A study of the binding energies of efavirenz to wild-type and K103N/Y181C HIV-1 reverse transcriptase based on the ONIOM method

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A study of the binding energies of efavirenz to wild-type and K103N/Y181C HIV-1 reverse transcriptase based on the ONIOM method is …
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scholarly articleQ13442814

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P356DOI10.1002/CMDC.200700181
P698PubMed publication ID18338369

P50authorSupa HannongbuaQ42871449
P2093author name stringPensri Srivab
P2860cites workStructural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptaseQ27628304
The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistanceQ27631898
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 inhibitorsQ27635069
Structural basis for the inhibitory efficacy of efavirenz (DMP-266), MSC194 and PNU142721 towards the HIV-1 RT K103N mutantQ27638329
High resolution structures of HIV-1 RT from four RT-inhibitor complexesQ27729427
Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistanceQ27766013
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozymeQ28291671
L-743, 726 (DMP-266): a novel, highly potent nonnucleoside inhibitor of the human immunodeficiency virus type 1 reverse transcriptaseQ28378789
The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errorsQ29039690
Structure of HIV-1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors.Q30342229
Perspectives of non-nucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infectionQ33631716
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Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.Q34575882
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Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activityQ35137594
New challenges in quantum chemistry: Quests for accurate calculations for large molecular systemsQ35153408
Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugsQ35796056
In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).Q36072382
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The molecular basis of resilience to the effect of the Lys103Asn mutation in non-nucleoside HIV-1 reverse transcriptase inhibitors studied by targeted molecular dynamics simulationsQ39268433
TMC125, a novel next-generation nonnucleoside reverse transcriptase inhibitor active against nonnucleoside reverse transcriptase inhibitor-resistant human immunodeficiency virus type 1.Q40425001
Benzophenone derivatives: a novel series of potent and selective inhibitors of human immunodeficiency virus type 1 reverse transcriptaseQ41346135
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.Q43678172
Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculationsQ43979142
Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptaseQ44570491
Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analoguesQ44844445
Quantum study of mutational effect in binding of efavirenz to HIV-1 RT.Q46403165
Molecular mechanics PBSA ligand binding energy and interaction of Efavirenz derivatives with HIV-1 reverse transcriptaseQ46558469
Performance Evaluation of the Three-Layer ONIOM Method:  Case Study for a Zwitterionic Peptide.Q51629310
Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.Q51630551
Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 VQ57480046
Conformational study of the HIV-1 reverse transcriptase inhibitor 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT)Q77296519
Computer-aided molecular design of highly potent HIV-1 RT inhibitors: 3D QSAR and molecular docking studies of efavirenz derivativesQ80141775
Binding energy analysis for wild-type and Y181C mutant HIV-1 RT/8-Cl TIBO complex structures: quantum chemical calculations based on the ONIOM methodQ81394699
P433issue5
P921main subjectefavirenzQ422645
P304page(s)803-811
P577publication date2008-05-01
P1433published inChemMedChemQ2962252
P1476titleA study of the binding energies of efavirenz to wild-type and K103N/Y181C HIV-1 reverse transcriptase based on the ONIOM method
P478volume3

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cites work (P2860)
Q48578132A toolkit to assist ONIOM calculations.
Q46230871Docking analysis and resistance evaluation of clinically relevant mutations associated with the HIV-1 non-nucleoside reverse transcriptase inhibitors nevirapine, efavirenz and etravirine
Q44285867Key role of hydrazine to the interaction between oxaloacetic against phosphoenolpyruvic carboxykinase (PEPCK): ONIOM calculations
Q54549089Multiple drugs and multiple targets: an analysis of the electrostatic determinants of binding between non-nucleoside HIV-1 reverse transcriptase inhibitors and variants of HIV-1 RT.