Design and Synthesis of Metabolically stable Tricyclic-SpiroLactams inhibitors of Mycobacterium tuberculosis type-II NADH dehydrogenase: Structure–Activity and Structure–Property Relationship Studies

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a critical global health challenge, as treatment efficacy is increasingly undermined by a high incidence of drug-resistant cases. Consequently, it is critical that novel antibiotics against Mtb are developed. Tricyclic spirolactam (TriSLa)-based inhibitors of mycobacterial type II NADH dehydrogenases (Ndh and NdhA) are a promising and novel class of anti-mycobacterial antibiotics that are efficacious in a zebrafish larvae model of M. marinum infection. However, the relatively low metabolic stability of the original TriSLa inhibitors prevented their evaluation in a murine model of Mtb infection. Here we report an extensive structure−activity relationship (SAR) and structure-property relationship (SPR) study of the TriSLa scaffold, leading to the discovery BDM91465 (compound 45), a potent and metabolically stable analog. The cryo-EM structure of BDM91465 bound to Ndh reveals the precise binding pocket of TriSLas and is consistent with the SAR. The tricyclic spirolactam core binds within the menaquinone pocket, with the distal aromatic rings embedded in the protein-micelle interface. Pharmacokinetic studies conducted on BDM91465 confirmed its bioavailability and low clearance, which together equated to extensive exposure above the antibioitic MIC. In vivo efficacy studies of BDM91465 found it to attenuate the growth of Mtb in mice, in line with results generated by the genetic inactivation of Ndh-2. Together this work provides a first example of the in vivo efficacy of an Ndh-2 inhibitor in a murine model of Mtb infection, confiming the proteins in vivo vulnerability and drugability and paving the way for the development of new anti-TB regimens.