In Silico Studies against Viral Sexually Transmitted Diseases

Author(s): Alex F.M. Monteiro, Jessika de Oliveira Viana, Engene Muratov, Marcus T. Scotti, Luciana Scotti*.

Journal Name: Current Protein & Peptide Science

Volume 20 , Issue 12 , 2019

Become EABM
Become Reviewer

Graphical Abstract:


Sexually Transmitted Diseases (STDs) refer to a variety of clinical syndromes and infections caused by pathogens that can be acquired and transmitted through sexual activity. Among STDs widely reported in the literature, viral sexual diseases have been increasing in a number of cases globally. This emphasizes the need for prevention and treatment. Among the methods widely used in drug planning are Computer-Aided Drug Design (CADD) studies and molecular docking which have the objective of investigating molecular interactions between two molecules to better understand the three -dimensional structural characteristics of the compounds. This review will discuss molecular docking studies applied to viral STDs, such as Ebola virus, Herpes virus and HIV, and reveal promising new drug candidates with high levels of specificity to their respective targets.

Keywords: Sexually transmitted diseases, antiviral drugs, in silico, molecular docking, HIV, infection.

Singh, S.K. Diagnostics to Pathogenomics of Sexually Trans-mitted Infections, 1st ed; Wiley Blackwell, 2018.
Satterwhite, C.L.; Torrone, E.; Meites, E.; Dunne, E.F.; Mahajan, R.; Ocfemia, M.C.B.; Su, J.; Xu, F.; Weinstock, H. Sexually transmitted infections among US women and men: prevalence and incidence estimates, 2008. Sex. Transm. Dis., 2013, 40(3), 187-193.
World Health Organization: Sexually transmitted infections 2016 (Accessed Set 15, . 2018.
Friedman, A.L.; Kachur, R.E.; Noar, S.M.; McFarlane, M. Health communication and social marketing campaigns for sexually transmitted disease prevention and control: What is the evidence of their effectiveness? Sex. Transm. Dis., 2016, 43(2)(Suppl. 1), S83-S101.
Center of Disease Control: Sexually transmitted diseases treatment guidelines, 2010. (Accessed Set 15, . 2018.
Ferreira, L.G.; Dos Santos, R.N.; Oliva, G.; Andricopulo, A.D. Molecular docking and structure-based drug design strategies. Molecules, 2015, 20(7), 13384-13421.
Chen, Y.; Shoichet, B.K. Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat. Chem. Biol., 2009, 5(5), 358-364.
Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov., 2004, 3(11), 935-949.
Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem., 2003, 46(12), 2287-2303.
Warren, G.L.; Andrews, C.W.; Capelli, A.M.; Clarke, B.; LaLonde, J.; Lambert, M.H.; Lindvall, M.; Nevins, N.; Semus, S.F.; Senger, S.; Tedesco, G.; Wall, I.D.; Woolven, J.M.; Peishoff, C.E.; Head, M.S. A critical assessment of docking programs and scoring functions. J. Med. Chem., 2006, 49(20), 5912-5931.
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 1996, 261(3), 470-489.
Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 1997, 267(3), 727-748.
Österberg, F.; Morris, G.M.; Sanner, M.F.; Olson, A.J.; Goodsell, D.S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins, 2002, 46(1), 34-40.
Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem., 2009, 30(16), 2785-2791.
Venkatachalam, C.M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model., 2003, 21(4), 289-307.
Jain, A.N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem., 2003, 46(4), 499-511.
McGann, M.R.; Almond, H.R.; Nicholls, A.; Grant, J.A.; Brown, F.K. Gaussian docking functions. Biopolymers, 2003, 68(1), 76-90.
Friesner, R.A.; Banks, J.L.; Murphy, R.B.; Halgren, T.A.; Klicic, J.J.; Mainz, D.T.; Repasky, M.P.; Knoll, E.H.; Shelley, M.; Perry, J.K.; Shaw, D.E.; Francis, P.; Shenkin, P.S. 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.
Trott, O.; Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2010, 31(2), 455-461.
Corbeil, C.R.; Williams, C.I.; Labute, P. Variability in docking success rates due to dataset preparation. J. Comput. Aided Mol. Des., 2012, 26(6), 775-786.
Zhao, H.; Caflisch, A. Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorg. Med. Chem. Lett., 2013, 23(20), 5721-5726.
Allen, W.J.; Balius, T.E.; Mukherjee, S.; Brozell, S.R.; Moustakas, D.T.; Lang, P.T.; Case, D.A.; Kuntz, I.D.; Rizzo, R.C. DOCK 6: Impact of new features and current docking performance. J. Comput. Chem., 2015, 36(15), 1132-1156.
Wang, Z.; Sun, H.; Yao, X.; Li, D.; Xu, L.; Li, Y.; Tian, S.; Hou, T. Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. Phys. Chem. Chem. Phys., 2016, 18(18), 12964-12975.
Leroy, E.M.; Kumulungui, B.; Pourrut, X.; Rouquet, P.; Hassanin, A.; Yaba, P.; Délicat, A.; Paweska, J.T.; Gonzalez, J.P.; Swanepoel, R. Fruit bats as reservoirs of Ebola virus. Nature, 2005, 438(7068), 575-576.
Briand, S.; Bertherat, E.; Cox, P.; Formenty, P.; Kieny, M.P.; Myhre, J.K.; Roth, C.; Shindo, N.; Dye, C. The International Ebola Emergency. N. Engl. J. Med., 2014, (Accessed May 23, 2004)
World Health Organization: Ebola situation report, 2016. (Accessed Oct 9, 2018).
Bwaka, M.A.; Bonnet, M.J.; Calain, P.; Colebunders, R.; De Roo, A.; Guimard, Y.; Katwiki, K.R.; Kibadi, K.; Kipasa, M.A.; Kuvula, K.J.; Mapanda, B.B.; Massamba, M.; Mupapa, K.D.; Muyembe-Tamfum, J.J.; Ndaberey, E.; Peters, C.J.; Rollin, P.E.; Van den Enden, E.; Van den Enden, E. Ebola hemorrhagic fever in Kikwit, Democratic Republic of the Congo: clinical observations in 103 patients. J. Infect. Dis., 1999, 179(Suppl. 1), S1-S7.
Centers for Disease Control and Prevention: Transmission Of Ebola (Ebola Virus Disease), 2014. transmission/index.html (Accessed Sep 18, 2018)
Hewlett, B.S.; Amola, R.P. Cultural contexts of Ebola in northern Uganda. Emerg. Infect. Dis., 2003, 9(10), 1242-1248.
Rodriguez, L.L.; De Roo, A.; Guimard, Y.; Trappier, S.G.; Sanchez, A. Bressler, Williams, D.A.J.; Rowe, A.K.; Bertolli, J.; Khan, A.S.; Ksiazek, T.G.; Peters, C.J.; Nichol, S.T. Persis-tence and genetic stability of Ebola virus during the outbreak in Kikwit, Democratic Republic of the Congo, 1995. J. Infect. Dis., 1999, 179, 170-176.
Rogstad, K.E.; Tunbridge, A. Ebola virus as a sexually transmitted infection. Curr. Opin. Infect. Dis., 2015, 28(1), 83-85.
Deen, G.F.; Broutet, N.; Xu, W.; Knust, B.; Sesay, F.R.; McDonald, S.L.; Ervin, E.; Marrinan, J.E.; Gaillard, P.; Habib, N.; Liu, H.; Liu, W.; Thorson, A.E.; Yamba, F.; Mas-saquoi, T.A.; James, F.; Ariyarajah, A.; Ross, C.; Bernstein, K.; Coursier, A.; Klena, J.; Carino, M.; Wurie, A.H.; Zhang, Y.; Dumbuya, M.S.; Abad, N.; Idriss, B.; Wi, T.; Bennett, S.D.; Davies, T.; Ebrahim, F.K.; Meites, E.; Naidoo, D.; Smith, S.J.; Ongpin, P.; Malik, T.; Banerjee, A.; Erickson, B.R.; Liu, Y.; Liu, Y. Xu, K.; Brault, A.; Durski, K.N.; Winter, J.; Sealy, T.; Nichol S.T.; Lamunu, M.; Bangura, J.; Landoulsi, S.; Jambai, A.; Morgan, A.; Wu, G.; Liang, M.; Su, Q.; Lan, Y.; Hao, Y.; Formenty, P.; Ströher, U.; Sahr, F. Ebola RNA persistence in semen of Ebola virus disease survivors. N. Engl. J. Med., 2017, 377(15), 1428-1437.
Christie, A.; Davies-Wayne, G.J.; Cordier-Lassalle, T.; Blackley, D.J.; Laney, A.S.; Williams, D.E.; Shinde, S.A.; Badio, M.; Lo, T.; Mate, S.E.; Ladner, J.T.; Wiley, M.R.; Kugelman, J.R.; Palacios, G.; Holbrook, M.R.; Janosko, K.B.; de Wit, E.; van Doremalen, N.; Munster, V.J.; Pettitt, J.; Schoepp, R.J.; Verhenne, L.; Evlampidou, I.; Kollie, K.K.; Sieh, S.B.; Gasasira, A.; Bolay, F.; Kateh, F.N.; Nyenswah, T.G.; De Cock, K.M. Possible sexual transmission of Ebola virus - Liberia, 2015. MMWR Morb. Mortal. Wkly. Rep., 2015, 64(17), 479-481.
World Health Organization. Interim advice on the sexual transmission of the Ebola virus disease, 2016. Set 21, . 2018.
Mate, S.E.; Kugelman, J.R.; Nyenswah, T.G.; Ladner, J.T.; Wiley, M.R.; Cordier-Lassalle, T.; Christie, A.; Schroth, G.P.; Gross, S.M.; Davies-Wayne, G.J.; Shinde, S.A.; Murugan, R.; Sieh, S.B.; Badio, M.; Fakoli, L.; Taweh, F.; de Wit, E.; van Doremalen, N.; Munster, V.J.; Pettitt, J.; Prieto, K.; Humrighouse, B.W.; Ströher, U.; DiClaro, J.W.; Hensley, L.E.; Schoepp, R.J.; Safronetz, D.; Fair, J.; Kuhn, J.H.; Blackley, D.J.; Laney, A.S.; Williams, D.E.; Lo, T.; Gasasira, A.; Nichol, S.T.; Formenty, P.; Kateh, F.N.; De Cock, K.M.; Bolay, F.; Sanchez-Lockhart, M.; Palacios, G. Molecular evidence of sexual transmission of Ebola virus. N. Engl. J. Med., 2015, 373(25), 2448-2454.
Judson, S.; Prescott, J.; Munster, V. Understanding ebola virus transmission. Viruses, 2015, 7(2), 511-521.
Gire, S.K.; Goba, A.; Andersen, K.G.; Sealfon, R.S.G.; Park, D.J.; Kanneh, L. Jalloh, s.; Momoh, M.; Fullah, M.; Dudas, G.; Wohl, S.; Moses, L.M.; Yozwiak, N.L.; Winnicki, S.; Matranga, C.B.; Malboeyf, C.M.; Qu, J.; Glandden, A.D.; Schaffner, S.F.; Yang, X.; Jiang, P.P.; Nekoui, M.; Colubri, A.; Coomber, M.R.; Fonnie, M.; Moigboi, A.; Gbakie, M.; Kama-ra, F.K.; Tucker, V.; Konuwa, E.; Saffa, S.; Sellu, J.; Jalloh, A.A.; Jovoma, A.; Koninga, J.; Mustapha, I.; Kargbo, K.; Fo-day, M.; Yillah, M.; Kanneh, F.; Robert, W.; Massally, J.L.B.; Chapman, S.B.; Bochicchio, J.; Murphy, C.; Nusbaum, C.; Young, S.; Birren, B.W.; Grant, D.S.; Scheiffelin, J.S.; Lander, E.S.; Happi, C.; Gevao, S.M.; Gnirke, A.; Rambaut, A.; Garry, R.F.; Khan, S.H.; Sabeti, P.C. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 out-break. Science, 2014, 345, 1369-1372.
Hulo, C.; de Castro, E.; Masson, P.; Bougueleret, L.; Bairoch, A.; Xenarios, I.; Le Mercier, P. ViralZone: A knowledge resource to understand virus diversity. Nucleic Acids Res., 2011, 39(Database issue), D576-D582.
Nanbo, A.; Watanabe, S.; Halfmann, P.; Kawaoka, Y. The spatio-temporal distribution dynamics of Ebola virus proteins and RNA in infected cells. Sci. Rep., 2013, 3, 1206.
Raj, U.; Varadwaj, P.K. Flavonoids as multi-target inhibitors for proteins associated with Ebola virus: In silico discovery using virtual screening and molecular docking studies. Interdiscip. Sci., 2016, 8(2), 132-141.
Chou, K.C. Impacts of bioinformatics to medicinal chemistry. Med. Chem., 2015, 11(3), 218-234.
Diehl, W.E.; Lin, A.E.; Grubaugh, N.D.; Carvalho, L.M.; Kim, K.; Kyawe, P.P.; McCauley, S.M.; Donnard, E.; Kucukural, A.; McDonel, P.; Schaffner, S.F.; Garber, M.; Rambaut, A.; Andersen, K.G.; Sabeti, P.C.; Luban, J. Ebola virus glycopro-tein with increased infectivity dominated the 2013-2016 epi-demic. Cell, 2016, 167(4), 1088-1098.e6.
Weissenhorn, W.; Carfí, A.; Lee, K.H.; Skehel, J.J.; Wiley, D.C. Crystal structure of the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain. Mol. Cell, 1998, 2(5), 605-616.
Takada, A.; Robison, C.; Goto, H.; Sanchez, A.; Murti, K.G.; Whitt, M.A.; Kawaoka, Y. A system for functional analysis of Ebola virus glycoprotein. Proc. Natl. Acad. Sci. USA, 1997, 94(26), 14764-14769.
Earp, L.J.; Delos, S.E.; Park, H.E.; White, J.M. The many mechanisms of viral membrane fusion proteins.Mem-brane trafficking in viral replication; Marsh, M., Ed.; Springer: Berlin, Heidelberg, 2004, Vol. 285, pp. 25-66.
Sakurai, Y.; Kolokoltsov, A.A.; Chen, C.C.; Tidwell, M.W.; Bauta, W.E.; Klugbauer, N.; Grimm, C.; Wahl-Schott, C.; Biel, M.; Davey, R.A. Ebola virus. Two-pore channels control Ebola virus host cell entry and are drug targets for disease treatment. Science, 2015, 347(6225), 995-998.
Lee, J.E.; Fusco, M.L.; Hessell, A.J.; Oswald, W.B.; Burton, D.R.; Saphire, E.O. Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor. Nature, 2008, 454(7201), 177-182.
Ahmad, N.; Farman, A.; Badshah, S.L.; Ur Rahman, A.; Ur Rashid, H.; Khan, K. Molecular modeling, simulation and docking study of ebola virus glycoprotein. J. Mol. Graph. Model., 2017, 72, 266-271.
Shinyguruce, A.; Sathya, D.; Keerthiga, K.; Pavithra, P.; Vin-itha, M.; Vaidheeswari, R.; Eswara, P.B. In Silico Antiviral Drug Screening and Molecular Docking Studies Against Ebola Virus Glycoprotein. J. Appl. Sci. Comput., 2018, 5(9), 211-216.
Basler, C.F.; Mikulasova, A.; Martinez-Sobrido, L.; Paragas, J.; Mühlberger, E.; Bray, M.; Klenk, H.D.; Palese, P.; García-Sastre, A. The Ebola virus VP35 protein inhibits activation of interferon regulatory factor 3. J. Virol., 2003, 77(14), 7945-7956.
Reynard, O.; Nemirov, K.; Page, A.; Mateo, M.; Raoul, H.; Weissenhorn, W.; Volchkov, V.E. Conserved proline-rich re-gion of Ebola virus matrix protein VP40 is essential for plas-ma membrane targeting and virus-like particle release. J. Infect. Dis., 2011, 204, 884-891.
Ekins, S.; Freundlich, J.S.; Coffee, M. A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus. F1000 Res., 2014, 3, 277.
Glanzer, J.G.; Byrne, B.M.; McCoy, A.M.; James, B.J.; Frank, J.D.; Oakley, G.G. In silico and in vitro methods to identify ebola virus VP35-dsRNA inhibitors. Bioorg. Med. Chem., 2016, 24(21), 5388-5392.
Ren, J.X.; Zhang, R.T.; Zhang, H.; Cao, X.S.; Liu, L.K.; Xie, Y. Identification of novel VP35 inhibitors: Virtual screening driven new scaffolds. Biomed. Pharmacother., 2016, 84, 199-207.
Sulaiman, K.O.; Kolapo, T.U.; Onawole, A.T.; Islam, A.; Adegoke, R.O.; Badmus, S.O. Molecular dynamics and com-bined docking studies for the identification of Zaire Ebola Vi-rus inhibitors. J. Biomol. Struct. Dyn., 2018, 2018, 1-31.
Hartlieb, B.; Muziol, T.; Weissenhorn, W.; Becker, S. Crystal structure of the C-terminal domain of Ebola virus VP30 reveals a role in transcription and nucleocapsid association. Proc. Natl. Acad. Sci. USA, 2007, 104(2), 624-629.
John, S.P.; Wang, T.; Steffen, S.; Longhi, S.; Schmaljohn, C.S.; Jonsson, C.B. Ebola virus VP30 is an RNA binding protein. J. Virol., 2007, 81(17), 8967-8976.
Biedenkopf, N.; Hartlieb, B.; Hoenen, T.; Becker, S. Phosphorylation of Ebola virus VP30 influences the composition of the viral nucleocapsid complex: impact on viral transcription and replication. J. Biol. Chem., 2013, 288(16), 11165-11174.
Martínez, M.J.; Biedenkopf, N.; Volchkova, V.; Hartlieb, B.; Alazard-Dany, N.; Reynard, O.; Becker, S.; Volchkov, V. Role of Ebola virus VP30 in transcription reinitiation. J. Virol., 2008, 82(24), 12569-12573.
Shah, R.; Panda, P.K.; Patel, P.; Panchal, H. Pharmacophore based virtual screening and molecular docking studies of inherited compounds against ebola virus receptor proteins. World J. Pharm. Pharm. Sci., 2015, 4(5), 1268-1282.
Setlur, A.S.; Naik, S.Y.; Skariyachan, S. Herbal lead as ideal bioactive compounds against probable drug targets of ebola virus in comparison with known chemical analogue: A computational drug discovery perspective. Interdiscip. Sci., 2017, 9(2), 254-277.
Vecchio, K.D.; Shwarz, A.; Saphire, E.O.; Stahelin, R. The ebola virus matrix protein vp40 interacts selectively with plasma membrane lipids to promote viral egress. FASEB J., 2017, 31, 945-951.
Gomis-Rüth, F.X.; Dessen, A.; Timmins, J.; Bracher, A.; Kolesnikowa, L.; Becker, S.; Klenk, H.D.; Weissenhorn, W. The matrix protein VP40 from Ebola virus octamerizes into pore-like structures with specific RNA binding properties. Structure, 2003, 11(4), 423-433.
Scianimanico, S.; Schoehn, G.; Timmins, J.; Ruigrok, R.H.; Klenk, H.D.; Weissenhorn, W. Membrane association induces a conformational change in the Ebola virus matrix protein. EMBO J., 2000, 19(24), 6732-6741.
Mirza, M.U.; Ikram, N. Integrated computational approach for virtual hit identification against ebola viral proteins VP35 and VP40. Int. J. Mol. Sci., 2016, 17(11), 1748.
M., Alam El-Din H.; A Loutfy, S.; Fathy, N.; H Elberry, M.; M Mayla, A.; Kassem, S.; Naqvi, A. Molecular docking based screening of compounds against VP40 from Ebola virus. Bioinformation, 2016, 12(3), 192-196.
Abazari, D.; Moghtadaei, M.; Behvarmanesh, A.; Ghannadi, B.; Aghaei, M.; Behruznia, M.; Rigi, G. Molecular docking based screening of predicted potential inhibitors for VP40 from Ebola virus. Bioinformation, 2015, 11(5), 243-247.
Karthick, V.; Nagasundaram, N.; Doss, C.G.P.; Chakraborty, C.; Siva, R.; Lu, A.; Zhang, G.; Zhu, H. Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus. Infect. Dis. Poverty, 2016, 5, 12.
Patel, J.; Chipkar, Y.; Momin, A. Comparitive study of vari-ous ebola virus Vp40 strains with modelling and docking studies to treat ebola virus infection. Intl. J. Pharm. Drug Res., 2013, 2(1), 1-10.
Skariyachan, S.; Acharya, A.B.; Subramaniyan, S.; Babu, S.; Kulkarni, S.; Narayanappa, R. Secondary metabolites extracted from marine sponge associated Comamonas testosteroni and Citrobacter freundii as potential antimicrobials against MDR pathogens and hypothetical leads for VP40 matrix protein of Ebola virus: an in vitro and in silico investigation. J. Biomol. Struct. Dyn., 2016, 34(9), 1865-1883.
Tamilvanan, T.; Hopper, W. High-throughput virtual screening and docking studies of matrix protein vp40 of ebola virus. Bioinformation, 2013, 9(6), 286-292.
Reid, S.P.; Leung, L.W.; Hartman, A.L.; Martinez, O.; Shaw, M.L.; Carbonnelle, C.; Volchkov, V.E.; Nichol, S.T.; Basler, C.F. Ebola virus VP24 binds karyopherin alpha1 and blocks STAT1 nuclear accumulation. J. Virol., 2006, 80(11), 5156-5167.
Watanabe, S.; Noda, T.; Halfmann, P.; Jasenosky, L.; Kawaoka, Y. Ebola virus (EBOV) VP24 inhibits transcription and replication of the EBOV genome. J. Infect. Dis., 2007, 196(Suppl. 2), S284-S290.
Hoenen, T.; Jung, S.; Herwig, A.; Groseth, A.; Becker, S. Both matrix proteins of Ebola virus contribute to the regulation of viral genome replication and transcription. Virology, 2010, 403(1), 56-66.
Tambunan, U.S.F.; Nasution, M.A.F. Identification of novel Ebola virus (EBOV) VP24 inhibitor from Indonesian natural products through in silico drug design approach. AIP Conf. Proc., 2017, 1862(1)030091
Tambunan, U.S.F.; Siregar, S.; Toepak, E.P. Ebola viral protein 24 (Vp24) inhibitor discovery by in silico fragment-based design. Int. J. Geomech., 2018, 15(49), 59-64.
Sharmila, R.; Jaikumar, B. Molecular docking study of bioac-tive compound of andrographolide against ebola virus. Int. J. Pharm. Sci. Res., 2016, 7(5), 250-253.
Sharma, D.; Pathak, M.; Sharma, R.; Tyagi, P.; Chawla, R.; Basu, M.; Ojha, H. Homology modeling and docking studies of VP24 protein of Ebola virus with an antiviral drug and its derivatives. Chem. Biol. Lett., 2017, 4(1), 27-32.
Sun, Y.; Guo, Y.; Lou, Z. A versatile building block: the structures and functions of negative-sense single-stranded RNA virus nucleocapsid proteins. Protein Cell, 2012, 3(12), 893-902.
Zhou, H.; Sun, Y.; Guo, Y.; Lou, Z. Structural perspective on the formation of ribonucleoprotein complex in negative-sense single-stranded RNA viruses. Trends Microbiol., 2013, 21(9), 475-484.
Baikerikar, S. Curcumin and natural derivatives inhibit ebola viral proteins: An in silico approach. Pharmacol. Res., 2017, 9(Suppl. 1), S15-S22.
Slots, J. Periodontal herpesviruses: prevalence, pathogenicity, systemic risk. Periodontol. 2000, 2015, 69(1), 28-45.
Whitley, R.J. Herpesviruses.University of Texas Medical Branch at Gal-veston; Microbiology, M.; Sam-uel, B., Eds.; Galveston, Texas, , 1996.
Robbins, G.; Lammert, S.; Rompalo, A.; Riley, L.; Daskalakis, D.; Morrow, R.; Lee, H.; Shui, A.; Gaydos, C.; Detrick, B.; Rosenber, E.; Crochiere, D.; Cunningham, K.; Bradley, H.; Markowitz, L.; Xu, F.; Felsenstein, D. Serologic assays for the diagnosis of herpes virus 1 (HSV-1) herpes virus 2 (HSV-2): test characteristics of FDA approved type-specific assays in an ethnically, racially, and economi-cally diverse patient population. In: Open Forum Infectious Diseases; Oxford University Press, 2015; p. 2.
Rohner, E.; Wyss, N.; Heg, Z.; Faralli, Z.; Mbulaiteye, S.M.; Novak, U.; Zwahlen, M.; Egger, M.; Bohlius, J. HIV and human herpesvirus 8 co-infection across the globe: Systematic review and meta-analysis. Int. J. Cancer, 2016, 138(1), 45-54.
World Health Organization: Herpes simplex virus, 2017. (Accessed Oct 2, 2018)
Burn, C.; Ramsey, N.; Garforth, S.J.; Almo, S.; Jacobs, W.R., Jr; Herold, B.C. A herpes simplex virus (HSV)-2 single-cycle candidate vaccine deleted in glycoprotein D protects male mice from lethal skin challenge with clinical isolates of HSV-1 and HSV-2. J. Infect. Dis., 2018, 217(5), 754-758.
Sripiboon, S.; Angkawanish, T.; Boonprasert, K.; Sombutputorn, P.; Langkaphin, W.; Ditcham, W.; Warren, K. Successful treatment of a clinical elephant endotheliotropic herpesvirus infection: The dynamics of viral load, genotype analysis, and treatment with acyclovir. J. Zoo Wildl. Med., 2017, 48(4), 1254-1259.
Troszok, A.; Kolek, L.; Szczygieł, J.; Wawrzeczko, J.; Borzym, E.; Reichert, M.; Kamińska, T.; Ostrowski, T.; Jurecka, P.; Adamek, M.; Rakus, K.; Irnazarow, I. Acyclovir inhibits Cyprinid herpesvirus 3 multiplication in vitro. J. Fish Dis., 2018, 41(11), 1709-1718.
Piret, J.; Boivin, G. Herpesvirus Resistance to Antiviral Drugs; Antimicrobial Drug Resistance, 2017, pp. 1185-1211.
Kolb, A.W.; Larsen, I.V.; Cuellar, J.A.; Brandt, C.R. Genomic, phylogenetic, and recombinational characterization of herpes simplex virus 2 strains. J. Virol., 2015, 89(12), 6427-6434.
Lehman, I.R.; Boehmer, P.E. Replication of herpes simplex virus DNA. J. Biol. Chem., 1999, 274(40), 28059-28062.
Matthews, J.T.; Terry, B.J.; Field, A.K. The structure and function of the HSV DNA replication proteins: Defining novel antiviral targets. Antiviral Res., 1993, 20(2), 89-114.
Hoog, S.S.; Smith, W.W.; Qiu, X.; Janson, C.A.; Hellmig, B.; McQueney, M.S.; O’Donnell, K.; O’Shannessy, D.; DiLella, A.G.; Debouck, C.; Abdel-Meguid, S.S. Active site cavity of herpesvirus proteases revealed by the crystal structure of herpes simplex virus protease/inhibitor complex. Biochemistry, 1997, 36(46), 14023-14029.
Kashyap, K.; Kakkar, R. Herpesvirus Proteases: Structure, Function, and Inhibition; Viral Proteases and Their Inhibitors, 2017, pp. 411-439.
Arunkumar, J.; Rajarajan, S. Study on antiviral activities, drug-likeness and molecular docking of bioactive compounds of Punica granatum L. to Herpes simplex virus - 2 (HSV-2). Microb. Pathog., 2018, 118, 301-309.
Chowdary, T.K.; Cairns, T.M.; Atanasiu, D.; Cohen, G.H.; Eisenberg, R.J.; Heldwein, E.E. Crystal structure of the conserved herpesvirus fusion regulator complex gH-gL. Nat. Struct. Mol. Biol., 2010, 17(7), 882-888.
Atanasiu, D.; Cairns, T.M.; Whitbeck, J.C.; Saw, W.T.; Rao, S.; Eisenberg, R.J.; Cohen, G.H. Regulation of herpes simplex virus gB-induced cell-cell fusion by mutant forms of gH/gL in the absence of gD and cellular receptors. MBio, 2013, 4(2), e00046-e13.
Connolly, C.S.A.; Jackson, J.O.; Jardetzky, T.S.; Longnecker, R. Fusing structure and function: a structural view of the her-pesvirus entry machinery. Nat. Rev. Microbiol., 2011, 9(5), 369.
Boyer, C.B.; Greenberg, L.; Chutuape, K.; Walker, B.; Monte, D.; Kirk, J.; Ellen, J.M.; Belzer, M.; Martinez, M.; Dudek, J. Adolescent medicine trials network. exchange of sex for drugs or money in adolescents and young adults: An examination of sociodemographic factors, HIV-related risk, and community context. J. Commun. Healthc., 2017, 42(1), 90-100.
Strategies, P.; Therapy, F.O.R.A.; Tecnol, D.; Cruz, O. Estratégias farmacológicas para a terapia anti-aids Emerson Poley Peçanha* e Octavio A. C. Antunes., 2002, 25(6), 1108-1116.
Morris, P.; DaSilva, Y.; Clark, E.; Hahn, W.E.; Barenholtz, E. Convolutional Neural Networks for Predicting Molecular Binding Affinity to HIV-1 Proteins. , 2018; pp. In: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB ’18); ACM, New York, NY, USA, . 220-225.
Mohammadi, A.A.; Taheri, S.; Amouzegar, A.; Ahdenov, R.; Halvagar, M.R.; Sadr, A.S. Diastereoselective synthesis and molecular docking studies of novel fused tetrahydro-pyridine derivatives as new inhibitors of HIV protease. J. Mol. Struct., 2017, 1139, 166-174.
Tong, J.; Wu, Y.; Bai, M.; Zhan, P. 3D-QSAR and molecular docking studies on HIV protease inhibitors. J. Mol. Struct., 2017, 1129, 17-22.
Zondagh, J.; Balakrishnan, V.; Achilonu, I.; Dirr, H.W.; Sayed, Y. Molecular dynamics and ligand docking of a hinge region variant of South African HIV-1 subtype C protease. J. Mol. Graph. Model., 2018, 82, 1-11.
Ahmad, R.; Sahidin, I.; Taher, M.; Low, C.; Noor, N.M.; Sillapachaiyaporn, C.; Chuchawankul, S.; Sarachana, T.; Tencomnao, T.; Iskandar, F.; Rajab, N.F.; Baharum, S.N. Polygonumins A, a newly isolated compound from the stem of Polygonum minus Huds with potential medicinal activities. Sci. Rep., 2018, 8(1), 4202.
Al-Shehri, M.M.; Al-Majed, A.R.A.; Aljohar, H.I.; El-Emam, A.A.; Pathak, S.K.; Sachan, A.K.; Prasad, O.; Sinha, L. First principle study of a potential bioactive molecule with tetrahydroisoquinoline, carbothiomide and adamantane scaffolds. J. Mol. Struct., 2017, 1143, 204-216.
Ghosh, A.K.; Osswald, H.L.; Glauninger, K.; Agniswamy, J.; Wang, Y-F.; Hayashi, H.; Aoki, M.; Weber, I.T.; Mitsuya, H. Probing lipophilic adamantyl group as the P1-ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. J. Med. Chem., 2016, 59(14), 6826-6837.
Debnath, U.; Kumar, P.; Agarwal, A.; Kesharwani, A.; Gupta, S.K.; Katti, S.B. N-hydroxy-substituted 2-aryl acetamide analogs: A novel class of HIV-1 integrase inhibitors. Chem. Biol. Drug Des., 2017, 90(4), 527-534.
Vyas, V.K.; Shah, S.; Ghate, M. Generation of new leads as HIV-1 integrase inhibitors: 3D QSAR, docking and molecular dynamics simulation. Med. Chem. Res., 2017, 26(3), 532-550.
Chander, S.; Pandey, R.K.; Penta, A.; Choudhary, B.S.; Sharma, M.; Malik, R.; Prajapati, V.K.; Murugesan, S. Molecular docking and molecular dynamics simulation based approach to explore the dual inhibitor against HIV-1 reverse transcriptase and integrase. Comb. Chem. High Throughput Screen., 2017, 20(8), 734-746.
Faridoon; Mnkandhla, D.; Isaacs, M.; Hoppe, H. C.; Kaye, P. T. Synthesis and evaluation of substituted 4-arylimino-3-hydroxybutanoic acids as potential HIV-1 integrase inhibitors. Bioorg. Med. Chem. Lett., 2018, 28(6), 1067-1070.
Zhang, F.H.; Debnath, B.; Xu, Z.L.; Yang, L.M.; Song, L.R.; Zheng, Y.T.; Neamati, N.; Long, Y.Q. Discovery of novel 3-hydroxypicolinamides as selective inhibitors of HIV-1 integrase-LEDGF/p75 interaction. Eur. J. Med. Chem., 2017, 125, 1051-1063.
Panwar, U.; Singh, S.K. Structure-based virtual screening toward the discovery of novel inhibitors for impeding the protein-protein interaction between HIV-1 integrase and hu-man lens epithelium-derived growth factor (LEDGF/P75). J. Biomol. Struct. Dyn., 2018, 36(12), 3199-3217.
Srivastav, V.K.; Tiwari, M. QSAR and Docking studies of coumarin derivatives as potent HIV-1 integrase inhibitors. Arab. J. Chem., 2017, 10, S1081-S1094.
Ericksen, S.S.; Wu, H.; Zhang, H.; Michael, L.A.; Newton, M.A.; Hoffmann, F.M.; Wildman, S.A. Machine learning consensus scoring improves performance across targets in structure-based virtual screening. J. Chem. Inf. Model., 2017, 57(7), 1579-1590.
Jin, K.; Yin, H.; De Clercq, E.; Pannecouque, C.; Meng, G.; Chen, F. Discovery of biphenyl-substituted diarylpyrimidines as non-nucleoside reverse transcriptase inhibitors with high potency against wild-type and mutant HIV-1. Eur. J. Med. Chem., 2018, 145, 726-734.
Kashid, A.M.; Dhawale, S. Design, Synthesis and Biological Screening of N 1 - (Substituted Pyridine-2-Yl) -N 3 - (Quinoline-2-Yl). Malonamide as Novel Anti-HIV-I Agents., Ind. J. Chem. Sec. B Org. Med. Chem., 2018, 57, 870-879.
Liu, G.; Wang, W.; Wan, Y.; Ju, X.; Gu, S. Application of 3D-QSAR, Pharmacophore, and Molecular Docking in the Molec-ular Design of Diarylpyrimidine Derivatives as HIV-1 Nonnucleoside Reverse Transcriptase Inhibitors. Int. J. Mol. Sci., 2018, 19(5), 1436.
Singh, A.; Singh, V.K.; Verma, R.; Singh, R.K. In Silico Studies on N - (Pyridin- 2-Yl) Thiobenzamides as NNRTIs against Wild and Mutant HIV-1 Strains. Philipp. J. Sci., 2018, 147(March), 37-46.
Peddi, S.R.; Mohammed, N.A.; Hussein, A.A.; Sivan, S.K.; Manga, V. Multiple-Receptor Conformation Docking, Dock Pose Clustering, and 3D QSAR-Driven Approaches Exploring New HIV-1 RT Inhibitors. Struct. Chem., 2018, 29(4), 999-1012.
Zhang, H.; Tian, Y.; Kang, D.; Huo, Z.; Zhou, Z.; Liu, H.; De Clercq, E.; Pannecouque, C.; Zhan, P.; Liu, X. Discovery of uracil-bearing DAPYs derivatives as novel HIV-1 NNRTIs via crystallographic overlay-based molecular hybridization. Eur. J. Med. Chem., 2017, 130, 209-222.
Samanta, P.N.; Das, K.K. Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations. J. Mol. Graph. Model., 2017, 75, 294-305.
Poongavanam, V.; Namasivayam, V.; Vanangamudi, M.; Al Shamaileh, H.; Veedu, R.N.; Kihlberg, J.; Murugan, N.A. In-tegrative Approaches in HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitor Design. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2018, 8(1), 1-26.
Monforte, A.M.; De Luca, L.; Buemi, M.R.; Agharbaoui, F.E.; Pannecouque, C.; Ferro, S. Structural optimization of N1-aryl-benzimidazoles for the discovery of new non-nucleoside reverse transcriptase inhibitors active against wild-type and mutant HIV-1 strains. Bioorg. Med. Chem., 2018, 26(3), 661-674.
Cabrera, A.; Huerta, H.L.; Chávez, D.; Medina-Franco, J.L. Molecular Modeling of Potential Dual Inhibitors of HIV Reverse Transcriptase and Integrase. Comput. Mol. Biosci., 2018, 8, 1-41.
Tang, J.; Vernekar, S.K.V.; Chen, Y.L.; Miller, L.; Huber, A.D.; Myshakina, N.; Sarafianos, S.G.; Parniak, M.A.; Wang, Z. Synthesis, biological evaluation and molecular modeling of 2-Hydroxyisoquinoline-1,3-dione analogues as inhibitors of HIV reverse transcriptase associated ribonuclease H and polymerase. Eur. J. Med. Chem., 2017, 133, 85-96.
Barberato, C.; Neto, Z.G. A AÇÃO coletiva como instrumento de tutela e concretização do direito à saúde. J. Popul., 2018, 1(3), 129-146.
Sousa, S.J.F.E.; Sousa, S.B.F.E. Eye bank procedures: donor selection criteria. Arq. Bras. Oftalmol., 2018, 81(1), 73-79.
Lemon, S.M.; Walker, C.M.; Hepatitis, A. Virus and Hepatitis E Virus: Emerging and Re-Emerging Enterically Transmitted Hepatitis Viruses. Cold Spring Harb. Perspect. Med., , 2019, 9(6), pii. A031823..
Majumdar, A.; Gilliam, B.L.; Arnold, R.; Rock, C.; Croft, L.; Morgan, D.J.; Donnenberg, M.S.; Majid, A.; McAninch, J.; Morgan, D.J. Grazoprevir Potassium. HCV NS3 NS4A Prote-ase Inhibitor, Anti-Hepatitis C Virus Drug. Drugs Future, 2016, 41(2), 85-109.
Pontarolo, R.; Borba, H.H.L.; Ferreira, V.L.; Pedroso, M.L.A.; Souza, A.W.; Siqueira, F.M. Direct-Acting Antivirals For Chronic Hepatitis C Treatment, ed. Berlin, Germany: Arid Science, , 2017. v., p.t.
Stanaway, J.D.; Flaxman, A.D.; Naghavi, M.; Fitzmaurice, C.; Vos, T.; Abubakar, I.; Abu-Raddad, L.J.; Assadi, R.; Bhala, N.; Cowie, B.; Forouzanfour, M.H.; Groeger, J.; Hanafiah, K.M.; Jacobsen, K.H.; James, S.L.; MacLachlan, J.; Malekzadeh, R.; Martin, N.K.; Mokdad, A.A.; Mokdad, A.H.; Murray, C.J.L.; Plass, D.; Rana, S.; Rein, D.B.; Richardus, J.H.; Sanabria, J.; Saylan, M.; Shahraz, S.; So, S.; Vlassov, V.V.; Weiderpass, E.; Wiersma, S.T.; Younis, M.; Yu, C.; El Sayed Zaki, M.; Cooke, G.S. The global burden of viral hepatitis from 1990 to 2013: findings from the Global Burden of Disease Study 2013. Lancet, 2016, 388(10049), 1081-1088.
Liver, E.A.F.T.S.O.T. EASL 2017 Clinical Practice Guidelines on the management of hepatitis B virus infection. J. Hepatol., 2017, 67(2), 370-398.
Kimberlin, D.W.; Brady, M.T.; Jackson, M.A.; Long, S.S. Red Book: 2015 Report of the Committee on Infec-tious Diseases, 30th ed; American Academy of Pediatrics: Elk Grove Village, IL, 2015.
Giesecke, J. Modern Infectious Disease Epidemiology; CRC Press, 2017.
Pilot-Matias, T.; Tripathi, R.; Cohen, D.; Gaultier, I.; Dekhtyar, T.; Lu, L.; Reisch, T.; Irvin, M.; Hopkins, T.; Pithawalla, R.; Middleton, T.; Ng, T.; McDaniel, K.; Or, Y.S.; Menon, R.; Kempf, D.; Molla, A.; Collins, C. In vitro and in vivo antiviral activity and resistance profile of the hepatitis C virus NS3/4A protease inhibitor ABT-450. Antimicrob. Agents Chemother., 2015, 59(2), 988-997.
Foureau, D.M.; Walling, T.L.; Maddukuri, V.; Anderson, W.; Culbreath, K.; Kleiner, D.E.; Ahrens, W.A.; Jacobs, C.; Watkins, P.B.; Fontana, R.J.; Chalasani, N.; Talwalkar, J.; Lee, W.M.; Stolz, A.; Serrano, J.; Bonkovsky, H.L. Comparative analysis of portal hepatic infiltrating leucocytes in acute drug-induced liver injury, idiopathic autoimmune and viral hepatitis. Clin. Exp. Immunol., 2015, 180(1), 40-51.
Sarrazin, C.; Lathouwers, E.; Peeters, M.; Daems, B.; Buelens, A.; Witek, J.; Wyckmans, Y.; Fevery, B.; Verbinnen, T.; Ghys, A.; Schlag, M.; Baldini, A.; De Meyer, S.; Lenz, O. Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region. Antiviral Res., 2015, 116, 10-16.
Appleby, T.C.; Perry, J.K.; Murakami, E.; Barauskas, O.; Feng, J.; Cho, A.; Fox, D.; Wetmore, D.R.; McGrath, M.E.; Ray, A.S. Structural Basis for RNA Replication by the Hepatitis C Virus Polymerase. Science, 2015, 347(6223), 771-775.
Patel, P.D.; Patel, M.R.; Kaushik-Basu, N.; Talele, T.T. 3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors. J. Chem. Inf. Model., 2008, 48(1), 42-55.
Vani, G.S.; Rajarajan, S. A Study on In-Silico Analysis of Phytochemicals Targeting the Proteins of Hepatitis B and C Virus. Int. J. Curr. Microbiol. Appl. Sci., 2015, 4(12), 683-691.
Wang, X.; Yang, W.; Xu, X.; Zhang, H.; Li, Y.; Wang, Y. Studies of benzothiadiazine derivatives as hepatitis C virus NS5B polymerase inhibitors using 3D-QSAR, molecular docking and molecular dynamics. Curr. Med. Chem., 2010, 17(25), 2788-2803.
Anithaa, K.; Singhb, N.; Shaikc, B.; Ahmadc, I.; Agrawald, V.K.; Guptac, S.P. QSAR and Docking Studies on 1, 1-Dioxo-2H-Benzothiadiazines Acting as HCV NS5B Polymerase In-hibitors. J. Mod. Med. Chem., 2015, 3, 49-68.
Liu, M-M.; Zhou, L.; He, P-L.; Zhang, Y-N.; Zhou, J-Y.; Shen, Q.; Chen, X-W.; Zuo, J-P.; Li, W.; Ye, D-Y. Discovery of flavonoid derivatives as anti-HCV agents via pharmacophore search combining molecular docking strategy. Eur. J. Med. Chem., 2012, 52, 33-43.
Scull, M.A.; Schneider, W.M.; Flatley, B.R.; Hayden, R.; Fung, C.; Jones, C.T.; van de Belt, M.; Penin, F.; Rice, C.M. The N-terminal Helical Region of the Hepatitis C Virus p7 Ion Channel Protein Is Critical for Infectious Virus Production. PLoS Pathog., 2015, 11(11)e1005297
Boukadida, C.; Fritz, M.; Blumen, B.; Fogeron, M-L.; Penin, F.; Martin, A. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities. PLoS Pathog., 2018, 14(2)e1006863
Lisboa Neto, G.; Noble, C.; Pinho, J.R.R.; Malta, F.M.; Gomes-Gouvea, M.S.; Alvarado-Mora, M.V.; Silva, M.H.; Leite, A.G.; Piccoli, L.Z.; Carrilho, F.J. Characterization of clinical predictors of naturally oc-curring ns3/ns4a protease polymorphism in genotype 1 hepatitis c virus infected patients. J. Hepatol; Elsevier Science BV, 2015, Vol. 62, pp. S686-S686.
Bailey, M.D.; Halmos, T.; Lemke, C.T. Discovery of novel P2 substituted 4-biaryl proline inhibitors of hepatitis C virus NS3 serine protease. Bioorg. Med. Chem. Lett., 2013, 23(15), 4436-4440.
Wei, Y.; Yang, J.; Kishore Sakharkar, M.; Wang, X.; Liu, Q.; Du, J.; Zhang, J-J. Evaluating the Inhibitory Effect of Eight Compounds from Daphne Papyracea against the NS3/4A Pro-tease of Hepatitis C Virus. Nat. Prod. Res., 2018, 17, 1-4.
Ashfaq, U.A.; Jalil, A.; Ul Qamar, M.T. Antiviral phytochemicals identification from Azadirachta indica leaves against HCV NS3 protease: an in silico approach. Nat. Prod. Res., 2016, 30(16), 1866-1869.
Shaw, J.; Harris, M.; Fishwick, C.W.G. Identification of a lead like inhibitor of the hepatitis C virus non-structural NS2 autoprotease. Antiviral Res., 2015, 124, 54-60.
Lulu, S.S.; Thabitha, A.; Vino, S.; Priya, A.M.; Rout, M. Naringenin and quercetin--potential anti-HCV agents for NS2 protease targets. Nat. Prod. Res., 2016, 30(4), 464-468.
Uddin, R.; Downard, K.M. Molecular basis of benzimidazole inhibitors to hepatitis C virus envelope glycoprotein. Chem. Biol. Drug Des., 2018, 92(3), 1638-1646.
Hung, T-C.; Jassey, A.; Liu, C-H.; Lin, C-J.; Lin, C-C.; Wong, S.H.; Wang, J.Y.; Yen, M-H.; Lin, L-T. Berberine inhibits hepatitis C virus entry by targeting the viral E2 glycoprotein. Phytomedicine, 2019, 53, 62-69.

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2019
Page: [1135 - 1150]
Pages: 16
DOI: 10.2174/1389203720666190311142747
Price: $65

Article Metrics

PDF: 27