Recent advances in mycobacterial membrane protein large 3 inhibitor drug design for mycobacterial infections

Abstract

Introduction: Tuberculosis and nontuberculous mycobacterial infections are notoriously difficult to treat, requiring long-courses of intensive multi-drug therapies associated with adverse side effects. To identify better therapeutics, whole cell screens have identified novel pharmacophores, a surprisingly high number of which target an essential lipid transporter known as MmpL3.

Areas covered: This paper summarizes what is known about MmpL3, its mechanism of lipid transport and therapeutic potential, and provides an overview of the different classes of MmpL3 inhibitors currently under development. It further describes the assays available to study MmpL3 inhibition by these compounds.

Expert opinion: MmpL3 has emerged as a target of high therapeutic value. Accordingly, several classes of MmpL3 inhibitors are currently under development with one drug candidate (SQ109) having undergone a Phase 2b clinical study. The hydrophobic character of most MmpL3 series identified to date seems to drive antimycobacterial potency resulting in poor bioavailability, which is a significant impediment to their development. There is also a need for more high-throughput and informative assays to elucidate the precise mechanism of action of MmpL3 inhibitors and drive the rational optimization of analogues.

Keywords: MmpL3; Mycobacterium; drug development; mycolic acids; non-tuberculous mycobacteria; tuberculosis.

Figure 1:. Schematic representation of the M. tuberculosis cell envelope.

Mycolic acid chains, major constituents of the OM of mycobacteria, are shown in red. MmpL3 is an inner membrane transporter that participates in the export of mycolic acids under the form of trehalose monomycolates (TMM) to the periplasmic space. The carrier(s) involved in the transport of TMM across the periplasmic space are not known. Once exported across the inner membrane and periplasm, mycolic acids are transferred by dedicated transferases onto either arabinogalactan (generating cell wall-bound mycolates) or another molecule of TMM to form outer membrane trehalose dimycolates (TDM). The overall schematic and individual structures are not drawn to scale. AG, arabinogalactan; IM, inner membrane; LAM, lipoarabinomannan; LM, lipomannan; OM, outer membrane; PG, peptidoglycan; PIM, phosphatidylinositol mannosides.

Figure 2:

A. Structure of a MmpL3 monomer (PDB ID: 6AJF) with the R1 and R2 repeats shown in teal and yellow, respectively. The TM2 and TM8 helices responsible for coupling of substrate efflux with proton translocation are shown in blue and orange, respectively. Two molecules of 6-n-dodecyl-α,α’-trehalose bound to the two binding sites in the periplasmic porter domain of MmpL3 are shown in green. B. Periplasmic view of the essential residues in TM4 and TM10 of MmpL3 (PDB ID: 6AJF). C. Stable docked complexes for an indolcarboxamide compound (compound 69 from ref.[70]). Dotted lines indicate hydrophobic interactions, and solid blue lines indicate hydrogen bonding. Yellow = inhibitor carbon atoms, blue = nitrogen atoms, lime green = chlorine atom, red = oxygen atoms, green = MmpL3 amino acid residues’ carbon atoms, light blue = fluorine atoms. Three subsites are indicated as layers with the Layer 2 containing the essential residues involved in proton translocation.

Figure 3:

Lead MmpL3 inhibitor scaffolds with potent whole cell mycobacterial MIC values.

Figure 4:

(A) Structural similarities between the diphenylpyrole scaffold and SQ109. (B) Design of the acetamide scaffold.