Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: EC:3.4.23.16 (HIV-1 protease)
 2,107 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A computer procedure TFIT, which uses a molecular superposition force field to flexibly match test compounds to a 3D pharmacophore, was evaluated to find out whether it could reliably predict the bioactive conformations of flexible ligands. The program superposition force field optimizes the overlap of those atoms of the test ligand and template that are of similar chemical type, by applying an attractive force between atoms of the test ligand and template which are close together and of similar type (hydrogen bonding, charge, hydrophobicity). A procedure involving Monte Carlo torsion perturbations, followed by torsional energy minimization, is used to find conformations of the test ligand which cominimize the internal energy of the ligand and the superposition energy of ligand and template. The procedure was tested by applying it to a series of flexible ligands for which the bioactive conformation was known experimentally. The 15 molecules tested were inhibitors of thermolysin, HIV-1 protease or endothiapepsin for which X-ray structures of the bioactive conformation were available. For each enzyme, one of the molecules served as a template and the others, after being conformationally randomized, were fitted. The fitted conformation was then compared to the known binding geometry. The matching procedure was successful in predicting the bioactive conformations of many of the structures tested. Significant deviation from experimental results was found only for parts of molecules where it was readily apparent that the template did not contain sufficient information to accurately determine the bioactive conformation.
 ...
PMID:Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: comparison of predicted and experimental conformations of inhibitors of three enzymes. 756 76

The peptides inhibiting HIV-1 protease were isolated from the hydrolysate of oyster (Crassostrea gigas) proteins prepared with thermolysin. The amino acid sequences of the peptides were determined as Leu-Leu-Glu-Tyr-Ser-Ile and Leu-Leu-Glu-Tyr-Ser-Leu. These sequences exist in some proteins of variola major virus or human cytomegalovirus. Chemically synthesized Leu-Leu-Glu-Tyr-Ser-Ile and Leu-Leu-Glu-Tyr-Ser-Leu showed IC50 values of 20 and 15 nM, respectively, and behaved as competitive inhibitors for HIV-1 protease with Ki values of 13 and 10 nM, respectively. These peptides were more potent as an HIV-1 protease inhibitor than pepstatin A.
 ...
PMID:Isolation of HIV-1 protease-inhibiting peptides from thermolysin hydrolysate of oyster proteins. 991 75