Journal of Molecular Modeling

, Volume 16, Issue 7, pp 1251–1268 | Cite as

Molecular docking and 3D-QSAR studies of HIV-1 protease inhibitors

  • Vijay M. Khedkar
  • Premlata K. Ambre
  • Jitender Verma
  • Mushtaque S. Shaikh
  • Raghuvir R. S. Pissurlenkar
  • Evans C. Coutinho
Original Paper


HIV-1 protease is an obligatory enzyme in the replication process of the HIV virus. The abundance of structural information on HIV-1PR has made the enzyme an attractive target for computer-aided drug design strategies. The daunting ability of the virus to rapidly generate resistant mutants suggests that there is an ongoing need for new HIV-1PR inhibitors with better efficacy profiles and reduced toxicity. In the present investigation, molecular modeling studies were performed on a series of 54 cyclic urea analogs with symmetric P2/P2′ substituents. The binding modes of these inhibitors were determined by docking. The docking results also provided a reliable conformational superimposition scheme for the 3D-QSAR studies. To gain insight into the steric, electrostatic, hydrophobic and hydrogen-bonding properties of these molecules and their influence on the inhibitory activity, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed. Two different alignment schemes viz. receptor-based and atom-fit alignment, were used in this study to build the QSAR models. The derived 3D-QSAR models were found to be robust with statistically significant r2 and r2pred values and have led to the identification of regions important for steric, hydrophobic and electronic interactions. The predictive ability of the models was assessed on a set of molecules that were not included in the training set. Superimposition of the 3D-contour maps generated from these models onto the active site of enzyme provided additional insight into the structural requirements of these inhibitors. The CoMFA and CoMSIA models were used to design some new inhibitors with improved binding affinity. Pharmacokinetic and toxicity predictions were also carried out for these molecules to gauge their ADME and safety profile. The computational results may open up new avenues for synthesis of potent HIV-1 protease inhibitors.


ADMET Atom-fit alignment CoMFA CoMSIA Docking HIV-1PR inhibitors Receptor-based alignment 



The computational facilities were jointly provided by the All India Council of Technical Education through grant (F. No. 8022/RID/NPROJ/RPS-5/2003–04), the Department of Science and Technology through their FIST program (SR/FST/LSI-163/2003) and the Council of Scientific and Industrial Research (01(1986)/05/EMR-II). Vijay M. Khedkar thanks the Amrut Mody Research Foundation (AMRF) and Jitender Verma, the CSIR, New Delhi for the financial support. The authors are also grateful to Dr. Krishna Iyer, Professor, Bombay College of Pharmacy for the ADME-Toxicity profiling of the designed molecules.


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Vijay M. Khedkar
    • 1
  • Premlata K. Ambre
    • 1
  • Jitender Verma
    • 1
  • Mushtaque S. Shaikh
    • 1
  • Raghuvir R. S. Pissurlenkar
    • 1
  • Evans C. Coutinho
    • 1
  1. 1.Department of Pharmaceutical ChemistryBombay College of PharmacyMumbaiIndia

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