestern Argentina. Parasitology. 2006; 132: 57-65. PMID: 16393354
5. Rassi A Jr, Rassi A, Marin-Neto JA. Chagas disease. Lancet. 2010; 375: 1388-1402. doi: 10.1016/S0140-6736(10)60061-X PMID: 20399979
6. Chagas C. Nova trypanozomiaze humana: estudos sobre a morfolojia e o ciclo evolutivo do Schizotrypanum cruzi n. gen., n. sp., ajente etiolojico de nova entidade morbida do homem. Mem Inst Oswaldo Cruz. 1909; 1: 159-218.
7. Kirchhoff LV. American trypanosomiasis (Chagas' disease). Gastroenterol Clin North Am. 1996; 25: 517-533. PMID: 8863038
8. Rossi MA, Bestetti RB. The challenge of chagasic cardiomyopathy. Cardiology. 1995; 86: 1-7. PMID: 7728781
9. Hugo VDB. Chemotherapy for parasitic infections. Nature. 1978; 273: 626-630. PMID: 351413
10. Linares GEG, Ravaschino EL, Rodriguez JB. Progresses in the field of drug design to combat tropical protozoan parasitic diseases. Curr Med Chem. 2006; 13: 335-360. PMID: 16475941
11. Maya JD, Cassels BK. Iturriaga-Vasquez P, Ferreira J, Faundez M, Galanti N, et al. Mode of action of natural and synthetic drugs against Trypanosoma cruzi and their interaction with the mammalian host. Comp Biochem Physiol A Mol Integr Physiol. 2007; 146: 601-620. PMID: 16626984
12. Buckner FS, Navabi N. Advances in Chagas disease drug development: 2009-2010. Curr Opin Infect Dis. 2010; 23: 609-616. doi: 10.1097/QCO.0b013e3283402956 PMID: 20885320
13. Jensen KF, Björnberg O. Evolutionary and functional families of dihydroorotate dehydrogenases. Paths Pyrimidines. 1998; 6:20-28.
14. Liu S, Neidhardt EA, Grossman TH, Ocain T, Clardy J. Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents. Structure. 2000; 8: 25-33. PMID: 10673429
15. Inaoka DK, Sakamoto S, Shimizu H, Shiba T, Kurisu G, Nara T, et al. Structures of Trypanosoma cruzi dihydroorotate dehydrogenase complexed with substrates and products: atomic resolution insights into mechanisms of dihydroorotate oxidation and fumarate reduction. Biochemistry. 2008; 47: 10881-10891. doi: 10.1021/bi800413r PMID: 18808149
16. Annoura T, Nara T, Makiuchi T, Hashimoto T, Aoki T. The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions. J Mol Evol. 2005; 60: 113-127. PMID: 15696374
17. Davies M, Heikkilä T, McConkey GA, Fishwick CW, Parsons MR, Johnson AP. Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases. J Med Chem. 2009; 52: 2683-2693. doi: 10.1021/jm800963t PMID: 19351152
18. Davis JP, Cain GA, Pitts WJ, Magolda RL, Copeland RA. The immunosuppressive metabolite of leflunomide is a potent inhibitor of human dihydroorotate dehydrogenase. Biochemistry. 1996; 35: 1270-1273. PMID: 8573583
19. Coteron JM, Marco M, Esquivias J, Deng X, White KL, White J, et al. Structure-guided lead optimization of triazolopyrimidine-ring substituents identifies potent Plasmodium falciparum dihydroorotate dehydrogenase inhibitors with clinical candidate potential. J Med Chem. 2011; 54: 5540-5561. doi: 10.1021/jm200592f PMID: 21696174
20. Phillips MA, Rathod PK. Plasmodium dihydroorotate dehydrogenase: a promising target for novel antimalarial chemotherapy. Infect Disord Drug Targets. 2010; 10: 226-239. PMID: 20334617
21. Copeland RA, Marcinkeviciene J, Haque TS, Kopcho LM, Jiang W, Wang K, et al. Helicobacter pyloriselective antibacterials based on inhibition of pyrimidine biosynthesis. J Biol Chem. 2000; 275: 33373-33378. PMID: 10938275
22. Diao Y, Lu W, Jin H, Zhu J, Han L, Xu M, et al. Discovery of Diverse Human Dihydroorotate Dehydrogenase Inhibitors as Immunosuppressive Agents by Structure-Based Virtual Screening. J Med Chem. 2012; 55: 8341-8349. doi: 10.1021/jm300630p PMID: 22984987
23. Marwaha A, White J, El Mazouni F, Creason SA, Kokkonda S, Buckner FS, et al. Bioisosteric Transformations and Permutations in the Triazolopyrimidine Scaffold To Identify the Minimum Pharmacophore Required for Inhibitory Activity against Plasmodium falciparum Dihydroorotate Dehydrogenase. J Med Chem. 2012; 55: 7425-7436 doi: 10.1021/jm300351w PMID: 22877245
24. Wermuth CG, Ganellin CR, Lindberg P, Mitscher LA. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure and Applied Chemistry. 1998; 70: 1129-1143.
25. Lingling J, Robert CR. Pharmacophore-based similarity scoring method for DOCK. J Phys Chem B. 2015 Jan 22; 119(3):1083-102. doi: 10.1021/jp506555w. Epub.2014.10.10. PMID: 25229837
26. Kitaura K, Sawai T, Asadaa T, Nakanob T, Uebayasi M. Pair interaction molecular orbital method: an approximate computational method for molecular interactions. Chem Phys Lett. 1999; 312: 319-324.
27. Tomonaga O, Kosuke O. CH/Π hydrogen bonds determine the selectivity of the Src homology 2 domain to tyrosine phosphotyrosyl peptides: an ab initio fragment molecular orbital study. Journal of Computational Chemistry. 2008; 29: 2656-2666. doi: 10.1002/jcc.20998 PMID: 18484636
28. Tomonaga O, Eiichi T, Motoyasu O, Cchiaki H, Harunobu M, Tochihiro N, et al. The importance of CH/Π hydrogen bonds in rational drug design: an ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase. Bioorganic and Medicinal Chemistry. 2008; 16: 10311-10318. doi: 10.1016/j.bmc.2008.10.041 PMID: 18977146
29. Tomonaga O, Kosuke O, Kazuo K. CH/Π hydrogen bonds play a role in ligand recognition and equilibrium between active and inactive states of the b2 adrenergic receptor: An ab initio fragment molecular orbital (FMO) study. Bioorganic and Medicinal Chemistry. 2011; 19: 5231-5237. doi: 10.1016/j.bmc.2011.07.004 PMID: 21820903
30. Tomonaga O, Kosuke O, Kazuo K. Importance of CH/Π hydrogen bonds in recognition of the core motif in proline-recognition domains: an ab initio fragment molecular orbital study. Journal of Computational Chemistry. 2011; 32: 2774-2782. doi: 10.1002/jcc.21857 PMID: 21710635
31. Kenichi F, Yoshimasa S. The role of fluorine atoms in a fluorinated prostaglandin agonist. Chem Med Chem. 2010; 5: 1254-1257. doi: 10.1002/cmdc.201000174 PMID: 20486154
32. Ohno K., Mori K., Orita M., Takeuchi M. Computational insights into binding of bisphosphates to farnesyl pyrophosphate synthase. Current Medicinal Chemistry. 2011; 18: 220-233. PMID: 21110804
33. Osamu I, John B, Richard JL, Mark W, Compound design by fragment linking. Molecular Informatics. 2011; 30: 298-306.
34. Michael PM, Osamu I, Richard JL, Mark W, Prediction of cyclin dependent kinase 2 inhibitor potency using the fragment molecular orbital method. Journal of Cheminformatics. 2011; 3: 2. doi: 10.1186/1758-2946-3-2 PMID: 21219630
35. Björnberg O., Jordan DB, Palfey BA, Jensen KF. Dihydrooxonate is a substrate of dihydroorotate dehydrogenase (DHOD) providing evidence for involvement of cysteine and serine residues in base catalysis. Arch. Biochem. Biophys. 2001; 391: 286-94. PMID: 11437361
36. Zbyszek O and Wladek M. Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology. 1997; 276: 307-326.
37. Emsley P and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004; 60: 2126-2132. PMID: 15572765
38. Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr. 1997; 53: 240-255. PMID: 15299926
39. http://www1.bbiq.jp/zzzfelis/Facio.html
40. Fedorov DG, Kazuo K. Pair interaction energy decomposition analysis. J Comput Chem. 2007; 28: 222-237. PMID: 17109433
41. Ozawa T, Tsuji E, Ozawa M, Handa C, Mukaiyama H, Nishimura T, et al. The importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase. Bioorg Med Chem. 2008; 16: 10311-10318. doi: 10.1016/j.bmc.2008.10.041 PMID: 18977146
42. Watanabe C, Fukuzawa K, Okiyama Y, Tsukamoto T, Kato A, Tanaka S, et al. Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design. J Mol Graph Model. 2013l; 41: 31-42. doi: 10.1016/j.jmgm.2013.01.006 PMID: 23467020
43. David. AC, Tom D, Thomas EC, Carlos S, Junmei. W, Robert. ED, et al., Amber 11. San Francisco. 2010
44. Michael WS, Kim KB, Jerry AB, Steven TE, Mark SG, Jan HJ, et al. General atomic and molecular electronic structure system. J Comput Chem. 1993; 14: 1347-1363.