5fve | pdb_00005fve
Crystal Structure of Helicobacter pylori beta clamp in complex with 3, 4-Difluorobenzamide
Structural highlights
Function[DPO3B_HELPY] DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The beta chain is required for initiation of replication once it is clamped onto DNA, it slides freely (bidirectional and ATP-independent) along duplex DNA (By similarity). Publication Abstract from PubMedThe characteristic of interaction with various enzymes and processivity-promoting nature during DNA replication makes beta-clamp an important drug target. Helicobacter pylori (H. pylori) have several unique features in DNA replication machinery that makes it different from other microorganisms. To find out whether difference in DNA replication proteins behavior accounts for any difference in drug response when compared to E. coli, in the present study, we have tested E. coli beta-clamp inhibitor molecules against H. pylori beta-clamp. Various approaches were used to test the binding of inhibitors to H. pylori beta-clamp including docking, surface competition assay, complex structure determination, as well as antimicrobial assay. Out of five shortlisted inhibitor molecules on the basis of docking score, three molecules, 5-chloroisatin, carprofen, and 3,4-difluorobenzamide were co-crystallized with H. pylori beta-clamp and the structures show that they bind at the protein-protein interaction site as expected. In vivo studies showed only two molecules, 5-chloroisatin, and 3,4-difluorobenzamide inhibited the growth of the pylori with MIC values in micro molar range, which is better than the inhibitory effect of the same drugs on E. coli. Therefore, the evaluation of such drugs against H. pylori may explore the possibility to use to generate species-specific pharmacophore for development of new drugs against H. pylori. Screening of E. coli beta-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.,Pandey P, Verma V, Dhar SK, Gourinath S Antibiotics (Basel). 2018 Jan 11;7(1). pii: antibiotics7010005. doi:, 10.3390/antibiotics7010005. PMID:29324718[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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