Structural Modelling of Platelet Activating Factor Acetyl Hydrolase in Leishmania donovani, Trypanosoma cruzi, and Trypanosoma brucei: Implications on Therapeutics for Leishmaniasis, Chagas Disease, and Sleeping Sickness

References

• Custodio H. Protozoan Parasites. Pediatr Rev. 2016;37(2):59–69;quiz 70–71. doi:10.1542/pir.2015-0006
   Google Scholar
• World Health Organization. Leishmaniasis; 2023. Available from: https://www.who.int/news-room/fact-sheets/detail/leishmaniasis. Accessed March 10, 2023.
   Google Scholar
• World Health Organization. Chagas disease (also known as American trypanosomiasis); 2022. Available from: https://www.who.int/news-room/fact-sheets/detail/chagas-disease-(american-trypanosomiasis). Accessed March 10, 2023.
   Google Scholar
• World Health Organization. Trypanosomiasis, human African (sleeping sickness); 2022. Available from: https://www.who.int/news-room/fact-sheets/detail/trypanosomiasis-human-african-(sleeping-sickness). Accessed March 10, 2023.
   Google Scholar
• Bi K, Chen Y, Zhao S, Kuang Y, John Wu CH. Current visceral leishmaniasis research: a research review to inspire future study. Biomed Res Int. 2018;2018:1–13. doi:10.1155/2018/9872095
   Web of Science ®Google Scholar
• Echeverria LE, Morillo CA. American trypanosomiasis (Chagas disease). Infect Dis Clin North Am. 2019;33(1):119–134. doi:10.1016/j.idc.2018.10.015
   PubMed Web of Science ®Google Scholar
• Ozioko K, Okoye C, Obiezue R, et al. Accelerating towards human African trypanosomiasis elimination: issues and opportunities. J Vector Borne Dis. 2020;57(2):105. doi:10.4103/0972-9062.310860
   PubMed Web of Science ®Google Scholar
• van Griensven J, Diro E. Visceral leishmaniasis. Infect Dis Clin North Am. 2012;26(2):309–322. doi:10.1016/j.idc.2012.03.005
   PubMed Web of Science ®Google Scholar
• Papadopoulou C, Kostoula A, Dimitriou D, Panagiou A, Bobojianni C, Antoniades G. Human and canine leishmaniasis in asymptomatic and symptomatic population in Northwestern Greece. J Infect. 2005;50(1):53–60. doi:10.1016/j.jinf.2004.05.004
   PubMed Web of Science ®Google Scholar
• Marin-Neto JA, Cunha-Neto E, Maciel BC, Simões M. Pathogenesis of chronic Chagas heart disease. Circulation. 2007;115(9):1109–1123. doi:10.1161/CIRCULATIONAHA.106.624296
   PubMed Web of Science ®Google Scholar
• Bonney KM, Luthringer DJ, Kim SA, Garg NJ, Engman DM. Pathology and pathogenesis of Chagas heart disease. Annu Rev Pathol. 2019;14:421–447. doi:10.1146/annurev-pathol-020117-043711
   PubMed Web of Science ®Google Scholar
• Rassi A, Rassi A, Marin-Neto JA. Chagas disease. Lancet. 2010;375(9723):1388–1402. doi:10.1016/S0140-6736(10)60061-X
   PubMed Web of Science ®Google Scholar
• Carvalho T, Trindade S, Pimenta S, Santos AB, Rijo-Ferreira F, Figueiredo LM. Trypanosoma brucei triggers a marked immune response in male reproductive organs. PLoS Negl Trop Dis. 2018;12(8):e0006690. doi:10.1371/journal.pntd.0006690
   PubMed Web of Science ®Google Scholar
• Greenwood BM, Whittle HC. The pathogenesis of sleeping sickness. Trans R Soc Trop Med Hyg. 1980;74(6):716–725. doi:10.1016/0035-9203(80
   PubMed Web of Science ®Google Scholar
• Kennedy PGE, Rodgers J. Clinical and neuropathogenetic aspects of human African trypanosomiasis. Front Immunol. 2019;10:39. doi:10.3389/fimmu.2019.00039
   PubMed Web of Science ®Google Scholar
• Pradhan S, Schwartz RA, Patil A, Grabbe S, Goldust M. Treatment options for leishmaniasis. Clin Exp Dermatol. 2022;47(3):516–521. doi:10.1111/ced.14919
   PubMed Web of Science ®Google Scholar
• Lascano F, García Bournissen F, Altcheh J. Review of pharmacological options for the treatment of Chagas disease. Br J Clin Pharmacol. 2022;88(2):383–402. doi:10.1111/bcp.14700
   PubMed Web of Science ®Google Scholar
• Büscher P, Cecchi G, Jamonneau V, Priotto G. Human African trypanosomiasis. Lancet. 2017;390(10110):2397–2409. doi:10.1016/S0140-6736(17
   PubMed Web of Science ®Google Scholar
• Pawlowic MC, Zhang K. Leishmania parasites possess a platelet-activating factor acetylhydrolase important for virulence. Mol Biochem Parasitol. 2012;186(1):11–20. doi:10.1016/j.molbiopara.2012.08.005
   PubMed Web of Science ®Google Scholar
• Shapiro J, Lui H. Vaniqa--eflornithine 13.9% cream. Skin Therapy Lett. 2001;6(7):1–3, 5.
   PubMedGoogle Scholar
• Kono N, Arai H. Platelet-activating factor acetylhydrolases: an overview and update. Biochimica Et Biophysica Acta. 2019;1864(6):922–931.
   Web of Science ®Google Scholar
• Ridgley EL, Ruben L. Phospholipase from Trypanosoma brucei releases arachidonic acid by sequential sn-1, sn-2 deacylation of phospholipids. Mol Biochem Parasitol. 2001;114(1):29–40. doi:10.1016/s0166-6851(01
   PubMed Web of Science ®Google Scholar
• Hariprasad G, Kaur P, Srinivasan A, Singh TP, Kumar M. Structural analysis of secretory phospholipase A2 from Clonorchis sinensis: therapeutic implications for hepatic fibrosis. J Mol Model. 2012;18(7):3139–3145. doi:10.1007/s00894-011-1333-8
   PubMed Web of Science ®Google Scholar
• Khan MI, Hariprasad G. Structural modeling of wild and mutant forms of human plasma platelet activating factor-acetyl hydrolase enzyme. J Inflamm Res. 2020;13:1125–1139. doi:10.2147/JIR.S274940
   PubMed Web of Science ®Google Scholar
• Machado FS, Mukherjee S, Weiss LM, Tanowitz HB, Ashton AW. Bioactive lipids in Trypanosoma cruzi infection. Adv Parasitol. 2011;76:1–31. doi:10.1016/B978-0-12-385895-5.00001-3
   PubMed Web of Science ®Google Scholar
• UniProt Consortium. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47(D1):D506–D515. doi:10.1093/nar/gky1049
   PubMed Web of Science ®Google Scholar
• Sievers F, Higgins DG. Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences. Springer; 2014:105–116. doi:10.1007/978-1-62703-646-7_6
   Google Scholar
• Waterhouse A, Bertoni M, Bienert S, et al. Swiss-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46(W1):W296–W303. doi:10.1093/nar/gky427
   PubMed Web of Science ®Google Scholar
• Combet C, Jambon M, Deleage G, Geourjon C. Geno3D: automatic comparative molecular modelling of protein. Bioinformatics. 2002;18(1):213–214. doi:10.1093/bioinformatics/18.1.213
   PubMed Web of Science ®Google Scholar
• Bowie JU, Lüthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991;253(5016):164–170. doi:10.1126/science.1853201
   PubMed Web of Science ®Google Scholar
• Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356(6364):83–85. doi:10.1038/356083a0
   PubMed Web of Science ®Google Scholar
• Colovos C, Yeates TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2(9):1511–1519. doi:10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 1993;26(2):283–291. doi:10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Schöning-Stierand K, Diedrich K, Fährrolfes R, et al. ProteinsPlus: interactive analysis of protein–ligand binding interfaces. Nucleic Acids Res. 2020;48(W1):W48–W53. doi:10.1093/nar/gkaa235
   PubMed Web of Science ®Google Scholar
• Volkamer A, Griewel A, Grombacher T, Rarey M. Analyzing the topology of active sites: on the prediction of pockets and subpockets. J Chem Inf Model. 2010;50(11):2041–2052. doi:10.1021/ci100241y
   PubMed Web of Science ®Google Scholar
• Madhavi Sastry G, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des. 2013;27(3):221–234. doi:10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Bowers KJ, Sacerdoti FD, Salmon JK, et al. Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the 2006 ACM/IEEE Conference on Supercomputing - SC’06. ACM Press; 2006:84. doi:10.1145/1188455.1188544.
   Google Scholar
• Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47(7):1739–1749. doi:10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Irwin JJ, Sterling T, Mysinger MM, Bolstad ES, Coleman RG. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012;52(7):1757–1768. doi:10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Shaikh F, Siu SWI. Identification of novel natural compound inhibitors for human complement component 5a receptor by homology modeling and virtual screening. Med Chem Res. 2016;25(8):1564–1573. doi:10.1007/s00044-016-1591-1
   PubMed Web of Science ®Google Scholar
• Carter P, Wells JA. Dissecting the catalytic triad of a serine protease. Nature. 1988;332(6164):564–568. doi:10.1038/332564a0
   PubMed Web of Science ®Google Scholar