Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs)

Abstract

Virtual screening was employed to identify new drug-like inhibitors of NAD synthetase (NADs) as antibacterial agents. Four databases of commercially available compounds were docked against three subsites of the NADs active site using FlexX in conjunction with CScore. Over 200 commercial compounds were purchased and evaluated in enzyme inhibition and antibacterial assays. 18 compounds inhibited NADs at or below 100 μM (7.6% hit rate), and two were selected for future SAR studies.With the increasing threat of pathogens, such as Bacillus anthracis, being used as bioweapons, 1 and the rise in the incidence of multi-drug resistant bacteria, 2 the need for new antibiotics that act at novel targets has never been greater. Previous studies within this group 3-5 have revealed that inhibition of one such target, the amidotransferase enzyme nicotinamide adenine dinucleotide (NAD) synthetase (NADs), could hinder both spore outgrowth and vegetative growth, which would provide antibacterial action at two different steps in the bacterial life cycle. 6-10The first class of NADs inhibitors designed by this group consisted of tethered dimers that contain two hydrophobic groups linked by a polymethylene tether, and a positively charged nitrogen on one end. 3-5 These inhibitors were antibacterial, and there was a correlation between the potencies of enzyme inhibition and antibacterial effects. However, the permanent positive charge and detergent-like properties of this class of compounds were unattractive for further drug development. 11,12 More drug-like lead inhibitors were, therefore, sought.Virtual screening of compound databases using the detailed structure of the drug target can serve to greatly enhance success in the lead discovery process. 13-17 Here we use the in silico screening program FlexX 1.20.1(BiosolveIT GmbH ® ) for the virtual screening of commercially available compounds within the catalytic site of NADs to identify new classes *Corresponding author. Tel. +1 205 934 8288; FAX +1 205 934 2543. Email address: wbrou@uab.edu (W. Brouillette). Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.Supplementary Data Supplementary data, including (a) structures of compounds from Table 1 not shown in Table 2, (b) graphical representations of the binding sites used and poses of selected docked ligands, and (c) a sample HPLC-chromatogram used in the enzyme assay, can be found in the online version. NADs is a large homodimer of approximately 60 kDa that contains two identical binding sites. The crystal structure of the protein from B. subtilis reveals two identical long, linear bind...

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