Application of Structure-based Methods to Analyze Resistance Mutations for Chemically Diverse Non-Nucleoside Reverse Transcriptase Inhibitors

Author(s): Tasnim Tabassum, Syeda M. Azeem, Alecia N. Muwonge, Kathleen M. Frey*

Journal Name: Current HIV Research
HIV and Viral Immune Diseases

Volume 18 , Issue 4 , 2020


Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Abstract:

Background: Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are used in combination with antiretroviral therapy to suppress viral loads in HIV patients. The chemical design of NNRTIs has changed in recent years in response to resistance-associated mutations (RAMs) and resistance. NNRTIs are chemically diverse compounds that bind an allosteric site of HIV RT. Resistance- associated mutations (RAMs) identified in HIV patients are associated with NNRTI resistance. RAMs confer amino acid changes that alter both structural and physiochemical properties of the allosteric site. Ultimately, these changes reduce NNRTI affinity. Previously, we used a combination of computational and experimental methods to analyze and validate RAMs for 3 diarylpyrimidine (DAPY) NNRTIs.

Objective: The objective of this study is to apply these methods to other chemically diverse, non- DAPY NNRTIs.

Materials and Methods: We selected MIV-150 (experimental microbicide) and doravirine for this study. A computational and molecular modeling strategy was used to evaluate the effects of RAMs. Calculated changes in drug affinity and stability (ΔS + ΔA) were used to determine overall resistance levels: susceptible, low, intermediate, and high. The ΔS + ΔA values for K101P suggest that this mutation confers intermediate/high-level resistance to MIV-150, but remains susceptible to doravirine. Based on the determined resistance levels, we analyzed the models and used Molecular Dynamics (MD) to compare the interactions of MIV-150/doravirine with RT wild-type (WT) and RT (K101P). From MD, we found that key interactions were lost with RT (K101P), but were retained with doravirine. To experimentally validate our findings, we conducted a fluorescence-based reverse transcription assay for MIV-150 with RT (WT) and RT (K101P). IC50 values determined in assays showed a 101-fold change in potency for MIV-150, but essentially no change for doravirine.

Results: Our computational and experimental results are also consistent with antiviral data reported in the literature.

Conclusion: We believe that this approach is effective for analyzing mutations to determine resistance profiles for chemically diverse NNRTIs in development.

Keywords: HIV, resistance, non-nucleoside reverse transcriptase inhibitor, mutation, structure-based drug design, molecular dynamics.

[1]
Wensing AM, Calvez V, Ceccherini-Silberstein F, et al. 2019 update of the drug resistance mutations in HIV-1. Top Antivir Med 2019; 27(3): 111-21.
[PMID: 31634862]
[2]
Rhee SY, Jordan MR, Raizes E, et al. HIV-1 Drug Resistance Mutations: Potential Applications for Point-of-Care Genotypic Resistance Testing. PLoS One 2015; 10(12)e0145772
[http://dx.doi.org/10.1371/journal.pone.0145772] [PMID: 26717411]
[3]
Das K, Arnold E. HIV-1 reverse transcriptase and antiviral drug resistance. Part 1. Curr Opin Virol 2013; 3(2): 111-8.
[http://dx.doi.org/10.1016/j.coviro.2013.03.012] [PMID: 23602471]
[4]
Das K, Arnold E. HIV-1 reverse transcriptase and antiviral drug resistance. Part 2. Curr Opin Virol 2013; 3(2): 119-28.
[http://dx.doi.org/10.1016/j.coviro.2013.03.014] [PMID: 23602470]
[5]
Spence RA, Kati WM, Anderson KS, Johnson KA. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Science 1995; 267(5200): 988-93.
[http://dx.doi.org/10.1126/science.7532321] [PMID: 7532321]
[6]
AIDSInfo. Clinical Guidelines https://aidsinfo.nih.gov/guidelines
[7]
Asahchop EL, Oliveira M, Wainberg MA, et al. Characterization of the E138K resistance mutation in HIV-1 reverse transcriptase conferring susceptibility to etravirine in B and non-B HIV-1 subtypes. Antimicrob Agents Chemother 2011; 55(2): 600-7.
[http://dx.doi.org/10.1128/AAC.01192-10] [PMID: 21135184]
[8]
Vingerhoets J, Azijn H, Fransen E, et al. TMC125 displays a high genetic barrier to the development of resistance: evidence from in vitro selection experiments. J Virol 2005; 79(20): 12773-82.
[http://dx.doi.org/10.1128/JVI.79.20.12773-12782.2005] [PMID: 16188980]
[9]
Azijn H, Tirry I, Vingerhoets J, et al. TMC278, a next-generation nonnucleoside reverse transcriptase inhibitor (NNRTI), active against wild-type and NNRTI-resistant HIV-1. Antimicrob Agents Chemother 2010; 54(2): 718-27.
[http://dx.doi.org/10.1128/AAC.00986-09] [PMID: 19933797]
[10]
Das K, Bauman JD, Clark AD Jr, et al. High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Proc Natl Acad Sci USA 2008; 105(5): 1466-71.
[http://dx.doi.org/10.1073/pnas.0711209105] [PMID: 18230722]
[11]
Lansdon EB, Brendza KM, Hung M, et al. Crystal structures of HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278): implications for drug design. J Med Chem 2010; 53(10): 4295-9.
[http://dx.doi.org/10.1021/jm1002233] [PMID: 20438081]
[12]
Friedland BA, Hoesley CJ, Plagianos M, et al. First-in-Human Trial of MIV-150 and Zinc Acetate Coformulated in a Carrageenan Gel: Safety, Pharmacokinetics, Acceptability, Adherence, and Pharmacodynamics. J Acquir Immune Defic Syndr 2016; 73(5): 489-96.
[http://dx.doi.org/10.1097/QAI.0000000000001136] [PMID: 27437826]
[13]
Hsu M, Keele BF, Aravantinou M, et al. Exposure to MIV-150 from a high-dose intravaginal ring results in limited emergence of drug resistance mutations in SHIV-RT infected rhesus macaques. PLoS One 2014; 9(2)e89300
[http://dx.doi.org/10.1371/journal.pone.0089300] [PMID: 24586674]
[14]
Seidman D, Weber S, Aaron E. Dapivirine Vaginal Ring for HIV-1 Prevention. N Engl J Med 2017; 376(10): 995.
[PMID: 28273024]
[15]
Côté B, Burch JD, Asante-Appiah E, et al. Discovery of MK-1439, an orally bioavailable non-nucleoside reverse transcriptase inhibitor potent against a wide range of resistant mutant HIV viruses. Bioorg Med Chem Lett 2014; 24(3): 917-22.
[http://dx.doi.org/10.1016/j.bmcl.2013.12.070] [PMID: 24412110]
[16]
Lai MT, Feng M, Falgueyret JP, et al. In vitro characterization of MK-1439, a novel HIV-1 nonnucleoside reverse transcriptase inhibitor. Antimicrob Agents Chemother 2014; 58(3): 1652-63.
[http://dx.doi.org/10.1128/AAC.02403-13] [PMID: 24379202]
[17]
Azeem SM, Muwonge AN, Thakkar N, Lam KW, Frey KM. Structure-based methods to predict mutational resistance to diarylpyrimidine non-nucleoside reverse transcriptase inhibitors. J Mol Graph Model 2018; 79: 133-9.
[http://dx.doi.org/10.1016/j.jmgm.2017.10.023] [PMID: 29156381]
[18]
Beard H, Cholleti A, Pearlman D, Sherman W, Loving KA. Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes. PLoS One 2013; 8(12)e82849
[http://dx.doi.org/10.1371/journal.pone.0082849] [PMID: 24340062]
[19]
Salam NK, Adzhigirey M, Sherman W, Pearlman DA. Structure-based approach to the prediction of disulfide bonds in proteins. Protein Eng Des Sel 2014; 27(10): 365-74.
[http://dx.doi.org/10.1093/protein/gzu017] [PMID: 24817698]
[20]
Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins 2014; 82(8): 1646-55.
[http://dx.doi.org/10.1002/prot.24551] [PMID: 24619874]
[21]
Smith SJ, Pauly GT, Akram A, et al. Rilpivirine and Doravirine Have Complementary Efficacies Against NNRTI-Resistant HIV-1 Mutants. J Acquir Immune Defic Syndr 2016; 72(5): 485-91.
[http://dx.doi.org/10.1097/QAI.0000000000001031] [PMID: 27124362]
[22]
Schrödinger Release 2020-1: LigPrep. Schrödinger, LLC, New York, NY,. 2020.
[23]
Schrödinger Release 2020-1: Glide,. Schrödinger, LLC, New York,NY,. 2020.
[24]
The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. Available from: https://pymol.org/2/support.html?#citing
[25]
Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field. J Chem Theory Comput 2010; 6(5): 1509-19.
[http://dx.doi.org/10.1021/ct900587b] [PMID: 26615687]
[26]
Schrödinger Release 2019-4: Desmond Molecular Dynamics System DESR, New York, NY, 2019 2019.
[27]
Schrödinger Release 2020-1: Maestro, Schrödinger, LLC, New York, NY, 2020..
[28]
Frey KM, Puleo DE, Spasov KA, Bollini M, Jorgensen WL, Anderson KS. Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants. J Med Chem 2015; 58(6): 2737-45.
[http://dx.doi.org/10.1021/jm501908a] [PMID: 25700160]
[29]
Gray WT, Frey KM, Laskey SB, et al. Potent inhibitors active against HIV reverse transcriptase with K101P, a mutation conferring rilpivirine resistance. ACS Med Chem Lett 2015; 6(10): 1075-9.
[http://dx.doi.org/10.1021/acsmedchemlett.5b00254] [PMID: 26487915]
[30]
Silprasit K, Thammaporn R, Tecchasakul S, Hannongbua S, Choowongkomon K. Simple and rapid determination of the enzyme kinetics of HIV-1 reverse transcriptase and anti-HIV-1 agents by a fluorescence based method. J Virol Methods 2011; 171(2): 381-7.
[http://dx.doi.org/10.1016/j.jviromet.2010.12.001] [PMID: 21167206]
[31]
Giacobbi NS, Sluis-Cremer N. In Vitro Cross-Resistance Profiles of Rilpivirine, Dapivirine, and MIV-150, Nonnucleoside Reverse Transcriptase Inhibitor Microbicides in Clinical Development for the Prevention of HIV-1 Infection. Antimicrob Agents Chemother 2017; 61(7): e00277-17.
[http://dx.doi.org/10.1128/AAC.00277-17] [PMID: 28507107]
[32]
Shafer RW. Rationale and uses of a public HIV drug-resistance database. J Infect Dis 2006; 194(Suppl. 1): S51-8.
[http://dx.doi.org/10.1086/505356] [PMID: 16921473]
[33]
Johnson M, Kumar P, Molina JM, et al. DRIVE-SHIFT Study Group. Switching to Doravirine/Lamivudine/Tenofovir Disoproxil Fumarate (DOR/3TC/TDF) Maintains HIV-1 Virologic Suppression Through 48 Weeks: Results of the DRIVE-SHIFT Trial. J Acquir Immune Defic Syndr 2019; 81(4): 463-72.
[http://dx.doi.org/10.1097/QAI.0000000000002056] [PMID: 30985556]
[34]
Namasivayam V, Vanangamudi M, Kramer VG, Kurup S, Zhan P, Liu X, et al. The journey of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) from lab to clinic. J Med Chem 2018.
[PMID: 30516990]
[35]
Günthard HF, Calvez V, Paredes R, et al. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clin Infect Dis 2019; 68(2): 177-87.
[http://dx.doi.org/10.1093/cid/ciy463] [PMID: 30052811]
[36]
Chan AH, Lee WG, Spasov KA, et al. Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography. Proc Natl Acad Sci USA 2017; 114(36): 9725-30.
[http://dx.doi.org/10.1073/pnas.1711463114] [PMID: 28827354]
[37]
Yang Y, Kang D, Nguyen LA, et al. Structural basis for potent and broad inhibition of HIV-1 RT by thiophene[3,2-d]pyrimidine non-nucleoside inhibitors. eLife 2018; 7: 7.
[http://dx.doi.org/10.7554/eLife.36340] [PMID: 30044217]


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 18
ISSUE: 4
Year: 2020
Page: [283 - 291]
Pages: 9
DOI: 10.2174/1570162X18666200603141209
Price: $65

Article Metrics

PDF: 40
HTML: 4