Design of Mutation‐resistant HIV Protease Inhibitors with the Substrate Envelope Hypothesis

There is a clinical need for HIV protease inhibitors that can evade resistance mutations. One possible approach to designing such inhibitors relies upon the crystallographic observation that the substrates of HIV protease occupy a rather constant region within the binding site. In particular, it has been hypothesized that inhibitors which lie within this region will tend to resist clinically relevant mutations. The present study offers the first prospective evaluation of this hypothesis, via computational design of inhibitors predicted to conform to the substrate envelope, followed by synthesis and evaluation against wild‐type and mutant proteases, as well as structural studies of complexes of the designed inhibitors with HIV protease. The results support the utility of the substrate envelope hypothesis as a guide to the design of robust protease inhibitors.

[1]  M. Kjeldgaard,et al.  O: A Macromolecule Modeling Environment , 1990 .

[2]  Ray Luo,et al.  Ligand-receptor docking with the Mining Minima optimizer , 2001, J. Comput. Aided Mol. Des..

[3]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[4]  K. N. Trueblood,et al.  On the rigid-body motion of molecules in crystals , 1968 .

[5]  C. Schiffer,et al.  Viability of a Drug-Resistant Human Immunodeficiency Virus Type 1 Protease Variant: Structural Insights for Better Antiviral Therapy , 2003, Journal of Virology.

[6]  HIV and AIDS--United States, 1981-2000. , 2001, MMWR. Morbidity and mortality weekly report.

[7]  Brian K. Shoichet,et al.  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..

[8]  Michael K. Gilson,et al.  Enhanced docking with the mining minima optimizer: Acceleration and side‐chain flexibility , 2002, J. Comput. Chem..

[9]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[10]  Richard J Morris,et al.  ARP/wARP's model-building algorithms. I. The main chain. , 2002, Acta crystallographica. Section D, Biological crystallography.

[11]  T. Schroer,et al.  Subunit organization in cytoplasmic dynein subcomplexes , 2002, Protein science : a publication of the Protein Society.

[12]  Celia A Schiffer,et al.  Lack of synergy for inhibitors targeting a multi‐drug‐resistant HIV‐1 protease , 2002, Protein science : a publication of the Protein Society.

[13]  M. Murcko,et al.  Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .

[14]  Charles E. Bugg,et al.  Crystallographic and Modeling Methods in Molecular Design , 1990, Springer New York.

[15]  J Kuriyan,et al.  Rigid protein motion as a model for crystallographic temperature factors. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Bryan Chan,et al.  Human immunodeficiency virus reverse transcriptase and protease sequence database , 2003, Nucleic Acids Res..

[17]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[18]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[19]  Irene T Weber,et al.  Ultra-high resolution crystal structure of HIV-1 protease mutant reveals two binding sites for clinical inhibitor TMC114. , 2006, Journal of molecular biology.

[20]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[21]  C. Schiffer,et al.  How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. , 2000, Journal of molecular biology.

[22]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[23]  Michael K. Gilson,et al.  Fast Assignment of Accurate Partial Atomic Charges: An Electronegativity Equalization Method that Accounts for Alternate Resonance Forms , 2003, J. Chem. Inf. Comput. Sci..

[24]  Akbar Ali,et al.  Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands. , 2006, Journal of medicinal chemistry.

[25]  E. Freire,et al.  Adaptive inhibitors of the HIV-1 protease. , 2005, Progress in biophysics and molecular biology.

[26]  Celia A Schiffer,et al.  Combating susceptibility to drug resistance: lessons from HIV-1 protease. , 2004, Chemistry & biology.

[27]  Celia A. Schiffer,et al.  Structural and Thermodynamic Basis for the Binding of TMC114, a Next-Generation Human Immunodeficiency Virus Type 1 Protease Inhibitor , 2004, Journal of Virology.

[28]  Michael K Gilson,et al.  Evaluation of the substrate envelope hypothesis for inhibitors of HIV‐1 protease , 2007, Proteins.