Structure-based design of RelSeq inhibitors: growth of an amino benzoic acid fragment

Bacterial resistance to antibiotics is a naturally occurring process that has been greatly accelerated by their misuse, resulting in an ever-increasing danger to global health. The bacterial genetic mutants that can specifically target and disarm an antibiotic’s mode of action, have long been known. As has the more obscure antibiotic tolerant variants, individuals found in isogenic populations, termed persisters. These elusive sub-populations are in a transient reduced metabolic state, sometimes occurring without environmental pressures. They can be multidrug tolerant and are a common cause of chronic infections, as is the case for opportunistic infections in cystic fibrosis patients. Furthermore, persisters have been credited as an evolutionary stepping stone to antibiotic resistance.[1] Persisters’ phenotypic downregulation of metabolism has a tight association with the stringent response and is therefore believed to be activated by the accumulation of the intracellular signalling alarmone, guanosine penta- or tetra-phosphate, (p)ppGpp.[2] The cellular concentration of (p)ppGpp is controlled by the superfamily of RSH (RelA/ SpoT Homologue) proteins (Fig.1), making them potential drug targets for drug development to reduce chronic infections and help curtail antibiotic resistance. The main objective of this study is to design small molecules to selectively inhibit the synthetase domain of Rel proteins. RelSeq from S. equisimilis has been chosen as our model protein. Among the chemotypes identified through in silico screening,[3,4] we present here the growth of the amino benzoic acid fragment into the first family of synthetase selective Rel inhibitors.[5] References (1) Levin-Reisman, et.al., Antibiotic Tolerance Facilitates the Evolution of Resistance. Science 2017, 355 (6327), 826–830.. (2) Irving, S. E., et.al. The Stringent Response and Physiological Roles of (Pp)PGpp in Bacteria. Nat. Rev. Microbiol. 2021, 19 (4), 256–271. (3) Civera, M.; Sattin, S. Homology Model of a Catalytically Competent Bifunctional Rel Protein. Front. Mol. Biosci. 2021, 8, 628596. (4) Coppa, C., et. al.,New Chemotypes for the Inhibition of (p)PpGpp Synthesis in the Quest for New Antimicrobial Compounds. Molecules. 2022, 27 (10), 3097. (5) Sattin, S., et. al. Manuscrtipt in preperation, 2023.