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BMC Systems Biology

Open Access

On the correlation between drug-resistant pattern of HIV-1 protease inhibitors and binding free energy and structural changes

  • Kitiyaporn Wittayanarakul1Email author,
  • Supot Hannongbua1 and
  • Michael Feig2
BMC Systems Biology20071(Suppl 1):P58

Published: 8 May 2007


Molecular DynamicRitonavirIndinavirSaquinavirNelfinavir


Protease inhibitor (PR) resistance remains the major limiting in the treatment of HIV infection. Understanding source of mutation at molecular level is a key of success in research and drug discovery. The present studies aim to examine relation between clinical data of drug resistance and the molecular properties obtained from molecular dynamics simulations (MD).

Materials and methods

MD simulations of 6 FDA-approved drugs, which are Lopinavir (LPV), Ritonavir (RTV), Saquinavir (SQV), Indinavir (IDV), Amprenavir (APV), and Nelfinavir (NFV), were performed using AMBER 8. The total inhibitor-enzyme binding free energy (ΔG total ) including entropic contributions of 6 complexes was estimated based on MM-PB(GB)SA approach. The decomposition free energy (ΔG DC ), representing interaction between inhibitor and each residue, was calculated and used as the criteria for the mutation prediction.


In comparison to the expermental binding free energy, the ΔG total for the 6 complexes yields the standard deviation of ± 2.29 kcal/mol, indicating reliability of the method used. To seek for the correlation between resistance according to the clinical data and the molecular properties according to the MD results, the ΔG DC and the structural changes (in term of the root mean square displacement, RMSD, of each residue) were evaluated. For simplicity, the notations F (favourable), U (unfavourable) and S (structure) were, then, used to represent the residue which gives the ΔG DC lower than -0.5 Kcal/mol, the ΔG DC higher than 0.5 kcal/mol and the RMSD higher than 2.0 Å, respectively. In addition, the notation I (indirect) was used to represent the residue which locates close to or between the two residues which have F, U and/or S character, i.e., mutation takes place due to the influence of the F, U and/or S residues. Table 1 contains the mutated residues which correlated with the level of resistance according to the clinical data [1] for 6 drugs. The F, U, S and I characteristic of each residue extracted from the MD trajectories for the 6 complexes were accordingly given. Subscripts a and b indicate its location in chain A and chain B of the HIV-1 PR, respectively. It can be clearly seen that most of the high-level resistance (very dark-blue) takes place at the residues which bind strongly to the inhibitor (F, ΔG DC < -0.5 kcal/mol) and/or residues which have high RMSD (S, RMSD > 2.0 Å). The data shows also that most of the indirect effect, I, effects lead to the low-level resistance (dark blue) and contribute to resistance (light blue). Figure 1 displays location of the residues for the LPV/enzyme complex with different levels of resistances; green for F, light-blue for U, brown for S. The pink and blue CPK represent the mutated residues which are intermediate and contributes to resistance level, respectively. It appears that the mutated residues due to the indirect effect are surrounded by those which have F, U and/or S characters.


Direct correlation between the experimental drug resistance and the calculated binding free energies obtained from the MM-PB(GB)SA as well as the structural changes was observed. Examination was performed for the 6 FDA-approval inhibitors.

See Table 1 & Figure 1 at

Authors’ Affiliations

Departments of Chemistry, Faculty Of Science, Chulalongkorn University, Bangkok, Thailand
Department of Biochemistry and Molecular Biology and Department Of Chemistry, Michigan State University, East Lansing, USA


  1. Richard T, Jonathan M: Drug Resistance Mutations. Special Contribution. 2002, 10: 21-25.Google Scholar


© Wittayanarakul et al; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd.