Identification of Adjacent NNRTI Binding Pocket in Multi-mutated HIV1- RT Enzyme Model: An in silico Study

Author(s): R.F. Kamil*, U. Debnath, S. Verma, Y.S. Prabhakar

Journal Name: Current HIV Research

Volume 16 , Issue 2 , 2018


Become EABM
Become Reviewer
Call for Editor

Graphical Abstract:


Abstract:

Introduction: A possible strategy to combat mutant strains is to have a thorough structural evaluation before and after mutations to identify the diversity in the non-nucleoside inhibitor binding pocket and their effects on enzyme-ligand interactions to generate novel NNRTI’s accordingly.

Objective: The primary objective of this study was to find effects of multiple point mutations on NNRTI binding pocket. This study included the contribution of each individual mutation in NNIBP that propose an adjacent binding pocket which can be used to discover novel NNRTI derivatives.

Methods: An in Silico model of HIV-1 RT enzyme with multiple mutations K103N, Y181C and Y188L was developed and evaluated. Two designed NNRTI pyridinone derivatives were selected as ligands for docking studies with the homology model through alignment based docking and residue based docking approaches. Binding pockets of wild type HIV-1 RT and multi-mutated homology model were compared thoroughly.

Result and Discussion: K103N mutation narrowed the entrance of NNRTI binding pocket and forbade electrostatic interaction with α amino group of LYS103. Mutations Y181C and Y188L prevented NNRTI binding by eliminating aromatic π interactions offered by tyrosine rings. Docking study against new homology model suggested an adjacent binding pocket with combination of residues in palm and connection domains. This pocket is approximately 14.46Å away from conventional NNRTI binding site.

Conclusion: Increased rigidity, steric hindrance and losses of important interactions cumulatively prompt ligands to adapt adjacent NNRTI binding pocket. The proposed new and adjacent binding pocket is identified by this study which can further be evaluated to generate novel derivatives.

Keywords: AIDS, HIV1-RT, NNRTIs, Non nucleoside inhibitor binding pocket, Docking, MD simulation.

[1]
Kent A, Sepkowitz MD. AIDS-the first 20 years. N Engl J Med 2001; 344(23): 1764-72.
[2]
Douek DC, Roederer M, Koup RA. Emerging Concepts in the Immunopathogenesis of AIDS. Annu Rev Med 2009; 60(1): 471-84.
[3]
Leitner T, Keuken C, Hahn B, et al. HIV sequence compendium 2008 los alamos HIV sequence database. HIV Seq Compend 2008; 1-7.
[4]
Hu WS, Hughes SH. HIV-1 reverse transcription. Cold Spring Harb Perspect Med 2012; 2(10): 1-22.
[5]
Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 1992; 256(5065): 1783-90.
[6]
Jacobo-Molina A, Ding J, Nanni RG, et al. Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci 1993; 90(13): 6320-4.
[7]
Castro HC, Loureiro NIV, Pujol-Luz M, et al. HIV-1 reverse transcriptase: a therapeutical target in the spotlight. Curr Med Chem 2006; 13(3): 313-24.
[8]
Alcaro S, Artese A, Ceccherini-Silberstein F, et al. Computational analysis of human immunodeficiency virus (HIV) Type-1 reverse transcriptase crystallographic models based on significant conserved residues found in Highly Active Antiretroviral Therapy (HAART)-treated patients. Curr Med Chem 2010; 17(4): 290-308.
[9]
Sluis-Cremer N, Arion D, Parniak MA. Molecular mechanisms of HIV-1 resistance to nucleoside reverse transcriptase inhibitors (NRTIs). C Cell Mol Life Sci 2000; 57(January): 1408-22.
[10]
Cihlar T, Ray AS. Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Res 2010; 85: 39-58.
[11]
Rittinger K, Divita G, Goody RS. Human immunodeficiency virus reverse transcriptase substrate-induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors. Proc Natl Acad Sci USA 1995; 92: 8046-9.
[12]
Huang H. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 1998; 282(5394): 1669-75.
[13]
Beyer A, Lawtrakul L, Hannongbua S, Wolschann P. Systematic investigation of non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). Monatshefte for Chemie/Chemical Mon 2004; 135(8): 1047-59.
[14]
Rodgers DW, Gamblin SJ. The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Proc Natl Acad Sci USA 1995; 92(4): 1222-6.
[15]
Sluis-Cremer N, Temiz NA, Bahar I. Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Curr HIV Res 2004; 2(4): 323-32.
[16]
Ren J, Esnouf R, Garman E, et al. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat Struct Biol 1995; 2(4): 293-302.
[17]
Hsiou Y, Ding J, Das K, Clark AD, Hughes SH, Arnold E. Structure of unliganded HIV-1 reverse transcriptase at 2.7 Å resolution: Implications of conformational changes for polymerization and inhibition mechanisms. Structure 1996; 4(7): 853-60.
[18]
Shen LL, Jiang HL. Steered molecular dynamics simulation on the binding of NNRTIs to HIV-1 RT. In: Biophysical Journal 2003; 3547-63.
[19]
Sluis-Cremer N, Arion D, Parniak MA. Destabilization of the HIV-1 reverse transcriptase dimer upon interaction with N-acyl hydrazone inhibitors. Mol Pharmacol 2002; 62(2): 398-405.
[20]
Mark A. Wainberg. HIV resistance to nevirapine and other non-nucleoside reverse transcriptase inhibitors.pdf. J of Acquir Immune Defic Syndr 2003; 34: S2-7.
[21]
Conway B, Wainberg MA, Hall D, et al. Development of drug resistance in patients receiving combinations of zidovudine, didanosine and nevirapine. AIDS 2001; 15(10): 1269-74.
[22]
Shulman N, Zolopa AR, Passaro D, et al. Phenotypic hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in treatment-experienced HIV-infected patients: Impact on virological response to efavirenz-based therapy. AIDS 2001; 15(9): 1125-32.
[23]
Jackson JB, Becker-Pergola G, Guay LA, et al. Identification of the K103N resistance mutationin Ugandan women receiving nevirapine to prevent HIV-1 vertical transmission. AIDS 2000; 14(11): 111-5.
[24]
Kuiken C, Korber B, Shafer RW. HIV sequence databases. AIDS Rev 2003; 5: 52-61.
[25]
Ren J, Stammers DK. Structural basis for drug resistance mechanisms for non-nucleoside inhibitors of HIV reverse transcriptase. Virus Res 2008; 134(1-2): 157-70.
[26]
Das K, Lewi PJ, Hughes SH, Arnold E. Crystallography and the design of anti-AIDS drugs: Conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors. Progress in Biophysics and Molecular Biology 2005; 88: 209-31.
[27]
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.
[28]
Ren J, Nichols C, Bird L, et al. Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors. J Mol Biol 2001; 312(4): 795-805.
[29]
Chong P, Sebahar P, Youngman M, et al. Rational design of potent non-nucleoside inhibitors of HIV-1 reverse transcriptase. J Med Chem 2012; 55(23): 10601-9.
[30]
Himmel DM, Das K, Clark AD, et al. Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: A new class of non-nucleoside inhibitors effective against a broad range of drug-resistant strains. J Med Chem 2005; 48(24): 7582-91.
[31]
Sahlberg C, Zhou X. Development of non-nucleoside reverse transcriptase inhibitors for Anti- HIV therapy. Antiinfect Agents Med Chem 2008; 7(2): 101-17.
[32]
Berman HM, Kleywegt GJ, Nakamura H, Markley JL. The Protein Data Bank archive as an open data resource. J Comput Aided Mol Des 2014; 28(10): 1009-14.
[33]
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41: 95-8.
[34]
Hall T, Biosciences I, Carlsbad C. BioEdit: An important software for molecular biology. GERF Bull Biosci 2011; 2: 60-1.
[35]
McWilliam H, Li W, Uludag M, et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013; 41: 597-600.
[36]
Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23(21): 2947-8.
[37]
Goujon M, McWilliam H, Li W, et al. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res 2010; 38(Suppl. 2): 695-9.
[38]
Webb B, Sali A. Comparative protein structure modeling using MODELLER Curr Protoc Bioinform 2014; 47: 5.6.1-32.
[39]
Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 1997; 18(15): 2714-23.
[40]
ChemicalComputingGroupInc. Molecular Operating Environment (MOE). Sci Comput Instrum 2004; 22(1): 32.
[41]
Humphrey W, Dalke A, Schulten K. Visual molecular dynamics. J Mol Graph 1996; 14(1): 33-8.
[42]
Ribeiro J V, Bernardi RC, Rudack T, et al. QwikMD — Integrative molecular dynamics toolkit for novices and experts. Nat Publ Gr 2016; (May): 1-14.
[43]
Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005; 26: 1781-802.
[44]
Debnath U, Verma S, Jain S, Katti SB, Prabhakar YS. Pyridones as NNRTIs against HIV-1 mutants: 3D-QSAR and protein informatics. J Comput Aided Mol Des 2013; 27(7): 637-54.
[45]
Guillemont J, Benjahad A, Oumouch S, et al. Synthesis and biological evaluation of C-5 methyl substituted 4-arylthio and 4-aryloxy-3-iodopyridin-2(1H)-one type anti-HIV agents. J Med Chem 2009; 52(23): 7473-87.
[46]
Mills N. ChemDraw Ultra 10.0. J Am Chem Soc 2006; 128(41): 13649-50.
[47]
Barakat MT, Dean PM. Molecular structure matching by simulated annealing. I. A comparison between different cooling schedules. J Comput Aided Mol Des 1990; 4(3): 295-316.
[48]
Murugesan V, Sethi N, Prabhakar YS, Katti SB. CoMFA and CoMSIA of diverse pyrrolidine analogues as dipeptidyl peptidase IV inhibitors: active site requirements. Mol Divers 2011; 15(2): 457-66.
[49]
Morris GM, Goodsell DS, Halliday RS, Huey R, Olson A. Automated docking using a lamarckian genetic algotithm and an empirical binding free energy function. J Comput Chem 1998; 19(14): 1639-62.
[50]
Morris GM, Huey R, Lindstrom W, et al. Software news and updates autodock4 and autodocktools4: automated docking with selective receptor flexibility. J Comput Chem 2009; 30: 2785-91.
[51]
Wiederstein M, Sippl MJ. ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007; 35(Suppl. 2): 407-10.
[52]
Benkert P, Tosatto SCE, Schomburg D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins-Structure Function and Bioinformatics 2008; 71(1): 261-77.
[53]
Willard L, Ranjan A, Zhang H, et al. VADAR: A web server for quantitative evaluation of protein structure quality. Nucleic Acids Res 2003; 31(13): 3316-9.
[54]
Colovos C, Yeates TO. Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Sci 1993; 2(9): 1511-9.
[55]
Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968; 23(C): 283-437.
[56]
Ramachandran GN, Ramakrishnan C, Sasisekharan V. Stereochemistry of polypeptide chain configurations. J of Mol Biol 1963; 7(1): 95-9.
[57]
Oberholser K. Proteopedia entry: ramachandran plots. Biochem Mol Biol Educ 2010; 38(6): 430.
[58]
Hollingsworth SA, Karplus PA. A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins. Biomol Concepts 2010; 1(3-4): 271-83.
[59]
Hsiou Y, Ding J, Das K, et al. The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. J Mol Biol 2001; 309(2): 437-45.
[60]
Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E. Crystal structures of clinically relevant lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside Inhibitor HBY 097. J Mol Biol 2007; 365(1): 77-89.
[61]
Esnouf R, Ren J, Ross C, Jones Y, Stammers D, Stuart D. Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. Nat Struct Biol 1995; 2(4): 303-8.
[62]
Bauman JD, Patel D, Dharia C, et al. Detecting allosteric sites of HIV-1 reverse transcriptase by X-ray crystallographic fragment screening. J Med Chem 2013; 56(7): 2738-46.


Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 16
ISSUE: 2
Year: 2018
Published on: 15 August, 2018
Page: [121 - 129]
Pages: 9
DOI: 10.2174/1570162X16666180412165004
Price: $65

Article Metrics

PDF: 28
HTML: 4