Metal-free synthesis of selenoesters directly from carboxylic acids using bifunctional selenoureas under batch and continuous-flow conditions.

A new metal-free method for the synthesis of selenoesters directly from carboxylic acids in a flow reactor is reported. The carboxylic acids, Michael acceptors, and bifunctional selenoureas (source of selenium and nucleophile, activator of carbonyl group) were reacted to obtain selenoesters (up to 70% yield). An evidence-backed plausible mechanism is also presented.

An update on ATP synthase inhibitors: A unique target for drug development in M. tuberculosis.

ATP synthase is a key protein in the oxidative phosphorylation process, as it aids in the effective production of ATP (Adenosine triphosphate) in all life's of kingdoms. ATP synthases have distinctive properties that contribute to efficient ATP synthesis. The ATP synthase of mycobacterium is of special relevance since it has been identified as a target for potential anti-TB molecules, especially Bedaquiline (BDQ). Better knowledge of how mycobacterial ATP synthase functions and its peculiar characteristics will aid in our understanding of bacterial energy metabolism adaptations. Furthermore, identifying and understanding the important distinctions between human ATP synthase and bacterial ATP synthase may provide insight into the design and development of inhibitors that target specific ATP synthase. In recent years, many potential candidates targeting the ATP synthase of mycobacterium have been developed. In this review, we discuss the druggable targets of the Electron transport chain (ETC) and recently identified potent inhibitors (including clinical molecules) from 2015 to 2022 of diverse classes that target ATP synthase of M. tuberculosis.

Importance of tautomerism in drugs.

Tautomerism is an important phenomenon exhibited by many drugs. As we discuss in this review, identifying the different tautomers of drugs and exploring their importance in the mechanisms of drug action are integral components of current drug discovery. Nuclear magnetic resonance (NMR), infrared (IR), ultraviolet (UV), Raman, and terahertz spectroscopic techniques, as well as X-ray diffraction, are useful for exploring drug tautomerism. Quantum chemical methods, in association with pharmacoinformatics tools, are being used to evaluate tautomeric preferences in terms of energy effects. Desmotropy (i.e., tautomeric polymorphism) of the drugs is particularly important in drug delivery studies.

Isolation of phytochemicals from Dolichandrone atrovirens followed by semisynthetic modification of ixoside via azomethine ylide cycloaddition; computational approach towards chemo-selection.

Aims of the study were the phytochemical investigation and chemical transformation of isolated compounds of medicinal plant listed in 'Ayurveda' like Dolichandrone atrovirens, endemic to Indian subcontinents. From chloroform extract of D. atrovirens four compounds; Ursolic acid (1), Maslinic acid (2), Lupeol (3), ß-sitosterol (4) and from methanol extract five compounds; ß-sitosterol-3-O-ß-D-glucopyranoside (5), 10-O-trans-p-Methoxycinnamoylcatalpol (6), Kaempferol-3-O-ß-D-glucopyranoside (7), 6-O-[6"(S)-hydroxy-2",6"dimethyl-2"(E)-7"-octadienoyl] catalpol (8) and Ixoside (9) were isolated. Ixoside was used for the semi-synthetic modification via azomethine ylide cycloaddition leading to novel spiro-oxindolo-pyrrolizidine adduct. The structures of novel adducts were elucidated by analysis of IR, MS and 1 D/2D NMR data. Furthermore, to confirm the chemo selection of only one double bond, we performed density functional theory (DFT) calculation, which confirms the chemo selectivity. In addition, in-silico ADME studies and atom-additive approach based on SASA was also examined for the molecules which suggest that they may be potential future candidates for drug discovery.

Tautomer Database: A Comprehensive Resource for Tautomerism Analyses.

We report a database of tautomeric structures that contains 2819 tautomeric tuples extracted from 171 publications. Each tautomeric entry has been annotated with experimental conditions reported in the respective publication, plus bibliographic details, structural identifiers (e.g., NCI/CADD identifiers FICTS, FICuS, uuuuu, and Standard InChI), and chemical information (e.g., SMILES, molecular weight). The majority of tautomeric tuples found were pairs; the remaining 10% were triples, quadruples, or quintuples, amounting to a total number of structures of 5977. The types of tautomerism were mainly prototropic tautomerism (79%), followed by ring-chain (13%) and valence tautomerism (8%). The experimental conditions reported in the publications included about 50 pure solvents and 9 solvent mixtures with 26 unique spectroscopic or nonspectroscopic methods. 1H and 13C NMR were the most frequently used methods. A total of 77 different tautomeric transform rules (SMIRKS) are covered by at least one example tuple in the database. This database is freely available as a spreadsheet at https://cactus.nci.nih.gov/download/tautomer/.

Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2.

We have collected 86 different transforms of tautomeric interconversions. Out of those, 54 are for prototropic (non-ring-chain) tautomerism, 21 for ring-chain tautomerism, and 11 for valence tautomerism. The majority of these rules have been extracted from experimental literature. Twenty rules, covering the most well-known types of tautomerism such as keto-enol tautomerism, were taken from the default handling of tautomerism by the chemoinformatics toolkit CACTVS. The rules were analyzed against nine differerent databases totaling over 400 million (non-unique) structures as to their occurrence rates, mutual overlap in coverage, and recapitulation of the rules' enumerated tautomer sets by InChI V.1.05, both in InChI's Standard and a Nonstandard version with the increased tautomer-handling options 15T and KET turned on. These results and the background of this study are discussed in the context of the IUPAC InChI Project tasked with the redesign of handling of tautomerism for an InChI version 2. Applying the rules presented in this paper would approximately triple the number of compounds in typical small-molecule databases that would be affected by tautomeric interconversion by InChI V2. A web tool has been created to test these rules at https://cactus.nci.nih.gov/tautomerizer.

A structural and functional perspective on the enzymes of Mycobacterium tuberculosis involved in the L-rhamnose biosynthesis pathway.

Tuberculosis is one of the leading causes of death from bacterial infections. The multi-drug resistant strain has warranted the development of new drug molecules which can inhibit the growth of Mycobacterium tuberculosis (M.tb). Most of the known drugs inhibit the enzymes in the cell wall biosynthesis pathway. One such pathway is L-rhamnose, which involves four druggable enzymes RmlA, B, C and D. The 3D structure analyses of these protein models (RmlA, B and D) and crystal structure (RmlC) has been carried out. Multiple sequence alignments of homologs from distant species of 32 taxa and analyses of available structures were performed in order to study the conservation of sequence and structural motifs, and catalytically important residues. Based on these results and reported mechanism in other organisms, we have predicted putative catalytic mechanism of M.tb enzymes involved in the L-rhamnose biosynthesis pathway.

Palladium-catalyzed arylation of 2H-chromene: a new entry to pyrano[2,3-c]carbazoles.

Pyrano[2,3-c]carbazoles which are biologically valuable and synthetically challenging frameworks are synthesized in high yields over five steps from commercially available resorcinol. Palladium-catalyzed arylation remains a key step in this novel strategy. The versatility of this protocol has been demonstrated by the synthesis of naturally occurring alkaloid clauraila C and 7-methoxyglycomaurin. The anti-proliferative activity of these designed compounds (5a, 5f, and 5l) has been evaluated in a cancer cell line (MOLT-4). The molecular docking study revealed that this pyrano[2,3-c]carbazole class of molecules selectively occupies the colchicine binding site of the tubulin-polymer.

DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme.

Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.

Cu-catalyzed arylation of the amino group in the indazole ring: regioselective synthesis of pyrazolo-carbazoles.

Cu(II)-catalyzed cross-coupling of various aryl boronic acids with 5 and 6-amino indazoles has resulted in (arylamino)-indazoles. These (arylamino)-indazoles have been utilized in synthesizing medicinally important pyrazole-fused carbazoles via Pd(II)-catalyzed cross-dehydrogenative coupling (CDC). This combined N-arylation/C-H arylation strategy has been successfully applied to the regioselective synthesis of polyheterocycles 3,6-dihydropyrazolo[3,4-c]carbazoles and 1,6-dihydro pyrazolo[4,3-c]carbazoles. Quantum chemical analysis has been carried out to understand the regioselectivity and to trace the potential energy surface of the entire reaction upon 5-N-aryl-indazole conversion to the corresponding carbazole.

On the stability of zwitterions of pyridine sulfonylureas: the effect of isosterism, acidity, and microsolvation.

Pyridine sulfonylureas (PSUs) are known to exist in zwitterionic form in the solid phase. For example, torsemide, a diuretic drug, exists in three polymorphic forms: two of them in the zwitterionic state and one in the "partial zwitterionic" state. Initial computational analysis showed that the energy difference between the canonical and the zwitterionic states of a model PSU is very large in the gas phase (∼15 kcal/mol), thus disfavoring the zwitterionic state. In order to understand the apparent dichotomy on the preferred state of PSUs, extensive computational analysis using density functional theory was taken up on a few analogues of PSU. The zwitterionic isomer was less stable than the canonical form in the model PSU, 4-amino-pyridyl-3-sulfonylurea. However, under implicit polar solvent conditions, the zwitterionic and the canonical forms of the model PSU were nearly isoenergetic. Furthermore, microsolvation calculations showed that the zwitterionic model of torsemide is thermodynamically more favorable over the canonical form in the presence of seven water molecules. A combined microsolvation-continuum solvent model showed that the zwitterionic form starts to dominate the canonical form under the influence of four water molecules. Analysis on the intramolecular interactions, the partial atomic charges, the conformational and tautomeric preferences was also carried out, which enabled the rationalization of the formation of stable zwitterionic species in PSUs.

Site-selective electrophilic cyclization and subsequent ring-opening: a synthetic route to pyrrolo[1,2-a]quinolines and indolizines.

An efficient strategy for the synthesis of pyrrolo[1,2-a]quinolines and indolizines from pyranoquinolines via site-selective electrophilic cyclization and subsequent opening of pyran ring using silver/iodine under mild reaction conditions is described. This approach involves the preferential attack of the pyridyl nitrogen over aryl ring and leads to the formation of 5-endo-dig cyclized products. Quantum chemical calculations between C-N (ΔE(a) = 9.01 kcal/mol) and C-C (ΔE(a) = 31.31 kcal/mol) bond formation were performed in order to rationalize the observed site selectivity. Structure of the products were confirmed by the X-ray crystallographic studies. Iodo-substituted compounds generated by the electrophilic iodocyclization were further diversified via Pd-catalyzed cross-coupling reactions.

Exploring the binding of HIV-1 integrase inhibitors by comparative residue interaction analysis (CoRIA).

Since the recognition of HIV-1 integrase as a novel and rational target for HIV therapeutics, remarkable progress has been made in the development of integrase inhibitors. Computational techniques have played a critical role in accelerating research in this area. However, most previous computational studies were based solely on ligand information. In the present work, we describe the application of one of our recently developed receptor-based 3D-quantitative structure activity relationships (QSAR) methods, i.e. comparative residue interaction analysis (CoRIA), in exploring the events involved in ligand-integrase binding. In this methodology, the non-bonded interaction energies (van der Waals and Coulombic) of the inhibitors with individual active site residues of the integrase enzyme are calculated and, along with other thermodynamic descriptors, are correlated with biological activity using chemometric methods. Different combinations of descriptors were used to develop three types of QSAR models, all of which were found to be statistically significant by internal and external validation. This is the first report of such a dedicated receptor-based 3D-QSAR approach being applied to comprehend the integrase-inhibitor recognition process. In addition, the study was performed on 13-different series of inhibitors, thereby exploring the most structurally diverse data set ever used in understanding the inhibition of HIV-1 integrase. The major advantage of this technique is that it can quantitatively extract crucial residues and identify the nature of interactions between the ligand and receptor that modulate activity. The models suggest that Asp64, Thr66, Val77, Asp116, Glu152 and Lys159 are the key residues influencing the binding of ligands with the integrase enzyme, and the majority of these results are in line with earlier studies. The approach facilitates easy lead-to-hit conversion and design of novel inhibitors by optimisation of the interaction of ligands with these specific residues of the integrase enzyme.