The central objective of Project 1 is to identify candidate ClpC1 modulators for translation into clinical anti- tuberculosis (TB) drugs. As recently emphasized by the NIAID Director, new oral TB drugs are sorely needed. Our work and that of others has identified ClpC1 as a novel protein target for TB treatment. Known natural product (NP) ClpC1 modulators display favorable in vitro anti-Mycobacterium tuberculosis (Mtb) properties, suggesting that TB drugs acting on this target would have utility against multi-drug/extensively drug-resistant (MDR/XDR)- TB, with potential to shorten treatment. The pharmacokinetic (PK) properties of the known ClpC1 modulators, ecumicin, rufomycin, cyclomarin-A and lassomycin, preclude direct use of these NP cyclic peptides as oral TB drugs. Thus, Project 1 seeks to identify and develop novel orally bioavailable ClpC1 modulators with potential for use within the TB treatment regimens envisioned in this CETR. Diverse approaches to lead identification include: identifying new NPs and novel small molecule ClpC1 modulators, and optimizing properties of known NPs. Each approach will leverage leading edge technologies in peptide chemistry, structure-based drug design (SBDD), NP discovery, and fragment-based drug design. Lead finding and optimization will utilize four orthogonal biophysical approaches to understand key factors in binding to ClpC1: surface plasmon resonance (SPR), X-ray crystallography, NMR, and Cryo-EM. Nanoencapsulation work aims at optimizing exposure of ecumicin, to fully explore its efficacy profile in Mtb-infected mice. The UIC Project 1 team is uniquely positioned to follow these objectives, having pioneered new NP technologies with unique utility in drug discovery and lead validation that led to the discovery, from actinomycetes, of ecumicin and rufomycin. UIC also conducted extensive work to gain mechanistic insights that demonstrate the vulnerability of Mtb ClpC1 protease, underpinning the proposed activities. Research conducted at UIC will help drive the translation of ClpC1 as an anti-Mtb drug target.
The Specific Aims of Project 1also have strong collaborative ties within the CETR. [AIM 1] is to optimize exposure of NP ClpC1 modulators to explore their anti-Mtb efficacy. This involves collaborations with Myongji (scale-up production) and Princeton University (nano-encapsulation for enhanced in vivo efficacy). Purity and NP integrity analysis of the oligopeptides will employ UIC?s qNMR methodology. PK and efficacy studies will be conducted w/Cores A+B. [AIM 2] will employ diverse approaches (large-scale NP isolation and characterization; NP-inspired structure-/SAR-guided design, NMR screening) to identify novel and orally available ClpC1 modulators. The array of methods involves Molecular Networking at UIC, fragment-based screening via collaboration with Eli Lilly, ClpC1 functional assays with Project 2, and at Core A, peptide and medicinal chemistry, SBDD, in vitro ADME, and mouse PK. [AIM 3] seeks to evaluate key factors in ClpC1 binding affinity of NPs, synthetic cyclic peptides and small molecules by using SPR, NMR, Cryo-EM, and co-crystallization X-ray analysis.
Aim 3 will also optimize leads emerging from Aim 2, followed by candidate selection and IND-enabling studies through Core C.
