Open Source Antibiotics: Simple Diarylimidazoles Are Potent against Methicillin-Resistant Staphylococcus aureus

Abstract

Antimicrobial resistance (AMR) is widely acknowledged as one of the most serious public health threats facing the world, yet the private sector finds it challenging to generate much-needed medicines. As an alternative discovery approach, a small array of diarylimidazoles was screened against the ESKAPE pathogens, and the results were made publicly available through the Open Source Antibiotics (OSA) consortium (https://github.com/opensourceantibiotics). Of the 18 compounds tested (at 32 μg/mL), 15 showed >90% growth inhibition activity against methicillin-resistant Staphylococcus aureus (MRSA) alone. In the subsequent hit-to-lead optimization of this chemotype, 147 new heterocyclic compounds containing the diarylimidazole and other core motifs were synthesized and tested against MRSA, and their structure-activity relationships were identified. While potent, these compounds have moderate to high intrinsic clearance and some associated toxicity. The best overall balance of parameters was found with OSA_975, a compound with good potency, good solubility, and reduced intrinsic clearance in rat hepatocytes. We have progressed toward the knowledge of the molecular target of these phenotypically active compounds, with proteomic techniques suggesting TGFBR1 is potentially involved in the mechanism of action. Further development of these compounds toward antimicrobial medicines is available to anyone under the licensing terms of the project.

Keywords: Drug discovery; antibacterials; antibiotics; bioactive molecules; open science; organic synthesis.

Figure 1

Literature optimization of diarylimidazole SB-400868A to generate ALK5 inhibitors and structure of a representative compound investigated in this work (OSA_822) toward compounds potent vs MRSA.

Scheme 1. Synthetic Routes to (A) General (Aryl–Aryl Linkage) Analogues and (B) N-Linked Analogues

Reagents and conditions for part A: (a) 2, DMF, 100 °C, 18 h; (b) NBS, DCM, rt, 1 h; (c) ArB(OH)₂ or ArB(pin), Na₂CO₃, Pd(PPh₃)₄ or PdCl₂(dppf)CH₂Cl₂, 3:1 PhMe:EtOH, 120 °C, 18 h (conventional heating) or 30 min (μW reactor); (d) 6, NaHCO₃, MeOH, reflux, 12 h; (e) 8, formalin (37% aq.), acetic acid, DCM, 18 h. Reagents and conditions for part B: (f) Yb(OTf)₃, 120 °C, 30 min (μW reactor); (g) 14, Cs₂CO₃, DMF, rt, 18 h. A phenyl ring containing a central “N” denotes a general (aza)aromatic. Yields are described in Supplementary Information - Chemistry.

Figure 2

Heat map of in vitro potency against MRSA of analogues with variations in the northwest and southwest substituents. Color gradient: green <4 μg/mL; yellow <16 μg/mL; red = 32 μg/mL.

Figure 3

Heat map of in vitro potency against MRSA of analogues containing fused bicyclic cores. Color gradient: green <4 μg/mL; yellow <16 μg/mL; red = 32 μg/mL.

Figure 4

Human and rat liver microsome and hepatocyte intrinsic clearance data and mammalian cell line toxicity results. MRSA MIC data units are μg/mL. Selectivity index (SI) = ratio of cytotoxic TC₅₀ to MRSA MIC.

Figure 5

Structure and MRSA activity of a metabolite of 821.

Figure 6

(a) D_max classification: compound toxicity at highest concentration is mapped against recovery status and detection output; compounds where D_max is lower than 50% are deemed non-toxic. (b) CC₅₀ classification: concentrations resulting in 50% reduction in viability were calculated by fitting logistic curves to viability data.

Figure 7

MIBs competition assay reveals potential kinase selectivity in mammalian cells. Shown is a subset of the kinome competition results from the incubation of HEK293 cell lysate with compounds 822 (active) and 820 (inactive). Following a brief incubation with these compounds, lysates were passed over MIBs (see Supporting Information - Biology), and the captured kinases were identified and quantified by mass spectrometry. Displaced kinases are shown to the left of the center line at the designated doses.