Virtual Screening and Experimental Verification to Identify Potential Inhibitors of the ErmC Methyltransferase Responsible for Bacterial Resistance against Macrolide Antibiotics

Abstract

Methyltransferases from the Erm family catalyze S-adenosyl-L-methionine-dependent modification of a specific adenine residue in bacterial 23S rRNA, thereby conferring resistance to clinically important macrolide, lincosamide, and streptogramin B antibiotics. Thus far, no inhibitors of these enzymes have been identified or designed that would effectively abolish the resistance in vivo. We used the crystal structure of ErmC' methyltransferase as a target for structure-based virtual screening of a database composed of 58,679 lead-like compounds. Among 77 compounds selected for experimental validation (63 predicted to bind to the catalytic pocket and 14 compounds predicted to bind to the putative RNA binding site), we found several novel inhibitors that decrease the minimal inhibitory concentration of a macrolide antibiotic erythromycin toward an Escherichia coli strain that constitutively expresses ErmC'. Eight of them have IC(50) values in the micromolar range. Analysis of docking models of the identified inhibitors suggests a novel strategy to develop potent and clinically useful inhibitors.

Structural Rearrangements in the Active Site of the Thermus thermophilus 16S rRNA Methyltransferase KsgA in a Binary Complex with 5′-Methylthioadenosine

“…The orientation of the equivalent Tyr104 in ErmC’ corresponds to the orientation of Tyr120 as observed in the KsgA3 crystal form. Tyr104 was found to be indispensable for ErmC’ function35 and computational docking calculations with ErmC’ indicated that a similar rearrangement of Tyr104 is likely to occur in this enzyme36. Together, these observations suggest that the conformational flexibility that we observed for the loop region near Tyr120 may have a function in coordinating the substrate base analogous to Tyr108 in M.TaqI.…”

Antibiotic adjuvants: identification and clinical use

“…The adjuvant cilastatin inhibits the action of this enzyme and protects imipenem from degradation prolonging its antibacterial effect when given in combination (Balfour et al ., ) (Table ). Inhibitors for aminoglycoside‐modifying enzymes and erythromycin ribosomal methylases have also been identified (Feder et al ., ; Vong et al ., ), but none of them has been considered sufficiently potent for further development as antibiotic adjuvants. Another way of preventing antibiotic degradation is by targeting the bacterial regulatory systems involved in the expression of antibiotic resistance genes.…”

Virtual screening strategies in drug design – methods and applications

“…A list of widely used protein-ligand docking software (Sousa et al, 2006). The main strengths and weaknesses are based on the work by Kellenberger et al, 2004, and (Feder et al, 2008) Hepatitis C virus NS5B polymerase inhibitors (Musmuca et al, 2010) summarized in Table 3 (Sousa et al, 2006). Although most of them require a commercial license, academic users and researchers can experiment using freely available software like DOCK (Lang et al, 2009) or Auto-Dock Vina (Trott and Olson, 2010).…”