Target-Based Design of Promysalin Analogues Identifies a New Putative Binding Cleft in Succinate Dehydrogenase

Abstract

Promysalin is a small-molecule natural product that specifically inhibits growth of the Gram-negative pathogen Pseudomonas aeruginosa (PA). This activity holds promise in the treatment of multidrug resistant infections found in immunocompromised patients with chronic illnesses, such as cystic fibrosis. In 2015, our lab completed the first total synthesis; subsequent analogue design and SAR investigation enabled identification of succinate dehydrogenase (Sdh) as the biological target in PA. Herein, we report the target-guided design of new promysalin analogues with varying alkyl chains, one of which is on par with our most potent analogue to date. Computational docking revealed that some analogues have a different orientation in the Sdh binding pocket, placing the terminal carbon proximal to a tryptophan residue. This inspired the design of an extended side chain analogue bearing a terminal phenyl moiety, providing a basis for the design of future analogues.

Structure-Based Design of Promysalin Analogues to Overcome Mechanisms of Bacterial Resistance

“…Due to the lack of an available crystal structure of PA Sdh, we utilized a homology model of the enzyme derived from Escherichia coli generated by the Karanicolas group for structural guidance. 24 Docking studies of promysalin in the ubiquinone binding site of this model reveal a nonpolar pocket composed of alanine, leucine, and isoleucine residues, which presumably stabilize the aliphatic side chain of promysalin through the hydrophobic effect. Additionally, hydrogen-bonding interactions to the nearby Tyr83, Ser27, and backbone of Ala24 are predicted to stabilize the amide terminus of promysalin's side chain (Figure 2A).…”

“…We were therefore interested in the investigation of the characteristics of the PA Sdh ubiquinone binding site adjacent to the anticipated localization of promysalin’s side chain (Figure ). Due to the lack of an available crystal structure of PA Sdh, we utilized a homology model of the enzyme derived from Escherichia coli generated by the Karanicolas group for structural guidance …”

Macrooxazoles A–D, New 2,5-Disubstituted Oxazole-4-Carboxylic Acid Derivatives from the Plant Pathogenic Fungus Phoma macrostoma

“…(R)-4-Benzyl-3-(hept-6-enoyl)oxazolidin-2-one ( 8 ) [ 25 ]: 6-Heptenoic acid ( 7 ; 100 μL, 738 μmol) in dry CH 2 Cl 2 (1 mL) at 0 °C was treated with DMAP (dimethylaminopyridine; 8.20 mg, 738 μmol), (R)-benzyl-2-oxazolidinone (119 mg, 671 μmol) and DCC (dicyclohexylcarbodiimide;152 mg, 738 μmol). The mixture was stirred for 23 h at room temperature.…”

Succinate Dehydrogenase, Succinate, and Superoxides: A Genetic, Epigenetic, Metabolic, Environmental Explosive Crossroad

“…Siccanin is another SDH inhibitor, initially isolated from a pathogenic fungus, that has been recently proposed as a new chemotherapeutic agent [ 146 ]. Promysalin, a secondary metabolite targeting SDH, produced by the bacteria Pseudomonas putida has been proposed to inhibit the growth of another Pseudomonas, namely the Gram-negative pathogen Pseudomonas aeruginosa [ 147 , 148 ]. SDH inhibitors are also found as secondary metabolites in various strains of Penicillium roqueforti used in the famous French Roquefort cheese.…”