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

A new computational method for the in situ generation of small molecules within the binding site of a protein is described. The method has been evaluated using two well-studied systems, dihydrofolate reductase and thymidylate synthase. The method has also been used to guide improvements to inhibitors of HIV-1 protease. One such improvement resulted in a compound selected for preclinical studies as an antiviral agent against AIDS.
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PMID:De novo design of enzyme inhibitors by Monte Carlo ligand generation. 785 40

Thymidylate synthase (TS) is an essential enzyme of DNA metabolism. We have carried out an extensive insertional mutagenesis of the Escherichia coli TS gene (thyA) using three different methods. Insertion of exogenous sequences at unique restriction sites or at random positions produced defective mutants, whereas comparison of TS sequences from different species allowed us to identify six zones permissive for insertions of exogenous sequences. The insertion of Human immunodeficiency virus type 1 (HIV-1) protease substrate sequences into the permissive sites converted TS to an HIV-1 protease substrate, and the in vivo cleavage of these insertions by the cloned HIV-1 protease conferred a thymidylate synthase-deficient phenotype in some of our E. coli mutant strains. In agreement with crystallographic data, these results show that the permissive sites are located in regions of the TS protein not essential for enzyme activity and accessible to cleavage by HIV protease. These results also show that it is possible to control a growth phenotype in E. coli through the protease-mediated destruction of an essential metabolic enzyme. Because both wild type and thymidylate synthase-deficient phenotypes are selectable on the appropriate growth medium, these thyA mutants could be used for genetic selections of protease inhibitors and analysis of protease specificities.
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PMID:Conversion of thymidylate synthase into an HIV protease substrate. 870 91

Structure-based design has emerged as a new tool in medicinal chemistry. A prerequisite for this new approach is an understanding of the principles of molecular recognition in protein-ligand complexes. If the three-dimensional structure of a given protein is known, this information can be directly exploited for the retrieval and design of new ligands. Structure-based ligand design is an iterative approach. First of all, it requires the crystal structure or a model derived from the crystal structure of a closely related homolog of the target protein, preferentially complexed with a ligand. This complex unravels the binding mode and conformation of a ligand under investigation and indicates the essential aspects determining its binding affinity. It is then used to generate new ideas about ways of improving an existing ligand or of developing new alternative bonding skeletons. Computational methods supplemented by molecular graphics are applied to assist this step of hypothesis generation. The features of the protein binding pocket can be translated into queries used for virtual computer screening of large compound libraries or to design novel ligands de novo. These initial proposals must be confirmed experimentally. Subsequently they are optimized toward higher affinity and better selectivity. The latter aspect is of utmost importance in defining and controlling the pharmacological profile of a ligand. A prerequisite to tailoring selectivity by rational design is a detailed understanding of molecular parameters determining selectivity. Taking examples from current drug development programs (HIV proteinase, t-RNA transglycosylase, thymidylate synthase, thrombin and, related serine proteinases), we describe recent advances in lead discovery via computer screening, iterative design, and understanding of selectivity discrimination.
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PMID:Recent developments in structure-based drug design. 1095 96

Insertional mutagenesis of the Escherichia coli thymidylate synthase (TS) was used to address substrate recognition of HIV-1 protease in a well characterized structural context. By modifying the TS conformation while maintaining its enzymic activity, we investigated the influence of protein folding on protease-substrate recognition. A slight destabilization of the TS structure permitted the cleavage of a target site, which was resistant in the native TS. This result supports a dynamic interpretation of HIV-1 protease specificity. Exposure time of the potential cleavage site, which depends on the stability of the global conformation, must be compatible with the cleavage kinetics, which are determined by the local sequence. Cleavage specificity has been described as the consequence of cumulative interactions, globally favourable, between at least six amino acids around the cleavage site. To investigate influence of local sequence, we introduced insertions of variable lengths in two exposed loops of the TS. In both environments, insertion of only two amino acids could determine specific cleavage. We then inserted libraries of dipeptides naturally cleaved by the HIV-1 protease in order to assess the limitations of established classifications of substrates in different conformational contexts.
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PMID:Local and spatial factors determining HIV-1 protease substrate recognition. 1151 51