All-Atom Models for the Non-Nucleoside Binding Site of HIV-1 Reverse Transcriptase Complexed with Inhibitors:  A 3D QSAR Approach†

1996 ◽  
Vol 39 (8) ◽  
pp. 1645-1650 ◽  
Author(s):  
Rick Gussio ◽  
Nagarajan Pattabiraman ◽  
Daniel W. Zaharevitz ◽  
Glen E. Kellogg ◽  
Igor A. Topol ◽  
...  
2019 ◽  
Vol 16 (8) ◽  
pp. 868-881
Author(s):  
Yueping Wang ◽  
Jie Chang ◽  
Jiangyuan Wang ◽  
Peng Zhong ◽  
Yufang Zhang ◽  
...  

Background: S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside reverse transcriptase inhibitors have received considerable attention during the last decade due to their high potency against HIV-1. Methods: In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2) was used to determine the most probable binding mode and to obtain reliable conformations for molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA (q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis of hybrid docking-based and ligand-based alignment. Results: The predictive ability of CoMFA and CoMSIA models was further validated using a test set of eight compounds with predictive r2 pred values of 0.843 and 0.723, respectively. Conclusion: The information obtained from the 3D contour maps can be used in designing new SDABO derivatives with improved HIV-1 inhibitory activity.


Biochemistry ◽  
2010 ◽  
Vol 49 (49) ◽  
pp. 10565-10573 ◽  
Author(s):  
Valerie A. Braz ◽  
Mary D. Barkley ◽  
Rebecca A. Jockusch ◽  
Patrick L. Wintrode

2011 ◽  
Vol 78 (3) ◽  
pp. 418-426 ◽  
Author(s):  
Ramaswamy Sree Latha ◽  
Ramadoss Vijayaraj ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Krishnaswamy Chitra ◽  
Venkatesan Subramanian

2008 ◽  
Vol 48 (8) ◽  
pp. 1706-1715 ◽  
Author(s):  
Monique Araújo de Brito ◽  
Carlos Rangel Rodrigues ◽  
José Jair Vianna Cirino ◽  
Ricardo Bicca de Alencastro ◽  
Helena Carla Castro ◽  
...  

2016 ◽  
Vol 18 (1) ◽  
pp. 310-317 ◽  
Author(s):  
A. Krzemińska ◽  
K. P. Świderek ◽  
P. Paneth

The 18O binding isotope effect allows us to distinguish the actual binding site of an inhibitor in HIV-1 reverse transcriptase.


2004 ◽  
Vol 78 (14) ◽  
pp. 7427-7437 ◽  
Author(s):  
Joeri Auwerx ◽  
Miguel Stevens ◽  
An R. Van Rompay ◽  
Louise E. Bird ◽  
Jingshan Ren ◽  
...  

ABSTRACT The phenylmethylthiazolylthiourea (PETT) derivative MSK-076 shows, besides high potency against human immunodeficiency virus type 1 (HIV-1), marked activity against HIV-2 (50% effective concentration, 0.63 μM) in cell culture. Time-of-addition experiments pointed to HIV-2 reverse transcriptase (RT) as the target of action of MSK-076. Recombinant HIV-2 RT was inhibited by MSK-076 at 23 μM. As was also found for HIV-1 RT, MSK-076 inhibited HIV-2 RT in a noncompetitive manner with respect to dGTP and poly(rC)·oligo(dG) as the substrate and template-primer, respectively. MSK-076 selected for A101P and G112E mutations in HIV-2 RT and for K101E, Y181C, and G190R mutations in HIV-1 RT. The selected mutated strains of HIV-2 were fully resistant to MSK-076, and the mutant HIV-2 RT enzymes into which the A101P and/or G112E mutation was introduced by site-directed mutagenesis showed more than 50-fold resistance to MSK-076. Mapping of the resistance mutations to the HIV-2 RT structure ascertained that A101P is located at a position equivalent to the nonnucleoside RT inhibitor (NNRTI)-binding site of HIV-1 RT. G112E, however, is distal to the putative NNRTI-binding site in HIV-2 RT but close to the active site, implying a novel molecular mode of action and mechanism of resistance. Our findings have important implications for the development of new NNRTIs with pronounced activity against a wider range of lentiviruses.


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