This project proposes to determine the crystal structure of HIV integrase in complex with various small-molecule compounds that inhibit the action of HIV Integrase. Presently, we have obtained high-quality crystals of the integrase catalytic domain (residues 50 to 212) that diffract X-rays beyond 1.8 A resolution. Our immediate aim is to refine the current protein structure model at the highest resolution possible. The high precision of the protein model will be essential for subsequent modeling efforts. A few potent inhibitors selected on the basis of the activity against preintegration complex, have been soaked successfully into crystals.
We aim to determine the crystal structure of the complex in order to define the stereochemistry of the bound inhibitors. Comparing conformations of these bound compounds will provide crucial information to design new drugs. To probe further the putative binding pocket of inhibitors, we will generate site-specific point mutants at positions in the vicinity of the drug-binding site. Based on the binding affinity measurements of these mutants, a computational strategy to design and screen new inhibitors will be guided. When the second-generation inhibitor is available, we will analyze its conformation and compare to those of other bound compounds by X-ray crystallography. We hope that iterative cycles of new design, chemical synthesis, biological assays, and structure determination will ultimately yield clinically useful drugs. In parallel, we aim to cocrystallize the full-length integrase in complex with a DNA substrate. The three-dimensional structure of the whole enzyme/DNA complex will permit a better understanding the catalytic mechanisms of this class of enzymes. Given the recent success of combination drug therapy targeting reverse transcriptase and protease simultaneously we hope to discover an inhibitor of HIV integrase that can be added as the third target in combination therapy.
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