Homology modeling, virtual screening and docking potential inhibitors of Shigella flexneri DHPS

Abstract

Increasing cases of resistance against Shigella flexneri (The bacteria responsible for Shigellosis) have encouraged the development of new antibiotics. Dihydropteroate synthase (DHPS) is an enzyme involved in folate biosynthesis pathway that has been targeted by sulfonamide drugs. DHPS mutations in PABA binding pocket were associated with sulfonamide resistance. However, it does not affect DHPPP binding site or also known as pterin pocket. This research aims to search for novel compounds that can potentially bind and inhibit Shigella flexneri DHPS on pterin pocket using AMPPD (Inhibitor of E. coli DHPS targeting pterin pocket) as a positive control employing in silico structure-based drug discovery. The main steps of this research were to build three-dimensional structure of Shigella flexneri DHPS using homology modeling with SWISS-MODEL and to perform virtual screening and docking on natural product database via MTi Open Screen webserver. Three-dimensional structure of Shigella flexneri DHPS was constructed using E.coli DHPS crystal structure as a template having 100% sequence identity and 1.7 A resolution. Based on the virtual screening results, three natural product compounds showed the highest binding affinity from -8,8 kcal/mol to -9,5 kcal/mol with Shigella flexneri DHPS as compared to AMPPD. They also occupied the same pterin binding pocket. It suggests that those three natural compounds could be potential inhibitors of Shigella flexneri DHPS targeting the pterin binding pocket. Hence, those compounds warrant further investigation by in vitro and in vivo experiments for validation.