Lead Optimization and Preclinical Development of a small molecule inhibitor of M. avium KasA

ABSTRACT. Non-tuberculous mycobacteria (NTM) constitute a major threat to global health with over 200,000 annual cases in the United States alone. Mycobacterium avium complex (MAC) infections are the most common cause of NTM pulmonary disease, producing a five-year all-cause mortality rate of 25%. M. avium (Mav) accounts for the majority of MAC with M. intracellulare (Mae) being the next most common pathogen in this group. MAC is usually treated with three drugs; however, the success rate of even multi-drug therapy is unacceptably low at ~60%. Furthermore, drug resistance can develop during treatment which may reduce cure rates to as low as 5%. Development of NTM-active drugs has lagged similar efforts for Mycobacterium tuberculosis (Mtb), the causative pathogen of tuberculosis (TB); however, important commonalities exist between these species. Both Mtb and MAC share similar liabilities in essential cell wall factors that could be good drug targets. For example, ethambutol (EMB) targets the biosynthesis of arabinogalactan, which is an essential cell wall component for both Mtb and MAC. EMB is part of first line anti-Mtb therapy and is also a cornerstone of multi-drug MAC regimens. Mycolic acids are another component of the mycobacterial cell wall that are similarly essential in both species. Mycolic acid biosynthesis is effectively targeted in Mtb by the first line drug isoniazid. Although isoniazid is not active against MAC because this complex lacks an enzyme necessary for isoniazid activation, we have developed JSF-3285, 4-fluoro-N-(3-methyl-1H-indazol-5-yl)butane-1-sulfonamide, which targets the ß-ketoacyl synthase KasA, another key enzyme in mycolic acid biosynthesis for both Mtb and MAC. JSF-3285 is highly effective against Mtb with a minimum inhibitory concentration (MIC) of 0.20 µM, excellent intracellular activity, oral bioavailability, pharmacokinetic (PK) profile in animals, and minimal toxicity, and it has an outstanding ability to increase total regimen potency in Mtb infected mice undergoing multi-drug treatments. This is critical as both Mtb and MAC infections are optimally treated with multi-drug regimens. JSF-3285 has an MIC of 3.1 – 6.2 µM against Mav, which is similar to the MICs of ethambutol and other pre-clinical and early clinical candidates against MAC; JSF-3285 potency against MAC can likely be further improved using an innovative blend of pharmaceutical drug discovery and development approaches. Here, we outline a proposal to deliver a first-in-class MAC KasA- targeting preclinical drug candidate as well as a backup candidate for effective therapy against MAC. We will also assemble a compound data package to share with the FDA in a pre-IND meeting with completion of non- GLP toxicology studies in two species. We will accomplish this in 2 aims: 1) Perform structure-based lead optimization of JSF-3285 to treat Mav and 2) Pursue the preclinical development of a Mav KasA-targeting compound.