Русская версия English version   
О журнале
Редакционная коллегия
Правила для авторов
Информация для читателей и авторов
Оглавление текущего номера
Архив
Контакты
Поиск

Отправить статью
 


Том 19   Выпуск 1   Год 2024
Андрианов А.М.1, Лайков Я.В.2, Тузиков А.В.2

Применение стратегии перепрофилирования лекарств для виртуального скрининга потенциальных ингибиторов проникновения ВИЧ-1, блокирующих домен NHR белка gp41 оболочки вируса

Математическая биология и биоинформатика. 2024;19(1):77-95.

doi: 10.17537/2024.19.77.

Список литературы

  1. Lyumkis D., Julien J.-P., de Val N., Cupo A., Potter C.S., Klasse P.-J., Burton D.R., Sanders R.W., Moore J.P., Carragher B., Wilson I.A., Ward A.B. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science. 2013;342:1484–1490. doi: 10.1126/science.1245627
  2. Julien J.-P., Cupo A., Sok D., Stanfield R.L., Lyumkis D., Deller M.C., Klasse P.J., Burton D.R., Sanders R.W., Moore J.P., Ward A.W., Wilson I.A. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science. 2013;342:1477–1483. doi: 10.1126/science.1245625
  3. Cocchi F., DeVico A.L., Garzino-Demo A., Cara A., Gallo R.C., Lusso P. The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for chemokine-mediated blockade of infection. Nat. Med. 1996;2:1244–1247. doi: 10.1038/nm1196-1244
  4. Feng Y., Broder C.C., Kennedy P.E., Berger E.A. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science. 1996;272:872–877. doi: 10.1126/science.272.5263.872
  5. Wilen C.B., Tilton J.C., Doms R.W. HIV: Cell binding and entry. Cold Spring Harb. Perspect. Med. 2012;2. a006866. doi: 10.1101/cshperspect.a006866
  6. Chan D.C., Fass D., Berger J.M., Kim P.S. Core structure of gp41 from the HIV envelope glycoprotein. Cell. 1997;89(2):263–273. doi: 10.1016/S0092-8674(00)80205-6
  7. Weissenhorn W., Dessen A., Harrison S.C., Skehel J.J., Wiley D.C. Atomic structure of the ectodomain from HIV-1 gp41. Nature. 1997;387(6631):426–430. doi: 10.1038/387426a0
  8. Tan K., Liu J., Wang J., Shen S., Liu M. Atomic structure of a thermostable subdomain of HIV-1 gp41. Proc. Natl. Acad. Sci. USA. 1997;94(23):12303–12308. doi: 10.1073/pnas.94.23.12303
  9. Chan D.C., Chutkowski C.T., Kim P.S. Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target. Proc. Natl. Acad. Sci. USA. 1998;95(26):15613–15617. doi: 10.1073/pnas.95.26.15613
  10. Arts E.J., Hazuda D.J. HIV-1 antiretroviral drug therapy. Cold Spring Harb. Perspect. Med. 2012;2. doi: 10.1101/cshperspect.a007161
  11. Kumari G., Singh R.K. Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario. HIV & AIDS Rev. 2012;11:5–14. doi: 10.1016/j.hivar.2012.02.003
  12. Matthews T., Salgo M., Greenberg M., Chung J., DeMasi R., Bolognesi D. Enfuvirtide: The first therapy to inhibit the entry of HIV-1 into host CD4 lymphocytes. Nat. Rev. Drug Discov. 2004;3:215–225. doi: 10.1038/nrd1331
  13. Kozal M., Aberg J., Pialoux G., Cahn P., Thompson M., Molina J.-M., Grinsztejn B., Diaz R., Castagna A., Kumar P., Latiff G., DeJesus E., et al., for the BRIGHTE Trial Team. Fostemsavir in adults with multidrug-resistant HIV-1 infection. N. Engl. J. Med. 2020;382:1232–1243. doi: 10.1056/NEJMoa1902493
  14. Chahine E.B. Fostemsavir: The first oral attachment inhibitor for treatment of HIV-1 infection. Am. J. Health Syst. Pharm. 2021;78(5):376–388. doi: 10.1093/ajhp/zxaa416
  15. MacArthur R.D., Novak R.M. Maraviroc: The first of a new class of antiretroviral agents. Clin. Infect. Dis. 2008;47:236–241. doi: 10.1086/589289
  16. Bettiker R.L., Koren D.E., Jacobson J.M. Ibalizumab. Curr. Opin. HIV AIDS. 2018;13(4):354–358. doi: 10.1097/COH.0000000000000473
  17. Rizza S.A., Bhatia R., Zeuli J., Temesgen Z. Ibalizumab for the treatment of multidrug-resistant HIV-1 infection. Drugs Today (Barc). 2019;55(1):25–34. doi: 10.1358/dot.2019.55.1.2895651
  18. Blair H.A. Ibalizumab: A Review in multidrug-resistant HIV-1 infection. Drugs. 2020;80(2):189–196. doi: 10.1007/s40265-020-01258-3
  19. Lai Y.-T. Small molecule HIV-1 attachment inhibitors: Discovery, mode of action and structural basis of inhibition. Viruses. 2021;13:843. doi: 10.3390/v13050843
  20. Jiang S., Tuzikov A.V., Andrianov A.M. Small-molecule HIV-1 entry inhibitors targeting the epitopes of broadly neutralizing antibodies. Cell Chem. Biol. 2022;29(5):757–773. doi: 10.1016/j.chembiol.2022.03.009
  21. Park K. A review of computational drug repurposing. Transl. Clin. Pharmacol. 2019;27(2):59–63. doi: 10.12793/tcp.2019.27.2.59
  22. Pushpakom S., Iorio F., Eyers P.A., Escott K.J., Hopper S., Wells A., Doig A., Guilliams T., Latimer J., McNamee C., Norris A., Sanseau P., Cavalla D., Pirmohamed M. Drug repurposing: progress, challenges and recommendations. Nat. Rev. Drug Discov. 2019;18(1):41–58. doi: 10.1038/nrd.2018.168
  23. Zhan P., Yu B., Ouyang L. Drug repurposing: An effective strategy to accelerate contemporary drug discovery. Drug Discov. Today. 2022;27(7):1785–1788. doi: 10.1016/j.drudis.2022.05.026
  24. Andrianov A.M., Furs K.V., Gonchar A.V., Aslanyan L.H., Tuzikov A.V. Application of Virtual Screening and Molecular Modeling Technologies to Identify Potential SARS-CoV-2 Main Protease Inhibitors. Mathematical Biology and Bioinformatics. 2023;18(1):15–32. doi: 10.17537/2023.18.15
  25. Fanke J., Andrianov A., Wang L., Furs K, Gonchar A., Wang Q., Xu W., Lu L., Xia S., Tuzikov A., Jiang S. Repurposing Navitoclax to block SARS-CoV-2 fusion and entry by targeting heptapeptide repeat sequence 1 in S2 protein. J. Med. Virol. 2023;95(10):e29145. doi: 10.1002/jmv.29145
  26. Palacio-Rodríguez K., Lans I., Cavasotto C.N., Cossio P. Exponential consensus ranking improves the outcome in docking and receptor ensemble docking. Sci. Rep. 2019;9(1). Article No. 5142. doi: 10.1038/s41598-019-41594-3
  27. Wishart D.S., Feunang Y.D., Guo A.C., Lo E.J., Marcu A., Grant J.R., Sajed T., Johnson D., Li C., Sayeeda Z., Assempour N., Iynkkaran I., Liu Y., Maciejewski A., Gale N., Wilson A., Chin L., Cummings R., Le D., Pon A., Knox C., Wilson M. DrugBank 5.0: a major update to the DrugBank database for 2018. Nucl. Acids Res. 2017;46:D1074–D1082. doi: 10.1093/nar/gkx1037
  28. Sterling T., Irwin J.J. ZINC 15 – Ligand discovery for everyone. J. Chem. Inf. Model. 2015;55(11):2324–2337. doi: 10.1021/acs.jcim.5b00559
  29. Landrum G. The RDKit documentation. https://www. rdkit.org/docs/ (accessed 26 March 2024).
  30. Trott O., Olson A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comp. Chem. 2010;31:455–461. doi: 10.1002/jcc.21334
  31. Zhang X., Zhu Y., Hu H., Zhang S., Wang P., Chong H., He J, Wang X., He Y. Structural insights into the mechanisms of action of short-peptide HIV-1 fusion inhibitors targeting the Gp41 pocket. Front. Cell. Infect. Microbiol. 2018;8:51. doi: 10.3389/fcimb.2018.00051
  32. Gordon J.C., Myers J.B., Folta T., Shoja V., Heath L.S., Onufriev A. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucl. Acids Res. 2005;33(suppl_2):W368–W371. doi: 10.1093/nar/gki464
  33. Wójcikowski M., Ballester P., Siedlecki P. Performance of machine-learning scoring functions in structure-based virtual screening. Sci. Rep. 2017;7:46710. doi: 10.1038/srep46710
  34. Durrant J.D., McCammon J.A. NNScore 2.0: A neural-network receptor–ligand scoring function. J. Chem. Inf. Model. 2011;51(11):2897–2903. doi: 10.1021/ci2003889
  35. Kaushik M. A review of innovative chemical drawing and spectra prediction computer software. Mediterr. J. Chem. 2014;3(1):759–766. doi: 10.13171/mjc.3.1.2014.04.04.16
  36. Case D.A., Ben-Shalom I.Y., Brozell S.R., Cerutti D.S., Cheatham T.E., III, Cruzeiro V.W.D., Darden T.A., Duke R.E., Ghoreishi D., Gilson M.K. et al. AMBER 2018. University of California, 2018.
  37. Ryckaert J.P., Ciccotti G., Berendsen H.J.C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23(3):327–341. doi: 10.1016/0021-9991(77)90098-5
  38. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 1995;103:8577–8593. doi: 10.1063/1.470117
  39. Genheden S., Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand- binding affinity. Expert Opin. Drug Discov. 2015;10(5):449–461. doi: 10.1517/17460441.2015.1032936
  40. Pu J., He X., Xu W., Wang C., Lan Q., Hua C., Wang K., Lu L., Jiang S. The analogs of furanyl methylidene rhodanine exhibit broad-spectrum inhibitory and inactivating activities against enveloped viruses, including SARS-CoV-2 and its variants. Viruses. 2022;14(3):489. doi: 10.3390/v14030489
  41. Katritzky A.R., Tala S.R., Lu H., Vakulenko A.V., Chen Q.Y., Sivapackiam J., Pandya K., Jiang S., Debnath A.K. Design, synthesis, and structure-activity relationship of a novel series of 2-aryl 5-(4-oxo-3-phenethyl-2-thioxothiazolidinylidenemethyl)furans as HIV-1 entry inhibitors. J. Med. Chem. 2009;52:7631–7639. doi: 10.1021/jm900450n
  42. Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 2001;46:3–26.
  43. Veber D.F., Johnson S.R., Cheng H.Y., Smith B.R., Ward K.W., Kopple K.D. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 2002;45(12):2615–2623. doi: 10.1021/jm020017n
  44. Daina A., Michielin O., Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep. 2017;7:42717. doi: 10.1038/srep42717
  45. Durrant J.D., McCammon J.A. BINANA: A novel algorithm for ligand-binding characterization. J. Mol. Graph. Model. 2011;29(6):888–893. doi: 10.1016/j.jmgm.2011.01.004
  46. Song F., Xu G., Gaul M.D., Zhao B., Lu T., Zhang R., DesJarlais R.L., DiLoreto K., Huebert N., Shook B., Rentzeperis D., Santulli R., Eckardt A., Demarest K. Design, synthesis and structure activity relationships of indazole and indole derivatives as potent glucagon receptor antagonists. Bioorg. Med. Chem. Lett. 2019;29(15):1974–1980. doi: 10.1016/j.bmcl.2019.05.036
  47. Jayne D.R., Merkel P.A., Schall T.J., Bekker P. Avacopan for the treatment of ANCA-associated vasculitis. New Eng. J. Med. 2021;384(7):599–609. doi: 10.1056/NEJMoa2023386
  48. Soulsby W.D. Journal Club Review of “Avacopan for the Treatment of ANCA-Associated Vasculitis”. ACR Open Rheumatol. 2022;4(7):558–561. doi: 10.1002/acr2.11412
  49. Gupta R., Mehan S., Sethi P., Prajapati A., Alshammari A., Alharbi M., Al-Mazroua H.A., Narula A.S. Smo-Shh agonist Purmorphamine prevents neurobehavioral and neurochemical defects in 8-OH-DPAT-induced experimental model of obsessive-compulsive disorder. Brain Sci. 2022;12(3):342. doi: 10.3390/brainsci12030342
  50. Blank B.R., Gut J., Rosenthal P.J., Renslo A.R. Artefenomel regioisomer RLA-3107 is a promising lead for the discovery of next-generation endoperoxide antimalarials. ACS Med. Chem. Lett. 2023;14(4):493–498. doi: 10.1021/acsmedchemlett.3c00039
  51. Schmidt A., Kimmel D.B., Bai C., Scafonas A., Rutledge S., Vogel R.L., McElwee-Witmer S., Chen F., Nantermet P.V., Kasparcova V., et al. Discovery of the selective androgen receptor modulator MK-0773 using a rational development strategy based on differential transcriptional requirements for androgenic anabolism versus reproductive physiology. J. Biol. Chem. 2010;285(22):17054–17064. doi: 10.1074/jbc.M109.099002
  52. Tack J., Schumacher K., Tonini G., Scartoni S., Capriati A., Maggi C.A. The neurokinin-2 receptor antagonist ibodutant improves overall symptoms, abdominal pain and stool pattern in female patients in a phase II study of diarrhoea-predominant IBS. Gut. 2016;66(8). doi: 10.1136/gutjnl-2015-310683
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2024;19(1):77-95
doi: 10.17537/2024.19.77
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы

 
  Copyright ИМПБ РАН © 2005-2024