Antiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection

References

• Aanouz, I., Belhassan, A., El-Khatabi, K., Lakhlifi, T., El-Ldrissi, M., & Bouachrine, M. (2020). Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1758790
   Google Scholar
• Ayerdi, O., Puerta, T., Clavo, P., Vera, M., Ballesteros, J., Fuentes, M. E., Estrada, V., Rodríguez, C., Del Romero, J., & Sandoval Study Group. (2020). Preventive efficacy of tenofovir/emtricitabine against severe acute respiratory syndrome coronavirus 2 among pre-exposure prophylaxis users. Open Forum Infectious Diseases, 7(11), ofaa455. https://doi.org/10.1093/ofid/ofaa455
   PubMed Web of Science ®Google Scholar
• Beigel, J. H., Tomashek, K. M., Dodd, L. E., Mehta, A. K., Zingman, B. S., Kalil, A. C., Hohmann, E., Chu, H. Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R. W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T. F., Paredes, R., Sweeney, D. A., Short, W. R., Touloumi, G., … ACTT-1 Study Group Members. (2020). Remdesivir for the treatment of Covid-19 - final report. New England Journal of Medicine, 383(19), 1813–1826. https://doi.org/10.1056/NEJMoa2007764
   PubMed Web of Science ®Google Scholar
• Blanco, J. L., Ambrosioni, J., Garcia, F., Martinez, E., Soriano, A., Mallolas, J., Miro, J. M., & COVID-19 in HIV Investigators. (2020). COVID-19 in patients with HIV: Clinical case series. Lancet HIV, 7(5), e314–e316. https://doi.org/10.1016/S2352-3018(20)30111-9
   Google Scholar
• Boettiger, D. C., Kerr, S., Ditangco, R., Chaiwarith, R., Li, P. C., Merati, T. P., Thi Thanh Pham, T., Kiertiburanakul, S., Kumarasamy, N., Vonthanak, S., Lee, C. K. C., Van Kinh, N., Pujari, S., Wong, W. W., Kamarulzaman, A., Zhang, F., Yunihastuti, E., Choi, J. Y., Oka, S., Ng, O. T., … TREAT Asia HIV Observational Database. (2016). Tenofovir-based antiretroviral therapy in HBV-HIV coinfection: Results from the TREAT Asia HIV Observational Database. Antiviral Therapy, 21(1), 27–35. https://doi.org/10.3851/IMP2972
   PubMed Web of Science ®Google Scholar
• Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1758788
   Web of Science ®Google Scholar
• Boulle, A., Davies, M. A., Hussey, H., Ismail, M., Morden, E., Vundle, Z., … Tamuhla, T. (2020). Risk factors for COVID-19 death in a population cohort study from the Western Cape Province, South Africa. Clinical Infectious Diseases. https://doi.org/10.1093/cid/ciaa1198
   Google Scholar
• Byrd, K. M., Beckwith, C. G., Garland, J. M., Johnson, J. E., Aung, S., Cu-Uvin, S., Farmakiotis, D., Flanigan, T., Gillani, F. S., Macias-Gil, R., Mileno, M., Ramratnam, B., Rybak, N. R., Sanchez, M., Tashima, K., Mylonakis, E., & Kantor, R. (2020). SARS-CoV-2 and HIV coinfection: Clinical experience from Rhode Island, United States. Journal of the International AIDS Society, 23(7), e25573. https://doi.org/10.1002/jia2.25573
   PubMed Web of Science ®Google Scholar
• Cao, B., Wang, Y., Wen, D., Liu, W., Wang, J., Fan, G., Ruan, L., Song, B., Cai, Y., Wei, M., Li, X., Xia, J., Chen, N., Xiang, J., Yu, T., Bai, T., Xie, X., Zhang, L., Li, C., … Wang, C. (2020). A trial of lopinavir-ritonavir in adults hospitalized with severe Covid-19. New England Journal of Medicine, 382(19), 1787–1799. https://doi.org/10.1056/NEJMoa2001282
   PubMed Web of Science ®Google Scholar
• Chen, Y. W., Yiu, C. B., & Wong, K. Y. (2020). Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: Virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Research, 9, 129. https://doi.org/10.12688/f1000research.22457.2
   PubMedGoogle Scholar
• Cheng, S. C., Chang, G. G., & Chou, C. Y. (2010). Mutation of Glu-166 blocks the substrate-induced dimerization of SARS coronavirus main protease. Biophysical Journal, 98(7), 1327–1336. https://doi.org/10.1016/j.bpj.2009.12.4272
   PubMed Web of Science ®Google Scholar
• Chien, M., Anderson, T. K., Jockusch, S., Tao, C., Li, X., Kumar, S., Russo, J. J., Kirchdoerfer, R. N., & Ju, J. (2020). Nucleotide analogues as inhibitors of SARS-CoV-2 polymerase, a key drug target for COVID-19. Journal of Proteome Research, 19(11), 4690–4697. https://doi.org/10.1021/acs.jproteome.0c00392
   PubMed Web of Science ®Google Scholar
• Chu, C. M., Cheng, V. C., Hung, I. F., Wong, M. M., Chan, K. H., Chan, K. S., … Group, H. U. S. S. (2004). Role of lopinavir/ritonavir in the treatment of SARS: Initial virological and clinical findings. Thorax, 59(3), 252–256. https://doi.org/10.1136/thorax.2003.012658
   PubMed Web of Science ®Google Scholar
• Dandachi, D., Geiger, G., Montgomery, M. W., Karmen-Tuohy, S., Golzy, M., Antar, A., Llibre, J. M., Camazine, M., Díaz-De Santiago, A., Carlucci, P. M., Zacharioudakis, I. M., Rahimian, J., Wanjalla, C. N., Slim, J., Arinze, F., Kratz, A., Jones, J. L., Patel, S. M., Kitchell, E., Francis, A., … HIV-COVID-19 consortium. (2020). Characteristics, comorbidities, and outcomes in a multicenter registry of patients with HIV and coronavirus disease-19. Clinical Infectious Diseases. https://doi.org/10.1093/cid/ciaa1339
   Google Scholar
• de Wilde, A. H., Jochmans, D., Posthuma, C. C., Zevenhoven-Dobbe, J. C., van Nieuwkoop, S., Bestebroer, T. M., van den Hoogen, B. G., Neyts, J., & Snijder, E. J. (2014). Screening of an FDA-approved compound library identifies four small-molecule inhibitors of Middle East respiratory syndrome coronavirus replication in cell culture. Antimicrobial Agents and Chemotherapy, 58(8), 4875–4884. https://doi.org/10.1128/AAC.03011-14
   PubMed Web of Science ®Google Scholar
• Del Amo, J., Polo, R., Moreno, S., Díaz, A., Martínez, E., Arribas, J. R., Jarrín, I., Hernán, M. A., & The Spanish HIV/COVID-19 Collaboration. (2020). Incidence and severity of COVID-19 in HIV-positive persons receiving antiretroviral therapy: A cohort study. Annals of Internal Medicine, 173(7), 536–541. https://doi.org/10.7326/M20-3689
   PubMed Web of Science ®Google Scholar
• Duarte, R. R. R., Copertino, D. C., Jr., Iñiguez, L. P., Marston, J. L., Nixon, D. F., & Powell, T. R. (2020). Repurposing FDA-approved drugs for COVID-19 using a data-driven approach. ChemRxiv. https://doi.org/10.26434/chemrxiv.12148764.v1
   Google Scholar
• Elfiky, A. A., & Azzam, E. B. (2020). Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1758789
   Google Scholar
• Elmezayen, A. D., Al-Obaidi, A., Sahin, A. T., & Yelekci, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1758791
   Web of Science ®Google Scholar
• Enayatkhani, M., Hasaniazad, M., Faezi, S., Guklani, H., Davoodian, P., Ahmadi, N., … Ahmadi, K. (2020). Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2020.1756411
   Google Scholar
• Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/10.1080/07391102.2020.1760136
   Google Scholar
• Ford, N., Vitoria, M., Rangaraj, A., Norris, S. L., Calmy, A., & Doherty, M. (2020). Systematic review of the efficacy and safety of antiretroviral drugs against SARS, MERS or COVID-19: Initial assessment. Journal of the International AIDS Society, 23(4), e25489. https://doi.org/10.1002/jia2.25489
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z., Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T., Zhang, B., … Rao, Z. (2020). Structure of the RNA-dependent RNA polymerase from COVID-19 virus. Science (New York, N.Y.), 368(6492), 779–782. https://doi.org/10.1126/science.abb7498
   PubMed Web of Science ®Google Scholar
• Gordon, C. J., Tchesnokov, E. P., Woolner, E., Perry, J. K., Feng, J. Y., Porter, D. P., & Gotte, M. (2020). Remdesivir is a direct-acting antiviral that inhibits RNA-dependent RNA polymerase from severe acute respiratory syndrome coronavirus 2 with high potency. Journal of Biological Chemistry, 295(20), 6785-6797. https://doi.org/10.1074/jbc.RA120.013679
   Google Scholar
• Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics, 1–11. https://doi.org/10.1080/07391102.2020.1751300
   PubMedGoogle Scholar
• Härter, G., Spinner, C. D., Roider, J., Bickel, M., Krznaric, I., Grunwald, S., Schabaz, F., Gillor, D., Postel, N., Mueller, M. C., Müller, M., Römer, K., Schewe, K., & Hoffmann, C. (2020). COVID-19 in people living with human immunodeficiency virus: A case series of 33 patients. Infection, 48(5), 681–686. https://doi.org/10.1007/s15010-020-01438-z
   PubMed Web of Science ®Google Scholar
• Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., Shahpasand, K., Saboury, A. A., & Falahati, M. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1754293
   Web of Science ®Google Scholar
• Hung, M., Tokarsky, E. J., Lagpacan, L., Zhang, L., Suo, Z., & Lansdon, E. B. (2019). Elucidating molecular interactions of L-nucleotides with HIV-1 reverse transcriptase and mechanism of M184V-caused drug resistance. Communications Biology, 2, 469. https://doi.org/10.1038/s42003-019-0706-x
   PubMed Web of Science ®Google Scholar
• Irwin, J. J., & Shoichet, B. K. (2005). ZINC-a free database of commercially available compounds for virtual screening. Journal of Chemical Information and Modeling, 45(1), 177–182. https://doi.org/10.1021/ci049714+
   PubMed Web of Science ®Google Scholar
• Jockusch, S., Tao, C., Li, X., Anderson, T. K., Chien, M., Kumar, S., Russo, J. J., Kirchdoerfer, R. N., & Ju, J. (2020). Triphosphates of the two components in DESCOVY and TRUVADA are inhibitors of the SARS-CoV-2 polymerase. BioRxiv. https://doi.org/10.1101/2020.04.03.022939
   Google Scholar
• Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shankar, S. S., Tellis, M. B., Pandya, V. K., … Kulkarni, M. J. (2020). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2020.1760137
   Google Scholar
• Karmen-Tuohy, S., Carlucci, P. M., Zervou, F. N., Zacharioudakis, I. M., Rebick, G., Klein, E., Reich, J., Jones, S., & Rahimian, J. (2020). Outcomes among HIV-positive patients hospitalized with COVID-19. Journal of Acquired Immune Deficiency Syndromes (1999), 85(1), 6–10. https://doi.org/10.1097/QAI.0000000000002423
   PubMed Web of Science ®Google Scholar
• Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1751298
   Web of Science ®Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
   PubMed Web of Science ®Google Scholar
• Ma, C., Sacco, M. D., Hurst, B., Townsend, J. A., Hu, Y., Szeto, T., Zhang, X., Tarbet, B., Marty, M. T., Chen, Y., & Wang, J. (2020). Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease. Cell Research, 30, 678–692. https://doi.org/10.1038/s41422-020-0356-z
   Google Scholar
• Mayer, K. H., Molina, J.-M., Thompson, M. A., Anderson, P. L., Mounzer, K. C., De Wet, J. J., DeJesus, E., Jessen, H., Grant, R. M., Ruane, P. J., Wong, P., Ebrahimi, R., Zhong, L., Mathias, A., Callebaut, C., Collins, S. E., Das, M., McCallister, S., Brainard, D. M., … Hare, C. B. (2020). Emtricitabine and tenofovir alafenamide vs emtricitabine and tenofovir disoproxil fumarate for HIV pre-exposure prophylaxis (DISCOVER): Primary results from a randomised, double-blind, multicentre, active-controlled, phase 3, non-inferiority trial. Lancet (London, England), 396(10246), 239–254. https://doi.org/10.1016/S0140-6736(20)31065-5
   PubMed Web of Science ®Google Scholar
• McKenna, C. E., Kashemirov, B. A., Peterson, L. W., & Goodman, M. F. (2010). Modifications to the dNTP triphosphate moiety: From mechanistic probes for DNA polymerases to antiviral and anti-cancer drug design. Biochimica et Biophysica Acta, 1804(5), 1223–1230. https://doi.org/10.1016/j.bbapap.2010.01.005
   PubMed Web of Science ®Google Scholar
• Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–6. https://doi.org/10.1080/07391102.2020.1752802
   Web of Science ®Google Scholar
• Oberg, B. (2006). Rational design of polymerase inhibitors as antiviral drugs. Antiviral Research, 71(2-3), 90–95. https://doi.org/10.1016/j.antiviral.2006.05.012
   PubMed Web of Science ®Google Scholar
• Pant, S., Singh, M., Ravichandiran, V., Murty, U. S. N., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1757510
   Google Scholar
• Park, L. S., Rentsch, C., Sigel, K., Rodriguez-Barradas, M., & Brown, S. T. (2020). COVID-19 in the largest US HIV cohort. Late-breaking poster LBPE023 presented at the AIDS 2020: 23rd International AIDS Conference Virtual. AIDS 2020, 6 – 10 July.
   Google Scholar
• Recovery-Collaborative-Group. (2020). Lopinavir-ritonavir in patients admitted to hospital with COVID-19 (RECOVERY): A randomised, controlled, open-label, platform trial. Lancet, 396(10259), 1345-1352. https://doi.org/10.1016/S0140-6736(20)32013-4
   Google Scholar
• Roos, K., Wu, C., Damm, W., Reboul, M., Stevenson, J. M., Lu, C., Dahlgren, M. K., Mondal, S., Chen, W., Wang, L., Abel, R., Friesner, R. A., & Harder, E. D. (2019). OPLS3e: Extending force field coverage for drug-like small molecules. Journal of Chemical Theory and Computation, 15(3), 1863–1874. https://doi.org/10.1021/acs.jctc.8b01026
   PubMed Web of Science ®Google Scholar
• Sanders, J. M., Monogue, M. L., Jodlowski, T. Z., & Cutrell, J. B. (2020). Pharmacologic treatments for coronavirus disease 2019 (COVID-19): A review. JAMA, 323(18), 1824-1836. https://doi.org/10.1001/jama.2020.6019
   Google Scholar
• Sarma, P., Shekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Singh, S., Kumar, H., Prakash, A., Dhibar, D. P., & Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1753580
   Google Scholar
• Shannon, A., Le, N. T.-T., Selisko, B., Eydoux, C., Alvarez, K., Guillemot, J.-C., Decroly, E., Peersen, O., Ferron, F., & Canard, B. (2020). Remdesivir and SARS-CoV-2: Structural requirements at both nsp12 RdRp and nsp14 Exonuclease active-sites. Antiviral Research, 178, 104793. https://doi.org/10.1016/j.antiviral.2020.104793
   PubMed Web of Science ®Google Scholar
• Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: A software program for pK(a) prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/s10822-007-9133-z
   PubMed Web of Science ®Google Scholar
• Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
   PubMed Web of Science ®Google Scholar
• Sluis-Cremer, N., & Tachedjian, G. (2008). Mechanisms of inhibition of HIV replication by non-nucleoside reverse transcriptase inhibitors. Virus Research, 134(1–2), 147–156. https://doi.org/10.1016/j.virusres.2008.01.002
   PubMed Web of Science ®Google Scholar
• Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., & Xiao, G. (2020). Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research, 30(3), 269–271. https://doi.org/10.1038/s41422-020-0282-0
   PubMed Web of Science ®Google Scholar
• Wang, Y., Zhang, D., Du, G., Du, R., Zhao, J., Jin, Y., Fu, S., Gao, L., Cheng, Z., Lu, Q., Hu, Y., Luo, G., Wang, K., Lu, Y., Li, H., Wang, S., Ruan, S., Yang, C., Mei, C., … Wang, C. (2020). Remdesivir in adults with severe COVID-19: A randomised, double-blind, placebo-controlled, multicentre trial. The Lancet, 395(10236), 1569–1578. https://doi.org/10.1016/S0140-6736(20)31022-9
   PubMed Web of Science ®Google Scholar
• Xu, X., Liu, Y., Weiss, S., Arnold, E., Sarafianos, S. G., & Ding, J. (2003). Molecular model of SARS coronavirus polymerase: Implications for biochemical functions and drug design. Nucleic Acids Research, 31(24), 7117–7130. https://doi.org/10.1093/nar/gkg916
   PubMed Web of Science ®Google Scholar
• Yamamoto, N., Yang, R., Yoshinaka, Y., Amari, S., Nakano, T., Cinatl, J., Rabenau, H., Doerr, H. W., Hunsmann, G., Otaka, A., Tamamura, H., Fujii, N., & Yamamoto, N. (2004). HIV protease inhibitor nelfinavir inhibits replication of SARS-associated coronavirus. Biochemical and Biophysical Research Communications, 318(3), 719–725. https://doi.org/10.1016/j.bbrc.2004.04.083
   PubMed Web of Science ®Google Scholar
• Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved alpha-ketoamide inhibitors. Science, 368(6489), 409–412. https://doi.org/10.1126/science.abb3405
   PubMed Web of Science ®Google Scholar