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Research Articles

In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes

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Pages 14977-14988 | Received 08 Dec 2022, Accepted 20 Feb 2023, Published online: 01 Mar 2023

References

  • Abecasis, A. B., Wensing, A. M., Paraskevis, D., Vercauteren, J., Theys, K., Van de Vijver, D. A., Albert, J., Asjö, B., Balotta, C., Beshkov, D., Camacho, R. J., Clotet, B., De Gascun, C., Griskevicius, A., Grossman, Z., Hamouda, O., Horban, A., Kolupajeva, T., Korn, K., … Vandamme, A.-M. (2013). HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics. Retrovirology, 10(1), 7. https://doi.org/10.1186/1742-4690-10-7
  • Abongwa, L. E., Nyamache, A. K., Torimiro, J. N., Okemo, P., & Charles, F. (2019). Human immunodeficiency virus type 1 (HIV-1) subtypes in the northwest region, Cameroon. Virology Journal, 16(1), 103. https://doi.org/10.1186/s12985-019-1209-6
  • Adamson, C. S., & Freed, E. O. (2009). Anti-HIV-1 therapeutics: From FDA-approved drugs to hypothetical future targets. Molecular Interventions, 9(2), 70–74. https://doi.org/10.1124/mi.9.2.5
  • Addo, M. M., Altfeld, M., Rosenberg, E. S., Eldridge, R. L., Philips, M. N., Habeeb, K., Khatri, A., Brander, C., Robbins, G. K., Mazzara, G. P., Goulder, P. J. R., Walker, B. D., & the HIV Controller Study Collaboration. (2001). The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals. Proceedings of the National Academy of Sciences of the United States of America, 98(4), 1781–1786. https://doi.org/10.1073/pnas.98.4.1781
  • Arkin, M. R., Tang, Y., & Wells, J. A. (2014). Small-molecule inhibitors of protein-protein interactions: Progressing toward the reality. Chemistry & Biology, 21(9), 1102–1114. https://doi.org/10.1016/j.chembiol.2014.09.001
  • Arts, E. J., & Hazuda, D. J. (2012). HIV-1 antiretroviral drug therapy. Cold Spring Harbor Perspectives in Medicine, 2(4), a007161. https://doi.org/10.1101/cshperspect.a007161
  • Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037–10041.
  • Barouch, D. H. (2008). Challenges in the development of an HIV-1 vaccine. Nature, 455(7213), 613–619. https://doi.org/10.1038/nature07352
  • Bbosa, N., Kaleebu, P., & Ssemwanga, D. (2019). HIV subtype diversity worldwide. Current Opinion in HIV and AIDS, 14(3), 153–160. https://doi.org/10.1097/COH.0000000000000534
  • Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. https://doi.org/10.1021/ct900549r
  • Brenke, R., Kozakov, D., Chuang, G. Y., Beglov, D., Hall, D., Landon, M. R., Mattos, C., & Vajda, S. (2009). Fragment-based identification of druggable 'hot spots’ of proteins using Fourier domain correlation techniques. Bioinformatics (Oxford, England), 25(5), 621–627. https://doi.org/10.1093/bioinformatics/btp036
  • Chaplin, B., Eisen, G., Idoko, J., Onwujekwe, D., Idigbe, E., Adewole, I., Gashau, W., Meloni, S., Sarr, A. D., Sankalé, J. L., Ekong, E., Murphy, R. L., & Kanki, P. (2011). Impact of HIV type 1 subtype on drug resistance mutations in Nigerian patients failing first-line therapy. AIDS Research and Human Retroviruses, 27(1), 71–80. https://doi.org/10.1089/aid.2010.0050
  • Corpet, F. (1988). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 16(22), 10881–10890. https://doi.org/10.1093/nar/16.22.10881
  • Darden, T., York, D., & Pedersen, L. (1998). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. Journal of Chemical Physics. 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • Drew, E. D., & Janes, R. W. (2020). Identification of a druggable binding pocket in the spike protein reveals a key site for existing drugs potentially capable of combating Covid-19 infectivity. BMC Molecular and Cell Biology, 21(1), 49. https://doi.org/10.1186/s12860-020-00294-x
  • Dunne, M. (2007). Antiretroviral drug development: The challenge of cost and access. AIDS, 21(Suppl 4), S73–S79. https://doi.org/10.1097/01.aids.0000279709.47298.8a
  • Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2.0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
  • Engelman, A., & Cherepanov, P. (2012). The structural biology of HIV-1: Mechanistic and therapeutic insights. Nature Reviews. Microbiology, 10(4), 279–290. https://doi.org/10.1038/nrmicro2747
  • Gatell, J. M. (2011). Antiretroviral therapy for HIV: Do subtypes matter? Clinical Infectious Diseases, 53(11), 1153–1155. https://doi.org/10.1093/cid/cir686
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Geretti, A. M., Harrison, L., Green, H., Sabin, C., Hill, T., Fearnhill, E., Pillay, D., Dunn, D., & On behalf of the UK Collaborative Group on HIV Drug Resistance and the UK Collaborative HIV Cohort Study. (2009). Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy. Clinical Infectious Diseases, 48(9), 1296–1305. https://doi.org/10.1086/598502
  • German Advisory Committee Blood (Arbeitskreis Blut), Subgroup ‘Assessment of Pathogens Transmissible by Blood’. (2016). Human immunodeficiency virus (HIV). Transfusion Medicine and Hemotherapy, 43(3), 203–222. https://doi.org/10.1159/000445852
  • Golmohammadi, R., Baesi, K., Moradi, A., Farrokhi, M., McFarland, W., & Parsamajd, S. (2017). The first characterization of HIV-1 subtypes and drug resistance mutations among antiretrovirally treated patients in Kermanshah, Iran. Intervirology, 60(1–2), 33–37. https://doi.org/10.1159/000478701
  • Golo, V. L., & Shaĭtan, K. V. (2002). Dynamic attractor for the Berendsen thermostat an the slow dynamics of biomacromolecules. Biofizika, 47(4), 611–617.
  • González, M. E. (2017). The HIV-1 Vpr protein: A multifaceted target for therapeutic intervention. International Journal of Molecular Sciences, 18(1), 126. https://doi.org/10.3390/ijms18010126
  • Guenzel, C. A., Hérate, C., & Benichou, S. (2014). HIV-1 Vpr—A still “enigmatic multitasker”. Frontiers in Microbiology, 5, 127. https://doi.org/10.3389/fmicb.2014.00127
  • Guilloux, V. L., Schmidtke, P., & Tuffery, P. (2009). Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics, 10, 168. https://doi.org/10.1186/1471-2105-10-168
  • Hagiwara, K., Ishii, H., Murakami, T., Takeshima, S.-n., Chutiwitoonchai, N., Kodama, E. N., Kawaji, K., Kondoh, Y., Honda, K., Osada, H., Tsunetsugu-Yokota, Y., Suzuki, M., & Aida, Y. (2015). Synthesis of a Vpr-binding derivative for use as a novel HIV-1 inhibitor. PLoS One, 10(12), e0145573. https://doi.org/10.1371/journal.pone.0145573
  • Izadi, S., Anandakrishnan, R., & Onufriev, A. V. (2014). Building water models: A different approach. The Journal of Physical Chemistry Letters, 5(21), 3863–3871. https://doi.org/10.1021/jz501780a
  • Kamata, M., Wu, R. P., An, D. S., Saxe, J. P., Damoiseaux, R., Phelps, M. E., Huang, J., & Chen, I. S. (2006). Cell-based chemical genetic screen identifies damnacanthal as an inhibitor of HIV-1 Vpr induced cell death. Biochemical and Biophysical Research Communications, 348(3), 1101–1106. https://doi.org/10.1016/j.bbrc.2006.07.158
  • Kantor, R., & Katzenstein, D. (2004). Drug resistance in non-subtype B HIV-1. Journal of Clinical Virology, 29(3), 152–159. https://doi.org/10.1016/S1386-6532(03)00115-X
  • Kantor, R., Katzenstein, D. A., Efron, B., Carvalho, A. P., Wynhoven, B., Cane, P., Clarke, J., Sirivichayakul, S., Soares, M. A., Snoeck, J., Pillay, C., Rudich, H., Rodrigues, R., Holguin, A., Ariyoshi, K., Bouzas, M. B., Cahn, P., Sugiura, W., Soriano, V., … Shafer, R. W. (2005). Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: Results of a global collaboration. PLoS Medicine, 2(4), e112. https://doi.org/10.1371/journal.pmed.0020112
  • Kogan, M., & Rappaport, J. (2011). HIV-1 accessory protein Vpr: Relevance in the pathogenesis of HIV and potential for therapeutic intervention. Retrovirology, 8, 25. https://doi.org/10.1186/1742-4690-8-25
  • Kozakov, D., Grove, L. E., Hall, D. R., Bohnuud, T., Mottarella, S. E., Luo, L., Xia, B., Beglov, D., & Vajda, S. (2015). The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nature Protocols, 10(5), 733–755. https://doi.org/10.1038/nprot.2015.043
  • Kumari, R., Kumar, R., Lynn, A., & Open Source Drug Discovery Consortium. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Lau, K. A., & Wong, J. J. (2013). Current trends of HIV recombination worldwide. Infectious Disease Reports, 5(Suppl 1), e4. https://doi.org/10.4081/idr.2013.s1.e4
  • Li, G., & Clercq, E. D. (2021). Chapter 1: Overview of antiviral drug discovery and development: Viral versus host targets. In Cesar Munoz-Fontela and Rafael Delgado (Eds.), Antiviral discovery for highly pathogenic emerging viruses (pp. 1–27). The Royal Society of Chemistry. https://doi.org/10.1039/9781788016858-00001
  • Lindahl, E., Abraham, M. J., Hess, B., & van der Spoel, D. (2021a). GROMACS 2020.5 Manual (2020.5). Zenodo. https://doi.org/10.5281/zenodo.4420784
  • Lindahl, E., Abraham, M. J., Hess, B., & van der Spoel, D. (2021b). GROMACS 2020.5 Source code (2020.5). Zenodo. https://doi.org/10.5281/zenodo.4420785
  • Lu, X., Zhao, H., Zhang, Y., Wang, W., Zhao, C., Li, Y., Ma, L., Cui, Z., & Chen, S. (2017). HIV-1 drug-resistant mutations and related risk factors among HIV-1-positive individuals experiencing treatment failure in Hebei Province, China. AIDS Research and Therapy, 14(1), 4. https://doi.org/10.1186/s12981-017-0133-3
  • Majumder, S., & Giri, K. (2021). An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: Molecular dynamics simulation, principal component analysis and binding free energy calculation study. Journal of Biomolecular Structure and Dynamics, 40(21), 10918–10930. https://doi https://doi.org/10.1080/07391102.2021.1954553
  • Mazzuti, L., Melengu, T., Falasca, F., Calabretto, M., Cella, E., Ciccozzi, M., Mezzaroma, I., Iaiani, G., Spaziante, M., d’Ettorre, G., Fimiani, C., Vullo, V., Antonelli, G., & Turriziani, O. (2020). Transmitted drug resistance mutations and trends of HIV-1 subtypes in treatment-naïve patients: A single-centre experience. Journal of Global Antimicrobial Resistance, 20, 298–303.
  • Miller, R. H., & Sarver, N. (1995). HIV accessory proteins: Emerging therapeutic targets. Molecular Medicine, 1(5), 479–485. https://doi.org/10.1007/BF03401585
  • Miyatake, H., Sanjoh, A., Murakami, T., Murakami, H., Matsuda, G., Hagiwara, K., Yokoyama, M., Sato, H., Miyamoto, Y., Dohmae, N., & Aida, Y. (2016). Molecular mechanism of HIV-1 Vpr for binding to importin-α. Journal of Molecular Biology, 428(13), 2744–2757. https://doi.org/10.1016/j.jmb.2016.05.003
  • Morellet, N., Bouaziz, S., Petitjean, P., & Roques, B. P. (2003). NMR structure of the HIV-1 regulatory protein VPR. Journal of Molecular Biology, 327(1), 215–227. https://doi.org/10.1016/s0022-2836(03)00060-3
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Neubert, J., Michalsky, N., Laws, H. J., Borkhardt, A., Jensen, B., & Lübke, N. (2016). HIV-1 subtype diversity and prevalence of primary drug resistance in a single-center pediatric cohort in Germany. Intervirology, 59(5–6), 301–306. https: https://doi.org/10.1159/000477811
  • Rawson, J. M., Landman, S. R., Reilly, C. S., & Mansky, L. M. (2015). HIV-1 and HIV-2 exhibit similar mutation frequencies and spectra in the absence of G-to-A hypermutation. Retrovirology, 12, 60. https: https://doi.org/10.1186/s12977-015-0180-6
  • Scherer, M., Trendelkamp-Schroer, B., Paul, F., Pérez-Hernández, G., Hoffmann, M., Plattner, N., Wehmeyer, C., Prinz, J. H., & Noé, F. (2015). PyEMMA 2: A software package for estimation, validation, and analysis of Markov models. Journal of Chemical Theory and Computation, 11(11), 5525–5542. https://doi.org/10.1021/acs.jctc.5b00743.
  • Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
  • Shaw, G. M., & Hunter, E. (2012). HIV transmission. Cold Spring Harbor Perspectives in Medicine, 2(11), a006965. https://doi.org/10.1101/cshperspect.a006965
  • Somasundaran, M., Sharkey, M., Brichacek, B., Luzuriaga, K., Emerman, M., Sullivan, J. L., & Stevenson, M. (2002). Evidence for a cytopathogenicity determinant in HIV-1 Vpr. Proceedings of the National Academy of Sciences of the United States of America, 99(14), 9503–9508. https://doi.org/10.1073/pnas.142313699
  • Strebel, K. (2013). HIV accessory proteins versus host restriction factors. Current Opinion in Virology, 3(6), 692–699. https://doi.org/10.1016/j.coviro.2013.08.004
  • The UniProt Consortium. (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100
  • Taylor, B. S., Sobieszczyk, M. E., McCutchan, F. E., & Hammer, S. M. (2008). The challenge of HIV-1 subtype diversity. The New England Journal of Medicine, 358(15), 1590–1602. https://doi.org/10.1056/NEJMra0706737
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461.
  • Tuble, C., Anwar, J., & Gale, J. D. (2004). An approach to developing a force field for molecular simulation of martensitic phase transitions between phases with subtle differences in energy and structure. Journal of the American Chemical Society, 126(1), 396–405. https://doi.org/10.1021/ja0356131
  • Venner, C. M., Nankya, I., Kyeyune, F., Demers, K., Kwok, C., Chen, P. L., Rwambuya, S., Munjoma, M., Chipato, T., Byamugisha, J., Van Der Pol, B., Mugyenyi, P., Salata, R. A., Morrison, C. S., & Arts, E. J. (2016). Infecting HIV-1 subtype predicts disease progression in women of Sub-Saharan Africa. EBioMedicine, 13, 305–314. https://doi.org/10.1016/j.ebiom.2016.10.014
  • Wang, C., Nguyen, P. H., Pham, K., Huynh, D., Le, T. B., Wang, H., Ren, P., & Luo, R. (2016). Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis. Journal of Computational Chemistry, 37(27), 2436–2446. https://doi.org/10.1002/jcc.24467
  • Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427
  • Wensing, A. M., Calvez, V., Ceccherini-Silberstein, F., Charpentier, C., Günthard, H. F., Paredes, R., Shafer, R. W., & Richman, D. D. (2019). 2019 update of the drug resistance mutations in HIV-1. Topics in Antiviral Medicine, 27(3), 111–121.
  • Win, N. N., Ngwe, H., Abe, I., & Morita, H. (2017). Naturally occurring Vpr inhibitors from medicinal plants of Myanmar. Journal of Natural Medicines, 71(4), 579–589. https://doi.org/10.1007/s11418-017-1104-7
  • Woo, S., Win, N. N., Wyine, M., Ngwe, H., Ito, T., Abe, I., & Morita, H. (2019). Viral protein R inhibitors from Swertia chirata of Myanmar. Journal of Bioscience and Bioengineering, 128(4), 445–449. https://doi.org/10.1016/j.jbiosc.2019.04.006
  • Wu, Y., Zhou, X., Barnes, C. O., DeLucia, M., Cohen, A. E., Gronenborn, A. M., Ahn, J., & Calero, G. (2016). The DDB1–DCAF1–Vpr–UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction. Nature Structural & Molecular Biology, 23(10), 933–940. https://doi.org/10.1038/nsmb.3284
  • Xiong, G., Wu, Z., Yi, J., Fu, L., Yang, Z., Hsieh, C., Yin, M., Zeng, X., Wu, C., Lu, A., Chen, X., Hou, T., & Cao, D. (2021). ADMETlab 2.0: An integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Research, 49(W1), W5–W14. https://doi.org/10.1093/nar/gkab255
  • Yang, Z., Wei, S., Liu, J., Piao, J., Xu, L., Sun, Y., Deng, X., Yang, X., Liu, C., Ma, S., Zhao, Q., & Huo, Y. (2020). Characterization of HIV-1 subtypes and drug resistance mutations in Henan Province, China (2017–2019). Archives of Virology, 165(6), 1453–1461. https://doi.org/10.1007/s00705-020-04606-6
  • Zhang, F., & Bieniasz, P. D. (2020). HIV-1 Vpr induces cell cycle arrest and enhances viral gene expression by depleting CCDC137. eLife, 9, e55806. https://doi.org/10.7554/eLife.55806
  • Zhao, R. Y., & Bukrinsky, M. I. (2014). HIV-1 accessory proteins: VpR. Methods in Molecular Biology (Clifton, N.J.), 1087, 125–134. https://doi.org/10.1007/978-1-62703-670-2_11
  • Zhao, R. Y., Li, G., & Bukrinsky, M. I. (2011). Vpr-host interactions during HIV-1 viral life cycle. Journal of Neuroimmune Pharmacology, 6(2), 216–229. https://doi.org/10.1007/s11481-011-9261-z
  • Zheng, X., Gan, L., Wang, E., & Wang, J. (2013). Pocket-based drug design: Exploring pocket space. The AAPS Journal, 15(1), 228–241. https://doi.org/10.1208/s12248-012-9426-6
  • Zotova, A., Atemasova, A., Pichugin, A., Filatov, A., & Mazurov, D. (2019). Distinct requirements for HIV-1 accessory proteins during cell coculture and cell-free infection. Viruses, 11(5), 390. https://doi.org/10.3390/v11050390

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