Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking.

This study details the separate analyses of binding specificity of HIV-1 integrase (IN) and viral B-DNA forms through ligand-receptor docking studies by means of a fast molecular docking method. The application of solvated electrostatics with the University of Houston Brownian Dynamics Program (UHBD) and configurational sampling by the Daughter of Turnip (DOT) docking program resulted in the computation of energies of more than 113 billion configurations for each ligand-receptor docking study, a procedure considered computationally intractable a few years ago. A specific binding pattern of viral DNA to the IN catalytic domain region has been predicted as a result of these calculations. In a representative docked configuration, we observe the 3'-hydroxyl of the conserved deoxyadenosine to be close to one of the two divalent metal ions that are necessary for catalysis. A superimposition of our energy-minimized docked complex on representative structures from a molecular dynamics (MD) simulation of a crystallographically resolved IN/inhibitor complex revealed an overlap of viral DNA with the inhibitor, indicating that the bound inhibitor might operate by blocking substrate binding. The DOT docking calculation also identified a second, adjacent DNA-binding site, which we believe is the nonspecific host DNA binding site. The binding pattern predicted by DOT complements previous electrostatics, MD simulation, photo-cross-linking, and mutagenesis studies and also provides a further refinement of the IN/viral DNA binding interaction as a basis for new structure-based design efforts.

[1]  M E Pique,et al.  Definition of the interaction domain for cytochrome c on cytochrome c oxidase. III. Prediction of the docked complex by a complete, systematic search. , 1999, The Journal of biological chemistry.

[2]  A. Skalka,et al.  Retroviral Integrase, Putting the Pieces Together* , 1996, The Journal of Biological Chemistry.

[3]  Kui Gao,et al.  Human immunodeficiency virus type 1 integrase: arrangement of protein domains in active cDNA complexes , 2001, The EMBO journal.

[4]  E. Asante-Appiah,et al.  Molecular mechanisms in retrovirus DNA integration. , 1997, Antiviral research.

[5]  G. Cohen,et al.  Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: a platform for antiviral drug design. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[6]  P. Brown,et al.  The Core Domain of HIV-1 Integrase Recognizes Key Features of Its DNA Substrates* , 1997, The Journal of Biological Chemistry.

[7]  R. Katz,et al.  Substrate recognition by retroviral integrases. , 1999, Advances in virus research.

[8]  Y. Pommier,et al.  Inhibitors of human immunodeficiency virus integrase. , 1999, Advances in virus research.

[9]  A. Skalka,et al.  Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases , 1992, Molecular and cellular biology.

[10]  J. Andrew McCammon,et al.  Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design , 1999 .

[11]  L. R. Scott,et al.  Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program , 1995 .

[12]  J Andrew McCammon,et al.  Modeling HIV-1 integrase complexes based on their hydrodynamic properties. , 2003, Biopolymers.

[13]  L. T. Ten Eyck,et al.  Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.

[14]  P. Brown,et al.  Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. , 1992, Science.

[15]  P. Brown,et al.  Photo-cross-linking studies suggest a model for the architecture of an active human immunodeficiency virus type 1 integrase-DNA complex. , 1998, Biochemistry.

[16]  M C Nicklaus,et al.  HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching. , 1997, Journal of medicinal chemistry.

[17]  J A McCammon,et al.  Active site binding modes of HIV-1 integrase inhibitors. , 2000, Journal of medicinal chemistry.

[18]  R. Plasterk,et al.  Structure-Based Mutational Analysis of the C-Terminal DNA-Binding Domain of Human Immunodeficiency Virus Type 1 Integrase: Critical Residues for Protein Oligomerization and DNA Binding , 1998, Journal of Virology.

[19]  M C Nicklaus,et al.  Depsides and depsidones as inhibitors of HIV-1 integrase: discovery of novel inhibitors through 3D database searching. , 1997, Journal of medicinal chemistry.

[20]  F E Cohen,et al.  Modeling protein-ligand complexes. , 1996, Current opinion in structural biology.

[21]  D. Esposito,et al.  Sequence specificity of viral end DNA binding by HIV‐1 integrase reveals critical regions for protein–DNA interaction , 1998, The EMBO journal.

[22]  Thomas Lengauer,et al.  Computational methods for biomolecular docking. , 1996, Current opinion in structural biology.

[23]  J Andrew McCammon,et al.  AutoDocking dinucleotides to the HIV-1 integrase core domain: exploring possible binding sites for viral and genomic DNA. , 2002, Journal of medicinal chemistry.

[24]  J A McCammon,et al.  Molecular dynamics studies on the HIV-1 integrase catalytic domain. , 1999, Biophysical journal.

[25]  R. Plasterk,et al.  Characterization of the minimal DNA-binding domain of the HIV integrase protein. , 1994, Nucleic acids research.

[26]  V. Nair HIV integrase as a target for antiviral chemotherapy , 2002, Reviews in medical virology.

[27]  D. Davies,et al.  Retroviral integrases and their cousins. , 1996, Current opinion in structural biology.

[28]  M C Nicklaus,et al.  Discovery of HIV-1 integrase inhibitors by pharmacophore searching. , 1997, Journal of medicinal chemistry.

[29]  R. Plasterk,et al.  Identification of amino acids in HIV-2 integrase involved in site-specific hydrolysis and alcoholysis of viral DNA termini. , 1993, Nucleic acids research.

[30]  J. Briggs,et al.  Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations. , 2000, Pharmacology & therapeutics.

[31]  P. Brown,et al.  Mapping features of HIV-1 integrase near selected sites on viral and target DNA molecules in an active enzyme-DNA complex by photo-cross-linking. , 1997, Biochemistry.

[32]  A. Engelman,et al.  Critical contacts between HIV‐1 integrase and viral DNA identified by structure‐based analysis and photo‐crosslinking , 1997, The EMBO journal.

[33]  A. Engelman,et al.  Identification of conserved amino acid residues critical for human immunodeficiency virus type 1 integrase function in vitro , 1992, Journal of virology.

[34]  A. Skalka,et al.  The retroviral enzymes. , 1994, Annual review of biochemistry.

[35]  J A McCammon,et al.  Ordered water and ligand mobility in the HIV-1 integrase-5CITEP complex: a molecular dynamics study. , 2001, Journal of medicinal chemistry.

[36]  F. Bushman,et al.  Developing a dynamic pharmacophore model for HIV-1 integrase. , 2000, Journal of medicinal chemistry.

[37]  D. Davies,et al.  Three new structures of the core domain of HIV-1 integrase: an active site that binds magnesium. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[38]  F. Bushman,et al.  HIV cDNA integration: molecular biology and inhibitor development , 1996, AIDS.

[39]  T. Steitz,et al.  Structural basis for the 3′‐5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. , 1991, The EMBO journal.