I36T↑T mutation in South African subtype C (C-SA) HIV-1 protease significantly alters protease-drug interactions

References

Ali, A., Bandaranayake, R.M., Cai, Y., King, N.M., Kolli, M., Mittal, S., Murzycki, J.F., Nalam, M.N., Nalivaika, E.A., and Özen, A. (2010). Molecular basis for drug resistance in HIV-1 protease. Viruses 2, 2509–2535.10.3390/v2112509Search in Google Scholar PubMed PubMed Central

Altman, M.D., Ali, A., Kumar Reddy, G.K., Nalam, M.N., Anjum, S.G., Cao, H., Chellappan, S., Kairys, V., Fernandes, M.X., and Gilson, M.K. (2008). HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J. Am. Chem. Soc. 130, 6099–6113.10.1021/ja076558pSearch in Google Scholar PubMed PubMed Central

Blanco-Heredia, J., Lecanda, A., Valenzuela-Ponce, H., Brander, C., Ávila-Ríos, S., and Reyes-Terán, G. (2016). Identification of immunogenic cytotoxic T lymphocyte epitopes containing drug resistance mutations in antiretroviral treatment-naïve HIV-infected individuals. PLoS One 11, e0147571.10.1371/journal.pone.0147571Search in Google Scholar PubMed PubMed Central

Clemente, J.C., Moose, R.E., Hemrajani, R., Whitford, L.R., Govindasamy, L., Reutzel, R., McKenna, R., Agbandje-McKenna, M., Goodenow, M.M., and Dunn, B.M. (2004). Comparing the accumulation of active-and nonactive-site mutations in the HIV-1 protease. Biochemistry 43, 12141–12151.10.1021/bi049459mSearch in Google Scholar PubMed

Fraser, C., Lythgoe, K., Leventhal, G.E., Shirreff, G., Hollingsworth, T.D., Alizon, S., and Bonhoeffer, S. (2014). Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science, 343, 1243727.10.1126/science.1243727Search in Google Scholar PubMed PubMed Central

Hayashi, H., Takamune, N., Nirasawa, T., Aoki, M., Morishita, Y., Das, D., Koh, Y., Ghosh, A.K., Misumi, S., and Mitsuya, H. (2014). Dimerization of HIV-1 protease occurs through two steps relating to the mechanism of protease dimerization inhibition by darunavir. Proc. Nat. Acad. USA 111, 12234–12239.10.1073/pnas.1400027111Search in Google Scholar PubMed PubMed Central

Hellen, C.U., Kraeusslich, H.G., and Wimmer, E. (1989). Proteolytic processing of polyproteins in the replication of RNA viruses. Biochemistry 28, 9881–9890.10.1021/bi00452a001Search in Google Scholar PubMed

Honarparvar, B., Govender, T., Maguire, G.E., Soliman, M.E., and Kruger, H.G. (2013). Integrated approach to structure-based enzymatic drug design: molecular modeling, spectroscopy, and experimental bioactivity. Chem. Rev. 114, 493–537.10.1021/cr300314qSearch in Google Scholar PubMed

Hong, L., Zhang, X.C., Hartsuck, J.A., and Tang, J. (2000). Crystal structure of an in vivo HIV‐1 protease mutant in complex with saquinavir: insights into the mechanisms of drug resistance. Protein Sci. 9, 1898–1904.10.1110/ps.9.10.1898Search in Google Scholar PubMed PubMed Central

Hornak, V. and Simmerling, C. (2007). Targeting structural flexibility in HIV-1 protease inhibitor binding. Drug Discov. Today 12, 132–138.10.1016/j.drudis.2006.12.011Search in Google Scholar PubMed PubMed Central

Kohl, N.E., Emini, E.A., Schleif, W.A., Davis, L.J., Heimbach, J.C., Dixon, R., Scolnick, E.M., and Sigal, I.S. (1988). Active human immunodeficiency virus protease is required for viral infectivity. Proc. Nat. Acad. Sci. USA 85, 4686–4690.10.1073/pnas.85.13.4686Search in Google Scholar PubMed PubMed Central

Kožíšek, M., Prejdová, J., Souček, M., Machala, L., Staňková, M., Linka, M., Brůčková, M., and Konvalinka, J. (2004). Characterisation of mutated proteinases derived from HIV-positive patients: enzyme activity, vitality and inhibition. Collect. Czech. Chem. Commun. 69, 703–714.10.1135/cccc20040703Search in Google Scholar

Kožíšek, M., Bray, J., Řezáčová, P., Šašková, K., Brynda, J., Pokorná, J., Mammano, F., Rulíšek, L., and Konvalinka, J. (2007). Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants. J. Mol. Biol. 374, 1005–1016.10.1016/j.jmb.2007.09.083Search in Google Scholar PubMed

Kuzmič, P., Sideris, S., Cregar, L.M., Elrod, K.C., Rice, K.D., and Janc, J.W. (2000). High-throughput screening of enzyme inhibitors: automatic determination of tight-binding inhibition constants. Anal. Biochem. 281, 62–67.10.1006/abio.2000.4501Search in Google Scholar PubMed

Lockhat, H.A., Silva, J.R., Alves, C.N., Govender, T., Lameira, J., Maguire, G.E., Sayed, Y., and Kruger, H.G. (2016). Binding free energy calculations of nine FDA‐approved protease inhibitors against HIV‐1 subtype C I36T↑ T containing 100 amino acids per monomer. Chem. Biol. Drug. Des. 87, 487–98.10.1111/cbdd.12690Search in Google Scholar PubMed

Luque, I., Todd, M.J., Gómez, J., Semo, N., and Freire, E. (1998). Molecular basis of resistance to HIV-1 protease inhibition: a plausible hypothesis. Biochemistry 37, 5791–5797.10.1021/bi9802521Search in Google Scholar PubMed

Mascolini, M. (2009). HIV DART 2008: Novel Agents, Strategies, and Assays to Control HIV, December 9–12, Rio Grande, Puerto Rico.Search in Google Scholar

Maseko, S.B., Natarajan, S., Sharma, V., Bhattacharyya, N., Govender, T., Sayed, Y., Maguire, G.E., Lin, J., and Kruger, H.G. (2016). Purification and characterization of naturally occurring HIV-1 (South African subtype C) protease mutants from inclusion bodies. Protein Expr. Purif. 122, 90–96.10.1016/j.pep.2016.02.013Search in Google Scholar PubMed

Mittal, S., Cai, Y., Nalam, M.N., Bolon, D.N., and Schiffer, C.A. (2012). Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. J. Am. Chem. Soc. 134, 4163–4168.10.1021/ja2095766Search in Google Scholar PubMed PubMed Central

Mosebi, S., Morris, L., Dirr, H.W., and Sayed, Y. (2008). Active site mutations in the South African HIV-1 subtype C protease impact significantly on clinical inhibitor binding: a kinetic and thermodynamic study. J. Virol. 82, 11476–11479.10.1128/JVI.00726-08Search in Google Scholar PubMed PubMed Central

Motulsky, H. (1999). Analyzing data with GraphPad prism: GraphPad Software Incorporated.Search in Google Scholar

Moyer, C.L., Besser, E.S., and Nemerow, G.R. (2016). A single maturation cleavage site in adenovirus impacts cell entry and capsid assembly. J. Virol. 90, 521–532.10.1128/JVI.02014-15Search in Google Scholar PubMed PubMed Central

Muzammil, S., Armstrong, A., Kang, L., Jakalian, A., Bonneau, P., Schmelmer, V., Amzel, L., and Freire, E. (2007). Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations. J. Virol. 81, 5144–5154.10.1128/JVI.02706-06Search in Google Scholar PubMed PubMed Central

Padayachee, E. and Whiteley, C. (2013). Etiology of Alzheimer’s disease: kinetic, thermodynamic and fluorimetric analyses of interactions of pseudo Aβ-peptides with neuronal nitric oxide synthase. Neuropeptides 47, 321–327.10.1016/j.npep.2013.08.001Search in Google Scholar PubMed

Park, J.H., Sayer, J.M., Aniana, A., Yu, X., Weber, I.T., Harrison, R.W., and Louis, J.M. (2016). Binding of clinical inhibitors to a model precursor of a rationally selected multidrug resistant HIV-1 protease is significantly weaker than that to the released mature enzyme. Biochemistry 55, 2390–2400.10.1021/acs.biochem.6b00012Search in Google Scholar PubMed PubMed Central

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25, 1605–1612.10.1002/jcc.20084Search in Google Scholar PubMed

Potempa, M., Lee, S.-K., Wolfenden, R., and Swanstrom, R. (2015). The triple threat of HIV-1 protease inhibitors. In: The Future of HIV-1 Therapeutics. Curr Top Microbiol Immunol 389, 203–241.10.1007/82_2015_438Search in Google Scholar PubMed

Robins, T. and Plattner, J. (1993). HIV protease inhibitors: their anti-HIV activity and potential role in treatment. JAIDS 6, 162–170.Search in Google Scholar

Santoro, M.M. and Perno, C.F. (2013). HIV-1 genetic variability and clinical implications. ISRN Microbiol. 2013. Article ID 481314. http://dx.doi.org/10.1155/2013/481314.10.1155/2013/481314Search in Google Scholar PubMed PubMed Central

Szeltner, Z. and Polgár, L. (1996). Conformational stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration. J. Biol. Chem. 271, 5458–5463.10.1074/jbc.271.10.5458Search in Google Scholar PubMed

Velazquez-Campoy, A., Muzammil, S., Ohtaka, H., Schon, A., Vega, S., and Freire, E. (2003). Structural and thermodynamic basis of resistance to HIV-1 protease inhibition: implications for inhibitor design. Curr. Drug Targets Infect. Disord 3, 311–328.10.2174/1568005033481051Search in Google Scholar PubMed

Wensing, A.M., Calvez, V., Günthard, H.F., Johnson, V.A., Paredes, R., Pillay, D., Shafer, R.W., and Richman, D.D. (2015). 2015 update of the drug resistance mutations in HIV-1. Topics Antiviral Med. 23, 132–141.Search in Google Scholar

Yanchunas, J., Langley, D.R., Tao, L., Rose, R.E., Friborg, J., Colonno, R.J., and Doyle, M.L. (2005). Molecular basis for increased susceptibility of isolates with atazanavir resistance-conferring substitution I50L to other protease inhibitors. Antimicrob. Agents Chemother. 49, 3825–3832.10.1128/AAC.49.9.3825-3832.2005Search in Google Scholar PubMed PubMed Central

Zhan, P., Pannecouque, C., De Clercq, E., and Liu, X. (2015). Anti-HIV drug discovery and development: current innovations and future trends: miniperspective. J. Med. Chem. 59, 2849–2878.10.1021/acs.jmedchem.5b00497Search in Google Scholar PubMed