Development of inhibitors to punish carbapenem-resistant acinetobacter baumannii

The National Institute of Allergy and Infectious Diseases awarded Emory University $100,228 on November 28, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855) to develop inhibitors targeting carbapenem-resistant Acinetobacter baumannii (CRAB).

The funded research focuses on structure-activity relationship studies and mechanism of action characterization of fendiline, a calcium channel blocker identified through high-throughput screening of FDA-approved small molecules. Prior work identified fendiline's potent activity against OXA-23-overexpressing strains of CRAB, with preliminary synthetic derivatives displaying fourfold better potency. The award supports continued optimization of fendiline analogs to increase activity against wild-type strains, leveraging diazirine photoaffinity probe methods to understand fendiline's protein targets and refine compound design.

Work is performed in Atlanta, Georgia. The period of performance runs through May 31, 2029. The assistance type is a project grant.

Abstract

Antibiotic resistance is a crisis that has been ongoing for decades, with 1 million deaths each year being directly caused by antibiotic resistance and predicted to rise to 2 million by 2050. Regardless of the evident need to uncover pharmacological solutions to this crisis, there have been scarce developments made in discovering new antibiotics that evade mechanisms of resistance, such as β-lactamase inhibitors. A bacterial pathogen that is of the highest concern is carbapenem-resistant acinetobacter baumannii (crab), a gram-negative bacterium. The crab strain of interest for this proposal is an OXA-23 overexpressing strain, to which OXA-23 is the most common β-lactamase in this bacterium. To address this issue, the rather lab performed a high-throughput screen of 3000+ FDA-approved small molecule drugs against a hyper-permeable and efflux-deficient OXA-23 overexpressing strain of AB. From this screen, fendiline, a calcium channel blocker, with no reported bactericidal activity was identified to have potent activity (MIC = 8 ΜG/ML) against the efflux deficient strain with the induction of OXA-23 expression. However, within wild-type (WT) strains, bactericidal activity lowered (MIC = 128 ΜG/ML). Further studies showed that the addition of a membrane permeabilizer, such as pmbn and colistin, increased activity back to MIC's ranging from 2-32 ΜG/ML in wild-type strains. Preliminary SAR studies have been conducted by synthesizing fendiline analogs that display 4-fold better potency and enantiomeric dependency in the WT strain. With the use of a diazirine photoaffinity probe, which covalently labels high-affinity protein targets upon irradiation, the mechanism of action (MOA) of fendiline was uncovered. The first goal of this proposal is to better understand the SAR of fendiline using the newly understand MOA to increase activity of the compounds in wild-type AB. To achieve this, regions of the fendiline scaffold have been highlighted that could lead to improvements in in drug accumulation and binding affinity. Within this goal, the hypothesis of the addition of a carboxylic acid to the fendiline scaffold to increase WT activity via increased drug accumulation and membrane permeability will be tested, as well as the addition of a primary ionizable amine. The second goal of this project is to test the synthesized analogs in clinically relevant strains of AB that are from various geographical and physiological sources. These small molecule drugs will be tested in combination with SPR741, an FDA-approved outer membrane permeabilizer, that is predicted to improve drug accumulation within the periplasm. This proposal will immensely aid my training as a medicinal chemist by providing me with hands-on training in drug discovery, as well as setting a synthetic foundation. In addition, this project aligns with my long-term career interests of working within the drug discovery field to repurpose and create new pharmaceuticals for the public.