Targeting NAD Biosynthesis in Bacterial Pathogens: Structure-Based Development of Inhibitors of Nicotinate Mononucleotide Adenylyltransferase NadD

Abstract

SUMMARY The emergence of multidrug-resistant pathogens necessitates the search for new antibiotics acting on previously unexplored targets. Nicotinate mononucleotide adenylyltransferase of the NadD family, an essential enzyme of NAD biosynthesis in most bacteria, was selected as a target for structure-based inhibitor development. Using iterative in silico and in vitro screens we identified small molecule compounds that efficiently inhibited target enzymes from Escherichia coli (ecNadD) and Bacillus anthracis (baNadD) but had no effect on functionally equivalent human enzymes. On-target antibacterial activity was demonstrated for some of the selected inhibitors. A 3D structure of baNadD was solved in complex with one of these inhibitors (3_02) providing mechanistic insights and guidelines for further improvement. Most importantly, the results of this study help validate NadD as a target for the development of antibacterial agents with potential broad-spectrum activity.

Genomics-driven Reconstruction of Acinetobacter NAD Metabolism

“…Moreover, enzymes of NadM, and not NadD, family are universally present in Archaea where they are expected to play the NaMNAT role in the de novo synthesis of NAD (38). 5 To distinguish between these two possibilities, in this study we set to experimentally determine the actual substrate preference of the purified recombinant abNadM and to use genetic techniques to address yet another (albeit unlikely) possibility; that is, the existence of an alternative NaMNAT nonhomologous to previously characterized enzymes.…”

“…Targeting essential enzymes involved in the biosynthesis of NAD(P), the indispensable redox cofactor, has been recognized as a promising strategy for the development of novel antibiotics (4,5,10,12). However, the rational choice of actual drug targets requires better understanding of pathways that comprise NAD metabolic subnetworks, especially in divergent and poorly explored organisms such as pathogenic species of Acinetobacter.…”

“…At the same time, the NadM (and not NadD) family is universally present in nearly all Archaea where it appears to function as the housekeeping NaMNAT/ NMNAT enzyme in NAD biogenesis. 5 None of the analyzed archaeal genomes revealed a presence of the bacterial-like NadM-NudF fusion protein. These observations as well as characteristic variations in gene patterns associated with deamidating and nondeamidating Nm salvage/recycling routes point to a likely archaeal origin of bacterial NadM (see supplemental Table S4 and the accompanying comments suggesting a possible evolutionary scenario).…”

“…Some isolates of A. baumannii display resistance to many known antibiotics (1,2), emphasizing the importance of pursuing new therapeutic targets for drug development. Biogenesis of nicotinamide adenine nucleotide (NAD), an indispensable cofactor involved in a multitude of biochemical transformations in metabolic networks of all species, was recently established as a target pathway for the development of new antibiotics (3)(4)(5)(6)(7). Beyond its main function as a redox cofactor, NAD is consumed as a co-substrate by a number of nonredox enzymes such as bacterial DNA ligase and protein deacetylase of the CobB/Sir2 family (8,9).…”

Quinolinate Salvage and Insights for Targeting NAD Biosynthesis in Group A Streptococci

“…1). The development of smallmolecule inhibitors targeting representative bacterial NadD and NadE enzymes that suppress the growth of various bacteria supported the choice of these enzymes as prospective broad-spectrum drug targets (6,(13)(14)(15)(16)(17)(18).…”