Abstract

The relaxed complex scheme, a virtual-screening methodology that accounts for protein receptor flexibility, was used to identify a low-micromolar, non-bisphosphonate inhibitor of farnesyl diphosphate synthase. Serendipitously, we also found that several predicted farnesyl diphosphate synthase inhibitors were low-micromolar inhibitors of undecaprenyl diphosphate synthase. These results are of interest because farnesyl diphosphate synthase inhibitors are being pursued as both anti-infective and anticancer agents, and undecaprenyl diphosphate synthase inhibitors are antibacterial drug leads.

Highlights

  • Two interesting new anti-infective targets involved in isoprenoid biosynthesis are farnesyl diphosphate synthase (FPPS) and undecaprenyl diphosphate synthase (UPPS) [18,19,20,21]

  • FPPS catalyzes the condensation of dimethylallyl diphosphate (DMAPP) with isopentenyl diphosphate (IPP) to form geranyl diphosphate (GPP) and thence, farnesyl diphosphate (FPP) [22], while UPPS elongates FPP via cis double-bond addition to produce undecaprenyl diphosphate (UPP) (Figure 1) [19]

  • Molecular dynamics (MD) simulations As the molecular motions of protein receptors play a critical role in ligand binding, we first studied FPPS dynamics before attempting to computationally identify non-bisphosphonate FPPS inhibitors

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Summary

Introduction

FPPS catalyzes the condensation of dimethylallyl diphosphate (DMAPP) with isopentenyl diphosphate (IPP) to form geranyl diphosphate (GPP) and thence, farnesyl diphosphate (FPP) [22], while UPPS elongates FPP via cis double-bond addition to produce undecaprenyl diphosphate (UPP) (Figure 1) [19]. Both enzymes are essential for bacterial cell growth, and UPPS is of particular interest because it is absent in humans.

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