Development of a generative adversarial neural network for identification of potential HIV-1 inhibitors by deep learning methods ; Разработка генеративной состязательной нейронной сети для идентификации потенциальных ингибиторов ВИЧ-1 методами глубокого обучения

Authors: G. I. Nikolaev, N. A. Shuldov, A. I. Anishenko, A. V. Tuzikov, A. M. Andrianov, Г. И. Николаев, Н. А. Шульдов, А. И. Анищенко, А. В. Тузиков, А. М. Андрианов

Source: Informatics; Том 17, № 1 (2020); 7-17 ; Информатика; Том 17, № 1 (2020); 7-17 ; 2617-6963 ; 1816-0301

Subject Terms: методы молекулярного моделирования, a generative adversarial neural network, gp120 protein, HIV-1 entry inhibitors, molecular modeling, генеративно-состязательный автоэнкодер, белок gp120, ингибиторы проникновения ВИЧ-1

File Description: application/pdf

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Expert Opinion on Therapeutic Patents, 2017, vol. 27, рр. 707–719.; Kadurin A., Aliper A., Kazennov A., Mamoshina P., Vanhaelen Q., Khrabrov K., Zhavoronkov A. The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology. Oncotarget, 2017, vol. 8, рр. 10883–10890.; Xu B., Wang N., Chen T., Li M. Empirical Evaluation of Rectified Activations in Convolutional Network, 2015. Available at: https://arxiv.org/abs/1505.00853 (accessed 12.11.2019).; Rudoy G. I. The Choice of the Activation Function in the Prediction of Neural Networks. Machine Learning and Data Analysis, 2011, no. 1, pp. 16–39. Available at: https://arxiv.org/abs/1412.6980 (accessed 12.11.2019).; Kingma D., Ba J. Adam: A Method for Stochastic Optimization, 2014.; Van der Maaten L. Visualizing data using t-SNE. Journal of Machine Learning Research, 2008, vol. 9, рр. 2579–2605.; Kolb H. C., Finn M. G., Sharpless K. B. Click chemistry: Diverse chemical function from a few good reactions. Angewandte Chemie International Edition, 2001, vol. 40, no. 11, рр. 2004–2021.; Irwin J. J., Shoichet B. K. ZINC  a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 2005, vol. 45, no. 1, рр. 177–182.; Irwin J. J., Sterling T., Mysinger M. M., Bolstad E. S., Coleman R. G. ZINC: a free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 2012, vol. 52, no. 7, рр. 1757–1768.; Courter J. R., Madani N., Sodroski J., Schön A., Freire E., …, Smith A. B. 3rd. Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: Conversion of a viral entry agonist to an antagonist. Accounts of Chemical Research, 2014, vol. 47, рр. 1228–1237.; Curreli F., Kwon Y. D., Zhang H., Scacalossi D., Belov D. S., …, Debnath A. K. Structure-based design of a small molecule CD4-antagonist with broad spectrum anti-HIV-1 activity. Journal of Medicinal Chemistry, 2015, vol. 58, рр. 6909–6927.; Durrant J. D., McCammon J. A. AutoClickChem: click chemistry in silico. PLOS Computational Biology, 2012, vol. 8, no. 3, e1002397. https://doi.org/10.1371/journal.pcbi.1002397; 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. Advanced Drug Delivery Reviews, 2001, vol. 46, no. 1–3, рр. 3–26.; Alhossary A., Handoko S. D., Mu Y., Kwoh C. K. Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics, 2015, vol. 31, no. 13, рр. 2214–2216.; Kwong P. D., Wyatt R., Robinson J., Sweet R. W., Sodroski J., Hendrickson W. A. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 1998, vol. 393, рр. 648–659.; Blahut R. E. Theory and Practice of Error Control Codes. Addison-Wesley, 1983, 500 р.; Tanimoto T. T. IBM Internal Report 17th. IBM Corp., Armonk, New York, 1957.; Myszka D. G., Sweet R. W., Hensley P., Brigham-Burke M., Kwong P. D., …, Doyle M. L. Energetics of the HIV gp120-CD4 binding reaction. Proceedings of the National Academy of Sciences, 2000, vol. 97, рр. 9026–9031.; Andrianov A. M., Nikolaev G. I., Kornoushenko Y. V., Xu W., Jiang S., Tuzikov A. V. In silico identification of novel aromatic compounds as potential HIV-1 entry inhibitors mimicking cellular receptor CD4. Viruses, 2019, vol. 11, E746. https://doi.org/10.3390/v11080746; Andrianov A. M., Nikolaev G. I., Kornoushenko Y. V., Huang J., Jiang S., Tuzikov A. V. Virtual screening and identification of potential HIV-1 inhibitors based on cross-reactive neutralizing antibody N6. Doklady of the National Academy of Sciences of Belarus, 2019, vol. 63, no. 4, рр. 445–456.; Andrianov A. M., Nikolaev G. I., Kornoushenko Y. V., Karpenko A. D., Huang J., Jiang S., Tuzikov A. V. Identification of functional mimetics of the neutralizing anti-HIV antibody N6 by virtual screening and molecular modeling N6. Doklady of the National Academy of Sciences of Belarus, 2019, vol. 63, no. 5, рр. 561–571.; Andrianov A. M., Nikolaev G. I., Kornoushenko Y. V., Huang J., Jiang S., Tuzikov A. V. In silico identification of high-affinity ligands of the HIV-1 gp120 protein, potential peptidomimetics of neutralizing antibody N6. Mathematical Biology and Bioinformatics, 2019, vol. 14, no. 2, рр. 430–449.; Curreli F., Kwon Y. D., Belov D .S., Ramesh R. R., Kurkin A. V., …, Debnath A. K. Synthesis, antiviral potency, in vitro ADMET, and X-ray structure of potent CD4 mimics as entry inhibitors that target the Phe43 cavity of HIV-1 gp120. Journal of Medicinal Chemistry, 2017, vol. 60, рр. 3124–3153.; https://inf.grid.by/jour/article/view/1045

Availability: https://inf.grid.by/jour/article/view/1045
https://doi.org/10.37661/1816-0301-2020-17-1-7-17

Identification of functional mimetics of anti-hiv antibody n6 by methods of virtual screening and molecular modeling ; Идентификация функциональных миметиков нейтрализующего анти-вич антитела n6 методами виртуального скрининга и молекулярного моделирования

Authors: Alexander M. Andrianov, Grigory I. Nikolaev, Yuri V. Kornoushenko, Anna D. Karpenko, Jinghe Huang, Shibo Jiang, Alexander V. Tuzikov, А. М. Андрианов, Г. И. Николаев, Ю. В. Корноушенко, А. Д. Карпенко, Дж. Хуанг, Ш. Дзян, А. В. Тузиков

Contributors: The study was supported by grants from the Belarusian Foundation for Basic Research (project Х18КИ-002) and the National Natural Science Foundation of China (project 84630090) within the cooperation and exchange Program, Работа поддержана Белорусским республиканским фондом фундаментальных исследований (проект Х18КИ-002) и Национальным фондом естественных наук Китая (проект 84630090) в рамках программы сотрудничества и обмена

Source: Doklady of the National Academy of Sciences of Belarus; Том 63, № 5 (2019); 561-571 ; Доклады Национальной академии наук Беларуси; Том 63, № 5 (2019); 561-571 ; 2524-2431 ; 1561-8323 ; 10.29235/1561-8323-2019-63-5

Subject Terms: лекарственные препараты против ВИЧ, gp120 protein, neutralizing antibody N6, HIV-1 entry inhibitors, virtual screening, molecular docking, molecular dynamics, anti-HIV drugs, белок gp120, нейтрализующее антитело N6, ингибиторы проникновения ВИЧ-1, виртуальный скрининг, молекулярный докинг, молекулярная динамика

File Description: application/pdf

Relation: https://doklady.belnauka.by/jour/article/view/713/713; Sharp, P. M. Origins of HIV and the AIDS pandemic / P. M. Sharp, B. H. Hahn // Cold Spring Harb. Perspect. Med. -2011. - Vol. 1, N 1. - P. a006841. https://doi.org/10.1101/cshperspect.a006841; UNAIDS %7C AIDSinfo [Electronic resource]. - Mode of access: http://aidsinfo.unaids.org/. - Date of access: 27.07.2019.; Kumari, G. Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario / G. Kumari, R.K. Singh // HiV AIDS Rev. - 2012. - Vol. 11, N 1. - P. 5-14. https://doi.org/10.1016/j.hivar.2012.02.003; Mann, J. K. HIV-1 vaccine immunogen design strategies / J. K. Mann, T. Ndung’u // Virol. J. - 2015. - Vol. 12, N 1. -P. 3. https://doi.org/10.1186/s12985-014-0221-0; Identification of a CD4-binding-site antibody to HIV that evolved near-pan neutralization breadth / J. Huang [et al.] // Immunity. - 2016. - Vol. 45, N 5. - P. 1108-1121. https://doi.org/10.10167j.immuni.2016.10.027; Виртуальный скрининг и идентификация потенциальных ингибиторов ВИЧ-1 на основе кросс-реактивного нейтрализующего антитела N6 / А. М. Андрианов [и др.] // Докл. Нац. акад. наук Беларуси. - 2019. - Т. 63, № 4. -С. 445-456. https://doi.org/10.29235/1561-8323-2019-63-4-445-456; Fast, accurate, and reliable molecular docking with QuickVina 2 / A. Alhossary [et al.] // Bioinformatics. - 2015. -Vol. 31, N 13. - P. 2214-2216. https://doi.org/10.1093/bioinformatics/btv082; AMBER 16 / D. A. Case [et al.]. - San Francisco, 2016.; Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody / P. D. Kwong [et al.] // Nature. - 1998. - Vol. 393, N 6686. - P. 648-659. https://doi.org/10.1038/31405; Identification of individual human-immunodeficiency-virus type-1 gp120 amino-acids important for CD4 receptor-binding / U. Olshevsky [et al.] // Virol. - 1990. - Vol. 64, N 12. - P. 5701-5707.; Liu, Y. Optimization of CD4/gp120 inhibitors by thermodynamic-guided alanine-scanning mutagenesis / Y. Liu, A. Schon, E. Freire // Chem. Biol. Drug Des. - 2013. - Vol. 81, N 1. - P. 72-78. https://doi.org/10.1111/cbdd.12075; Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: Conversion of a viral entry agonist to an antagonist / J. R. Courter [et al.] // Acc. Chem. Res. - 2014. - Vol. 47, N 4. - P. 1228-1237. https://doi.org/10.1021/ar4002735; Energetics of the HIV gp120-CD4 binding reaction / D. G. Myszka [et al.] // Proc. Natl. Acad. Sci. USA. - 2000. -Vol. 97, N 16. - P. 9026-9031. https://doi.org/10.1073/pnas.97.16.9026; https://doklady.belnauka.by/jour/article/view/713

Availability: https://doklady.belnauka.by/jour/article/view/713
https://doi.org/10.29235/1561-8323-2019-63-5-561-571

Virtual screening and identification of potential HIV-1 inhibitors based on the cross-reactive neutralizing antibody N6 ; Виртуальный скрининг и идентификация потенциальных ингибиторов ВИЧ-1 на основе кросс-реактивного нейтрализующего антитела N6

Authors: Alexander M. Andrianov, Gregory I. Nikolaev, Yuri V. Kornoushenko, Jinghe Huang, Shibo Jiang, Alexander V. Tuzikov, А. М. Андрианов, Г. И. Николаев, Ю. В. Корноушенко, Дж. Хуанг, Ш. Дзян, А. В. Тузиков

Contributors: The study was supported by grants from the Belarusian Foundation for Fundamental Research (project X18КИ-002) and the National Natural Science Foundation of China (project 84630090) within the cooperation and exchange Program., Работа поддержана Белорусским республиканским фондом фундаментальных исследований (проект X18КИ-002) и Национальным фондом естественных наук Китая (проект 84630090) в рамках программы сотрудничества и обмена.

Source: Doklady of the National Academy of Sciences of Belarus; Том 63, № 4 (2019); 445-456 ; Доклады Национальной академии наук Беларуси; Том 63, № 4 (2019); 445-456 ; 2524-2431 ; 1561-8323 ; 10.29235/1561-8323-2019-63-4

Subject Terms: лекарственные препараты против ВИЧ, gp120 protein, antibody N6, HIV-1 entry inhibitors, virtual screening, molecular docking, molecular dynamics, anti-HIV drugs, белок gp120, антитело N6, ингибиторы проникновения ВИЧ-1, виртуальный скрининг, молекулярный докинг, молекулярная динамика

File Description: application/pdf

Relation: https://doklady.belnauka.by/jour/article/view/632/637; Arts, E. J. HIV-1 antiretroviral drug therapy / E. J. Arts, D. J. Hazuda // Cold Spring Harb. Perspect. Med. – 2012. – Vol. 2, N 4. – P. a007161. https://doi.org/10.1101/cshperspect.a007161; kumari, G. Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario / G. kumari, R.k. Singh // HIV AIDS Rev. – 2012. – Vol. 11, N 1. – P. 5–14. https://doi.org/10.1016/j.hivar.2012.02.003; Wang, H.-B. HIV vaccine research: The challenge and the way forward / H.-B. Wang, Q.-H. Mo, Z. yang // J. Immunol. Res. - 2015. – Vol. 2015. – Art. 503978. https://doi.org/10.1155/2015/503978; Barouch, D. H. Challenges in the development of an HIV-1 vaccine / D. H. Barouch // Nature. – 2008. – Vol. 455, N 7213. – P. 613–619. https://doi.org/10.1038/nature07352; Mann, J. k. HIV-1 vaccine immunogen design strategies / J. k. Mann, T. Ndung’u // Virol. J. – 2015. – Vol. 12, N 1. – P. 3. https://doi.org/10.1186/s12985-014-0221-0; Identifcation of a CD4-binding-site antibody to HIV that evolved near-pan neutralization breadth / J. Huang [et al.] // Immunity. – 2016. – Vol. 45, N 5. – P. 1108–1121. https://doi.org/10.1016/j.immuni.2016.10.027; Sunseri, J. Pharmit: interactive exploration of chemical space / J. Sunseri, D. R. Koes // Nucl. Acids Res. – 2016. – Vol. 44. – P. W442–W448. https://doi.org/10.1093/nar/gkw287; Fast, accurate, and reliable molecular docking with QuickVina 2 / A. Alhossary [et al.] // Bioinformatics. – 2015. – Vol. 31, N 13. – P. 2214–2216. https://doi.org/10.1093/bioinformatics/btv082; Structure-based design of a small molecule CD4-antagonist with broad spectrum anti-HIV-1 activity / F. Curreli [et al.] // J. Med. Chem. – 2015. – Vol. 58, N 17. – P. 6909–6927. https://doi.org/10.1021/acs.jmedchem.5b00709; Structure-based design, synthesis and validation of CD4-mimetic small molecule inhibitors of HIV-1 entry: Conversion of a viral entry agonist to an antagonist / J. R. Courter [et al.] // Acc. Chem. Res. – 2014. – Vol. 47, N 4. – P. 1228–1237. https://doi.org/10.1021/ar4002735; AMBER 16 / D. A. Case [et al.]. – San Francisco, 2016.; Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody / P. D. kwong [et al.] // Nature. – 1998. – Vol. 393, N 6686. – P. 648–659. https://doi.org/10.1038/31405; Identifcation of individual human-immunodefciency-virus type-1 gp120 amino-acids important for CD4 receptor-binding / U. Olshevsky [et al.] // Virol. – 1990. – Vol. 64, N 12. – P. 5701–5707.; Liu, y. Optimization of CD4/gp120 inhibitors by thermodynamic-guided alanine-scanning mutagenesis / y. Liu, A. Schön, E. Freire // Chem. Biol. Drug Des. – 2013. – Vol. 81, N 1. – P. 72–78. https://doi.org/10.1111/cbdd.12075; Energetics of the HIV gp120-CD4 binding reaction / D. G. Myszka [et al.] // Proc. Natl. Acad. Sci. USA. – 2000. – Vol. 97, N 16. – P. 9026–9031. https://doi.org/10.1073/pnas.97.16.9026; https://doklady.belnauka.by/jour/article/view/632

Availability: https://doklady.belnauka.by/jour/article/view/632
https://doi.org/10.29235/1561-8323-2019-63-4-445-456

Molecular dynamics for structural complexes of potential HIV-1 inhibitors with the viral envelope gp120 protein ; Молекулярная динамика структурных комплексов потенциальных ингибиторов ВИЧ-1 с белком gp120 оболочки вируса

Authors: I. A. Kashyn, G. I. Nikolaev, M. A. Tuzikov, A. M. Andrianov, И. А. Кашин, Г. И. Николаев, А. В. Тузиков, А. М. Андрианов

Contributors: Belarusian Republican Foundation for Fundamental Research, projects no. X17-022, Х18КИ-002, Белорусский республиканский фонд фундаментальных исследований, проекты Х17-022, Х18КИ-002

Source: Doklady of the National Academy of Sciences of Belarus; Том 62, № 5 (2018); 576-584 ; Доклады Национальной академии наук Беларуси; Том 62, № 5 (2018); 576-584 ; 2524-2431 ; 1561-8323 ; 10.29235/1561-8323-2018-62-5

Subject Terms: лекарственные препараты против ВИЧ, gp120 protein, HIV-1 entry inhibitors, molecular dynamics, anti-HIV drugs, белок gp120, ингибиторы проникновения ВИЧ-1, молекулярная динамика

File Description: application/pdf

Relation: https://doklady.belnauka.by/jour/article/view/555/559; Wang, H.-B. HIV vaccine research: The challenge and the way forward / H.-B. Wang, Q.-H. Mo, Z. J. Yang // J. Immunol. Res. - 2015. - Vol. 2015. - Article 503978. https://doi.org/10.1155/2015/503978; Kumari, G. Highly active antiretroviral therapy for treatment of HIV/AIDS patients: current status and future prospects and the Indian scenario / G. Kumari, R. K. Singh // HIV AIDS Rev. - 2012. - Vol. 11, N 1. - P. 5-14. https://doi.org/10.1016/j. hivar.2012.02.003; Corti, D. Broadly neutralizing antiviral antibodies / D. Corti, A. Lanzavecchia // Annu. Rev. Immunol. - 2013. -Vol. 31, N 1. - P. 705-742. https://doi.org/10.1146/annurev-immunol-032712-095916; Mann, J. K. HIV-1 vaccine immunogen design strategies / J. K. Mann, T. Ndung’u // Virol. J. - 2015. - Vol. 12, N 1. -P. 3. https://doi.org/10.1186/s12985-014-0221-0; Small-molecule HIV-1 entry inhibitors targeting gp120 and gp41: a patent review (2010-2015) / W. Li [et al.] // Expert Opin. Ther. Pat. - 2017. - Vol. 27, N 6. - P. 707-719. https://doi.org/10.1080/13543776.2017.1281249; Wilen, C. B. HIV: Cell binding and entry / C. B. Wilen, J. S. Tilton, R. W. Doms // Cold Spring Harb. Perspect. Med. -2012. - Vol. 2, N 8. - P. a006866. https://doi.org/10.1101/cshperspect.a006866; Computational methods in drug discovery / G. Sliwoski [et al.] // Pharmacol. Rev. - 2014. - Vol. 66, N 1. - P. 334-395. https://doi.org/10.1124/pr.112.007336; In silico дизайн и оценка потенциальной активности новых ингибиторов ВИЧ-1 - миметиков первичного рецептора CD4 белка gp120 оболочки вируса / А. М. Андрианов [и др.] // Докл. Нац. акад. наук Беларуси. - 2017. - Т. 61, № 3. - С. 47-57.; AMBER 11 / D. A. Case [et al.]. - San Francisco, Univ. California, 2010. - 296 p.; MMPBSA.py: An efficient program for end-state free energy calculations / B. R. Miller [et al.] // J. Chem. Theory Comput. - 2012. - Vol. 8, N 9. - P. 3314-3321. https://doi.org/10.1021/ct300418h; Structure-based design of a small molecule CD4-antagonist with broad spectrum anti-HIV-1 activity / F. Curreli [et al.] // J. Med. Chem. - 2015. - Vol. 58, N 17. - P. 6909-6927. https://doi.org/10.1021/acs.jmedchem.5b00709; Energetics of the HIV gp120-cD4 binding reaction / D. G. Myszka [et al.] // Proc. Natl. Acad. Sci. USA. - 2000. -Vol. 97, N 16. - P. 9026-9031. https://doi.org/10.1073/pnas.97.16.9026; Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody / P. D. Kwong [et al.] // Nature. - 1998. - Vol. 393, N 6686. - P. 648-659. https://doi.org/10.1038/31405; Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings / C. A. Lipinski [et al.] // Adv. Drug Deliv. Rev. - 2001. - Vol. 46, N 1-3. - P. 3-26. https://doi.org/10.1016/s0169-409x(00)00129-0; Brase S., Banert K. Organic Azides: Syntheses and applications. - Wiley, 2009. - 507 p. https://doi.org/10.1002/9780470682517; https://doklady.belnauka.by/jour/article/view/555

Availability: https://doklady.belnauka.by/jour/article/view/555
https://doi.org/10.29235/1561-8323-2018-62-5-576-584

IN SILICO DESIGN AND EVALUATION OF THE POTENTIAL ACTIVITY OF NOVEL HIV-1 INHIBITORS – MIMETICS OF THE PRIMARY RECEPTOR CD4 OF THE VIRAL ENVELOPE GP120 PROTEIN ; IN SILICO ДИЗАЙН И ОЦЕНКА ПОТЕНЦИАЛЬНОЙ АКТИВНОСТИ НОВЫХ ИНГИБИТОРОВ ВИЧ-1 − МИМЕТИКОВ ПЕРВИЧНОГО РЕЦЕПТОРА CD4 БЕЛКА GP120 ОБОЛОЧКИ ВИРУСА

Authors: A. M. Andrianov, I. A. Kashyn, G. I. Nikolaev, A. V. Tuzikov, А. М. Андрианов, И. А. Кашин, Г. И. Николаев, А. В. Тузиков

Source: Doklady of the National Academy of Sciences of Belarus; Том 61, № 3 (2017); 47-57 ; Доклады Национальной академии наук Беларуси; Том 61, № 3 (2017); 47-57 ; 2524-2431 ; 1561-8323 ; undefined

Subject Terms: молекулярный докинг, gp120 protein, HIV-1 entry inhibitors, computer-aided drug design, click chemistry methodology, molecular docking, белок gp120, ингибиторы проникновения ВИЧ-1, компьютерное конструирование лекарств, методология клик-химии

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