Discovery of Imidazo[1,2-a]pyridine Ethers and Squaramides as Selective and Potent Inhibitors of Mycobacterial Adenosine Triphosphate (ATP) Synthesis.

The approval of bedaquiline to treat tuberculosis has validated adenosine triphosphate (ATP) synthase as an attractive target to kill Mycobacterium tuberculosis (Mtb). Herein, we report the discovery of two diverse lead series imidazo[1,2-a]pyridine ethers (IPE) and squaramides (SQA) as inhibitors of mycobacterial ATP synthesis. Through medicinal chemistry exploration, we established a robust structure-activity relationship of these two scaffolds, resulting in nanomolar potencies in an ATP synthesis inhibition assay. A biochemical deconvolution cascade suggested cytochrome c oxidase as the potential target of IPE class of molecules, whereas characterization of spontaneous resistant mutants of SQAs unambiguously identified ATP synthase as its molecular target. Absence of cross resistance against bedaquiline resistant mutants suggested a different binding site for SQAs on ATP synthase. Furthermore, SQAs were found to be noncytotoxic and demonstrated efficacy in a mouse model of tuberculosis infection.

Whole cell screen based identification of spiropiperidines with potent antitubercular properties.

Whole cell based screens to identify hits against Mycobacterium tuberculosis (Mtb), carried out under replicating and non-replicating (NRP) conditions, resulted in the identification of multiple, novel but structurally related spiropiperidines with potent antitubercular properties. These compounds could be further classified into three classes namely 3-(3-aryl-1,2,4-oxadiazol-5-yl)-1'-alkylspiro[indene-1,4'-piperidine] (abbr. spiroindenes), 4-(3-aryl-1,2,4-oxadiazol-5-yl)-1'-alkylspiro[chromene-2,4'-piperidine] (abbr. spirochromenes) and 1'-benzylspiro[indole-1,4'-piperidin]-2(1H)-one (abbr. spiroindolones). Spiroindenes showed ⩾ 4 log10 kill (at 2-12 µM) on replicating Mtb, but were moderately active under non replicating conditions. Whole genome sequencing efforts of spiroindene resistant mutants resulted in the identification of I292L mutation in MmpL3 (Mycobacterial membrane protein Large), required for the assembly of mycolic acid into the cell wall core of Mtb. MIC modulation studies demonstrated that the mutants were cross-resistant to spirochromenes but not to spiroindolones. This Letter describes lead identification efforts to improve potency while reducing the lipophilicity and hERG liabilities of spiroindenes. Additionally, as deduced from the SAR studies, we provide insights regarding the new chemical opportunities that the spiroindolones can offer to the TB drug discovery initiatives.

Computational and experimental investigations of mono-septanoside binding by Concanavalin A: correlation of ligand stereochemistry to enthalpies of binding.

Structure-energy relationships for a small group of pyranose and septanose mono-saccharide ligands are developed for binding to Concanavalin A (ConA). The affinity of ConA for methyl "manno"ß-septanoside 7 was found to be higher than any of the previously reported mono-septanoside ligands. Isothermal titration calorimetry (ITC) in conjunction with docking simulations and quantum mechanics/molecular mechanics (QM/MM) modeling established the specific role of binding enthalpy in the structure-energy relations of ConA bound to natural mono-saccharides and unnatural mono-septanosides. An important aspect in the differential binding among ligands is the deformation energy required to reorganize internal hydroxyl groups upon binding of the ligand to ConA.

Stereoselectivity in the epoxidation of carbohydrate-based oxepines.

The facial selectivity in the DMDO epoxidation of carbohydrate-based oxepines derived from glucose, galactose, and mannose has been determined by product analysis and density functional theory (DFT, B3LYP/6-31+G**//B3LYP/6-31G*) calculations. Oxepines 3 and 4, derived from d-galactose and d-mannose, largely favor alpha- over beta-epoxidation. The results reported here, along with selectivities in the DMDO-mediated epoxidation of d-xylose-based oxepine 1 and d-glucose-based oxepines 2 and 5 reported earlier, support a model in which electronic effects, guided by the stereochemistry of the oxygens on the oxepine ring, largely determine the stereoselectivity of epoxidation. Other contributing factors included conformational issues in the oxepine's transition state relative to the reactant, the asynchronicity in bond formation of the epoxide, and the overall steric bulk on the alpha- and beta-faces of the oxepine. Considered together, these factors should generally predict facial selectivity in the DMDO-epoxidation of cyclic enol ethers.

Polyhydroxylated homoazepanes and 1-deoxy-homonojirimycin analogues: Synthesis and glycosidase inhibition study.

The Johnson-Claisen rearrangement of D-gluco and L-ido-derived allylic orthoesters afforded gamma,delta-unsaturated ester that on ester reduction, epoxidation, regioselective oxirane opening by sodium azide and hydrogenation led to sugar amino alcohols--immediate precursors for 1-deoxy-homonojirimycin 3a,b, and polyhydroxylated homoazepanes 4a,b. Our synthetic approach and glycosidase inhibitory activity is reported.

Synthesis of pentahydroxy indolizidine alkaloids using ring closing metathesis: attempts to find the correct structure of uniflorine A.

Ring closing metathesis of d-glucose derived diene-substrate containing nitrogen functionality followed by asymmetric dihydroxylation afforded sugar substituted dihydroxylated pyrrolidines 8a-c which on 1,2-acetonide deprotection and reductive amination afforded putative uniflorine A 2a and its analogues 2b-c, respectively.

Synthesis of tetrahydroxy perhydroaza-azulenes: tandem Johnson-Claisen rearrangement of D-glucose-derived allylic alcohols.

The Johnson-Claisen rearrangement of D-glucose-derived allylic alcohols 5a,b, afforded sugar-substituted gamma,delta-unsaturated ester in high yield. Conversion of the ester group to an azidomethyl group, epoxidation of the double bond and hydrogenation gave pyrrolidine ring skeletons 13a and 13b, which were transformed to tetrahydroxy perhydroaza-azulenes 1a and 1b, respectively. Glycosidase inhibitory activity was also evaluated.

Intramolecular 5-endo-trig aminomercuration of beta-hydroxy-gamma-alkenylamines: efficient route to a pyrrolidine ring and its application for the synthesis of (+)-castanospermine and analogues.

The intramolecular aminomercuration reaction of sugar-derived beta-hydroxy-gamma-alkenylamines 8a-c undergoes 5-endo-trig cyclization in high yield. The sugar-substituted pyrrolidines thus obtained were elaborated to the synthesis of polyhydroxylated indolizidine alkaloids, namely, castanospermine 1a, 1-epi-castanospermine 1b, and 8a-epi-castanospermine 1c, having promising glycosidase inhibitory activities.

Synthesis and evaluation of glycosidase inhibitory activity of N-butyl 1-deoxy-D-gluco-homonojirimycin and N-butyl 1-deoxy-L-ido-homonojirimycin.

Conjugate addition of n-butyl amine to d-glucose derived alpha,beta-unsaturated ester 4 afforded beta-amino esters 5a,b that on reduction of ester group, 1,2-acetonide deprotection, and reductive amination led to the formation of corresponding N-butyl 1-deoxy-D-gluco-homonojirimycin 2c and N-butyl 1-deoxy-L-ido-homonojirimycin 2d which were found to be selective beta-glucosidase inhibitors with an IC(50) value in millimolar range.

1,3-Dipolar cycloaddition reaction of D-glucose-derived nitrone with allyl alcohol: synthesis of 2-hydroxy-1-deoxycastanospermine analogues.

[reaction: see text] The synthesis and evaluation of glycosidase inhibitory activity of polyhydroxylated indolizidine alkaloids namely 2-hydroxy-1-deoxycastanospermine 3a,b and 2-hydroxy-1-deoxy-8a-epi-castanospermine 3c,d is reported. The key step involves the intermolecular 1,3-dipolar cycloaddition of allyl alcohol to d-glucose-derived nitrone 4, followed by tosylation, that afforded four diastereomeric sugar-substituted isoxazolidines 5a-d with the desired regioselectivity. The one-pot conversion of 5a-d to pyrrolidines 8a-d by hydrogenolysis, removal of 1,2-acetonoide functionality, and hydrogenation afforded corresponding target molecules 3a-d.

Asymmetric dihydroxylation of d-glucose derived alpha,beta-unsaturated ester: synthesis of azepane and nojirimycin analogues.

The asymmetric dihydroxylation of a d-glucose derived alpha,beta-unsaturated ester 3 afforded syn vicinal diols in good to high diastereoselectivity. The conversion of these vicinal diols to the corresponding cyclic sulfate, regio-, stereoselective nucleophilic ring opening by sodium azide, and LAH reduction afforded amino heptitols 7a,b that were converted to azepane 1c,d and nojirimycin analogues 2c,d.