The D2 code analysis of a large collection of crystal structures of human immunodeficiency virus type 1 protease (HIV-1 PR) variants can provide a new perspective to the problem of drug resistance and lead to new ideas on designing more efficient drugs.

The D2 code analysis can be also useful in rational drug design. For instance, analysis of the distribution of D2-variable regions may lead to a more detailed description of the mechanism of multi-drug resistance due to non-active site mutations. As an example, let's consider mutations in HIV-1 protease which produce resistance to HIV-1 protease inhibitors, one of the major anti-HIV-1 drug targets, in the therapy of HIV-1 infection [1].

Because of the short life cycle and the high mutation rate of HIV-1, every mutation of HIV-1 protease is created thousands of time each day in each patient [2]. As a result, HIV-1 protease exists within a patient as a mixture of genetically related but distinguishable variants often referred to as a ``swarm'' or ``quasi-species'' [3]. Drug-resistant HIV-1 strains are then developed under the selective pressure of protease inhibitor therapy.

More than 60 mutations are currently associated with protease inhibitor resistance [4], which could be classified as active site or non-active site mutations depending on their location within the protease molecule. The mechanism of resistance due to non-active site mutations is not immediately apparent unlike the case of active site mutations, and extensive studies have been made on this topic ([5]--[9]), although the detailed mechanisms of drug resistance are yet to be clarified.

In the following, superposition of molecules and their Z-scores and RMSDs are computed by the DaliLite server ([10]--[11]).

(0) About the structure of HIV-1 PR

HIV-1 PR is a homodimeric molecule, consisted of two identical 99-residue polypeptide chains.
HIV-1 PR is a C2-symmetric molecule, with a twofold axis transversing the active site (residues Asp25, Thr26, and Gly27).

(1) X-ray crystal structures of HIV-1 PR variants from the PDB database

  1. Crystal structures of space group P 61
  2. Crystal structures of space group P 21 21 2
    • HIV-1 PR complexed with the FDA approved drugs
    • HIV-1 PR complexed with peptidomimetic inhibitors
    • HIV-1 PR complexed with non-peptide based inhibitors

  3. Crystal structures of space group P 21 21 21
    • HIV-1 PR complexed with the FDA approved drugs
    • HIV-1 PR complexed with peptidomimetic inhibitors
    • HIV-1 PR complexed with non-peptide based inhibitors

  4. Crystal structures of the other space groups
    • HIV-1 PR complexed with the FDA approved drugs
    • HIV-1 PR complexed with peptidomimetic inhibitors
    • HIV-1 PR complexed with non-peptide based inhibitors

  5. Deviation from C2-symmetry upon ligand-binding
    • Difference between the D2 codes of chain A and chain B

*) FDA:= U.S. Food and Drug Administration.

(2) NMR structures (solution structures) of HIV-1 PR variants

  1. Wlodawer A, Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct 1998;27:249-84.
  2. Shafera RW, Rheea S-Y, Pillayb D, Millerc V, Sandstromd P, Schapiroa JM, Kuritzkese DR, Bennettf D. HIV-1protease and reverse transcriptase mutations for drug resistance surveillance. AIDS 2007;21:215-223.
  3. Rhee SY, Gonzales MJ, Kantor R, Betts BJ, Ravela J, Shafer RW. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 2003;31:298-303.
  4. Shafer RW, Schapiro JM. HIV-1 drug resistance mutations: an updated framework for the second decade of HAART, AIDS Rev. 2008;10:67-84. 
  5. Piana S, Carloni P, Rothlisberger U. Drug resistance in HIV-1 protease: flexibility-assisted mechanism of compensatory mutations. Protein Sci 2002;11: 2393-2402.
  6. Zoete V, Michielin O, Karplus M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol 2002;315:21-52.
  7. Ohtaka H, Schon A, Freire E. Multidrug resistance to HIV-1 protease inhibition requires cooperative coupling between distal mutations. Biochemistry 2003;42:13659-66. 
  8. Prabu-Jeyabalan M, Nalivaika EA, King NM, Schiffer CA. Viability of a drug-resistant human immunodeficiency virus type 1 protease variant: structural insights for better antiviral therapy. Virol 2003;77:1306-15.
  9. Ode H, Neya S, Hata M, Sugiura W, Hoshino T. Computational simulations of HIV-1 proteases-multi-drug resistance due to nonactive site mutation L90M. J Am Chem Soc 2006;128:7887 -7895.
  10. Holm, L. and Park J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics, 16:566-567.
  11. The pairwise DaliLite server : http://www.ebi.ac.uk/DaliLite/