SecA inhibitors as potential antimicrobial agents: differential actions on SecA-only and SecA-SecYEG protein-conducting channels

Abstract

Sec-dependent protein translocation is an essential process in bacteria. SecA is a key component of the translocation machinery and has multiple domains that interact with various ligands. SecA acts as an ATPase motor to drive the precursor protein/peptide through the SecYEG protein translocation channels. As SecA is unique to bacteria and there is no mammalian counterpart, it is an ideal target for the development of new antimicrobials. Several reviews detail the assays for ATPase and protein translocation, as well as the search for SecA inhibitors. Recent studies have shown that, in addition to the SecA-SecYEG translocation channels, there are SecA-only channels in the lipid bilayers, which function independently from the SecYEG machinery. This mini-review focuses on recent advances on the newly developed SecA inhibitors that allow the evaluation of their potential as antimicrobial agents, as well as a fundamental understanding of mechanisms of SecA function(s). These SecA inhibitors abrogate the effects of efflux pumps in both Gram-positive and Gram-negative bacteria. We also discuss recent findings that SecA binds to ribosomes and nascent peptides, which suggest other roles of SecA. A model for the multiple roles of SecA is presented.

Figure 1.

Proposed multiple roles of SecA; (a) Soluble, symmetric dimer SecA (cryo-EM image; Chen et al.2008); (b) Membrane-associated, asymmetric ring-pore structures (TEM image of SecA on the lipids, Wang et al.2003); (c) Membrane-associated, SecA-only protein conducting channels, which are active for proteins with or without signal peptides (albeit inefficiently) in ion channel activity and protein translocation (Hsieh et al.; You et al.2013), (d) More efficient SecA-SecYEG-DFC channels require precursors with signal peptides, and can be converted from SecA-only channels (TEM image of SecA-SecYEG, Tang et al.2011); (e) SecA binds to ribosomes (cryo-EM-based SecA-ribosome structures from Singh et al.2014), presumably leading to (f) SecA-mediated co-translational translocation with the exiting nascent peptide providing the sole source for stable association of ribosome and membrane? (Smith et al., , ; Herskovits and Bibi ; Halbedel et al.; Rawat et al.; Wang, Yang and Shan 2017)

Figure 2.

Three classes of small molecule SecA inhibitors: Class A, RB analogs; Class B, Thiouracil-pyrimidine analogs and Class C, Triazole-pyrimidine analogs (From Jin et al.2016).

Figure 3.

Molecular modeling of three classes of small molecule SecA inhibitors. The program used is SYBYL 2.0 for file PDB ID- 2FSG with SecA dimers A and B. (A) Class A inhibitor (see Fig. 2), SCA-50, binds close to the ATP site of monomer B; (B) Class B inhibitor, SCA-15, binds at the interface of A and B; close to the ATP site of the B momoner and (C) Class C inhibitor, SCA-107, binds to the interface of A and B monomers (slightly closer to the ATP site of A, partially blocking the entrance to this ATP site). SCA-15 binds relatively closer to ATP site of the B monomer, followed by SCA-50, then the SCA-107. At the interface, SCA-15 binds to the B monomer, facing the A monomer. Lower panels: Inhibitors bindings relative to surrounding amino acid residues. (SCA-50 modified from Jin et al., SCA-15 from Chaudhary et al., SCA-107, from Cui et al.2016).