Cancer pharmacoinformatics: Databases and analytical tools.

Cancer is a subject of extensive investigation, and the utilization of omics technology has resulted in the generation of substantial volumes of big data in cancer research. Numerous databases are being developed to manage and organize this data effectively. These databases encompass various domains such as genomics, transcriptomics, proteomics, metabolomics, immunology, and drug discovery. The application of computational tools into various core components of pharmaceutical sciences constitutes "Pharmacoinformatics", an emerging paradigm in rational drug discovery. The three major features of pharmacoinformatics include (i) Structure modelling of putative drugs and targets, (ii) Compilation of databases and analysis using statistical approaches, and (iii) Employing artificial intelligence/machine learning algorithms for the discovery of novel therapeutic molecules. The development, updating, and analysis of databases using statistical approaches play a pivotal role in pharmacoinformatics. Multiple software tools are associated with oncoinformatics research. This review catalogs the databases and computational tools related to cancer drug discovery and highlights their potential implications in the pharmacoinformatics of cancer.

Monovalent cation binding to model systems and the macrocyclic depsipeptide, emodepside.

This study focuses on the systematic exploration of the emodepside conformations bound to monovalent K+ ion using quantum mechanical density functional theory (DFT) calculations at the M06-2X/6-31+G(d,p) level of theory. Nine conformers of emodepside and their complexes with K+ ion were characterized as stationary points on the potential energy surface. The conformational isomers were examined for their 3D structures, bonding, energetics, and interactions with the cation. A cavitand-like structure (CC) is identified to be the energetically most stable arrangement. To arrive at a better understanding of the K+ ion binding, calculations were initially performed on complexes formed by the K+ and Na+ ions with model ligands (methyl ester and N,N-dimethyl acetamide). Both the natural bond orbital (NBO) method and the block-localized wavefunction (BLW) energy decomposition approach was employed to assess the bonding and energetic contributions stabilizing the ion-bound model complexes. Finally, the solvent effect was evaluated through complete geometry optimizations and energy minimizations for the model ion-ligand complexes and the emodepside-K+ bound complexes using an implicit solvent model mimicking water and DMSO.

Directed regioselective arylation of imidazo[1,2-a]pyridine-3-carboxamides using Rh(III) catalysis.

In contrast to previously reported free-radical pathways to functionalize imidazo[1,2-a]pyridines at the C-5 centre, directing group approaches are rare. Herein, we demonstrate a rhodium(III) catalyzed efficient and regioselective strategy for directed C-5 functionalization of imidazo[1,2-a]pyridines using N-methoxyamide as a directing group. This methodology facilitates directed arylation without the necessity for pre-functionalization. It also allows for gram-scale synthesis and post-functionalization.

Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6.

Cytochrome P450 2D6 (CYP2D6) is one of the most important enzymes involved in drug metabolism. Genetic polymorphism can influence drug metabolism by CYP2D6 such that a therapy is seriously affected by under- or overdosing of drugs. However, a general explanation at the atomistic level for poor activity is missing so far. Here we show for the 20 most common single nucleotide polymorphisms (SNPs) of CYP2D6 that poor metabolism is driven by four mechanisms. We found in extensive all-atom molecular dynamics simulations that the rigidity of the I-helix (central helix), distance between central phenylalanines (stabilizing bound substrate), availability of basic residues on the surface of CYP2D6 (binding of cytochrome P450 reductase), and position of arginine 132 (electron transfer to heme) are essential for an extensive function of the enzyme. These results were applied to SNPs with unknown effects, and potential SNPs that may lead to poor drug metabolism were identified. The revealed molecular mechanisms might be important for other drug-metabolizing cytochrome P450 enzymes.

The importance of four-membered NHCs in stabilizing Breslow intermediates on benzoin condensation pathway.

N-heterocyclic carbenes (NHCs) have been established to be effective organocatalysts for facilitating the benzoin condensation and many other reactions. These reactions involve the formation of a Breslow intermediate (BI), which exhibits umpolung chemistry. To facilitate organocatalysis, several new cyclic carbenes are being introduced, four-membered NHCs are of special interest. Whether these NHCs can exhibit catalytic influence or not, can be evaluated by exploring the potential energy surface (PES) of the benzoin condensation reaction. Quantum chemical analysis has been carried out to compare the PES of these four-membered NHCs with that of standard five-membered NHCs to explore their catalytic ability. The barrier for the first step of the reaction for the formation of BI is comparable in all the cases. But the barrier for the second step of the reaction leading to the benzoin formation from BI is estimated to be very high for the four membered NHCs. These results indicate that the probability of identifying and isolating the BI is very high in comparison to the completion of benzoin condensation reaction in the case of the four-membered NHCs.

Bronsted Acid-Catalyzed Regioselective Carboxamidation of 2-Indolylmethanols with Isonitriles.

A regioselective direct carboxamidation reaction of 2-indolylmethanols with readily available isocyanoesters/isocyanides has been reported in this work. The reaction was catalyzed by Bronsted acid such as p-TsOH to deliver the benzylic regioselective amides in 67-86% yield under mild conditions. The developed methodology provides alternative access to traditional metal-free carboxamidation via C-C and C-O bond formation with high atom economy. Furthermore, the developed approach was diversified to synthesize chiral indole-2-carboxamide derivatives with a moderate enantiomeric excess (61-73% ee) using an (R)-chiral phosphoric acid.

Iodocycloisomerization/Nucleophile Addition Cascade Transformations of 1,2-Alkynediones.

A general electrophilic iodocyclization/nucleophile addition cascade transformation for 1,2-alkynediones for the synthesis of various oxygen heterocycles and access to regioselective alkyne hydroxylation is reported. Furan-tethered ynediones resulted in the construction of exo-enol ethers via carbonyl-alkyne cyclization-initiated heteroarene dearomatization, whereas other (hetero)arene-, alkenyl-, and alkyl-tethered ynediones resulted in the formation of highly functionalized 3(2H)-furanones. Importantly, the developed domino protocols involve the construction of important heterocyclic scaffolds and installation of two functional groups in a single operation. Moreover, the use of water as a nucleophile resulted in regioselective alkyne hydroxylation via furanone ring opening. The developed protocols are characterized by a wide substrate scope, and their utility has been demonstrated by a number of postsynthetic transformations.

Synthesis of 3-sulfenylindole derivatives from 4-hydroxy-2H-chromene-2-thione and indole using oxidative cross-dehydrogenative coupling reaction and anti-proliferative activity study of some of their sulfone derivatives.

The synthesis of hitherto unreported 3-sulfenylindole derivatives is achieved from 4-hydroxy-2H-chromene-2-thione (1) and indole (2) by employing an oxidative cross-dehydrogenative coupling reaction using a combination of 10 mol% of molecular iodine and 1 equivalent of TBHP in DMSO at room temperature. Then, the 3-sulfenylindole derivatives 3a, 3b, 3d, 3f, 3 h, and 3 k were converted into their corresponding sulfone derivatives because of lead likeness properties. Subsequently, a target prediction and docking study of six sulfone derivatives (5a-f) was performed, and four sulfones, namely 5a, 5d, 5e, and 5f, were selected for further in-vitro studies. The four sulfones mentioned above exhibited prominent anti-proliferative activity on breast cancer (MCF7) cell lines. In addition, this reaction was exergonic through quantum chemical analysis of the mechanistic steps. The salient features of this reaction are mild reaction conditions, good yields, and broad substrate scope.

Understanding Poor Milling Behavior of Voriconazole from Crystal Structure and Intermolecular Interactions.

The study investigated the milling behavior of voriconazole (VRZ) subjected to particle size reduction using air jet mill at differential air pressures of 5, 6, 7, and 8 bar for five cycles at each pressure. The crystal structure of VRZ was probed for understanding the fracture behavior from crystal packing and intermolecular interactions using molecular modeling tools of attachment energy (Eatt), density functional theory, and energy framework analysis. Upon milling for different cycles, VRZ showed that size reduction from (D90) 20 to 9 µm and 100% particles could not be milled to sizes below 9 µm, with the increase in either the milling intensity or cycle. The milled samples retained the original crystal lattice as evident from consistent melting endotherm (Tm = 130.75 °C); heat of fusion (ΔHf = 96.52 J/g) values; and the plate-shaped morphology. The powder X-ray diffraction pattern of milled samples consistently showed characteristic peaks of stable form B of VRZ. The crystallographic plane (001) was found to be the most prominent slip and the cleavage plane due to least Eatt and weak noncovalent interactions (6.996 kJ/mol) between 3'H and 4'F functional groups of the neighboring planes. The predicted indentation hardness value of 228.67 MPa further indicated toward the plastic nature of VRZ crystals. Corroborating outcomes from the different molecular modeling tools for VRZ, cleavage along the plane (001) was determined to be energetically favorable, whereas cleavage of isotropic 2D molecular sheets was energetically unfavorable. As milling proceeds and crystal reduces in size, contact surface area and overall interaction energy decrease contributing to plastic behavior of the crystal. It was concluded that crystal plasticity and isotropic 2D molecular sheets along with the orientation of particles to the direction of stress and attrition energy during air jet milling are contributing factors for nonuniform size reduction of VRZ particles.

Thiazetidin-2-ylidenes as four membered N-heterocyclic carbenes: theoretical studies and the generation of complexes with N+ center.

Thiazetidin-2-ylidenes have been designed as four membered N-heterocyclic carbenes (NHCs) using quantum chemical studies. These species are smaller analogs of thiazol-2-ylidenes, possess high singlet stability (57 kcal mol-1) and large nucleophilicity (3.4 eV). The possible existence of these carbenes has been established by synthesizing and crystalizing compounds with NHC→N+←(thiazetidin-2-ylidene) coordination bonds.

Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity.

Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.

Iodine Catalyzed Oxidative Coupling of Diaminoazines and Amines for the Synthesis of 3,5-Disubstituted-1,2,4-Triazoles.

A simple, convenient, transition metal-free one pot synthesis of 3,5-disubstituted-1,2,4-triazoles has been established. The innovation in this reaction is the use of easily available 1,1-diaminoazines as substrates. This method provides the products with wider substrate scope, at an expedited rate, and with relatively better yields in comparison to the reported methods. The reaction mechanism involves an initial intermolecular nucleophilic addition (facilitated by I2) followed by intramolecular nucleophilic cyclization.

F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism.

Of 57 human cytochrome P450 (CYP) enzymes, 12 metabolize 90% of xenobiotics. To our knowledge, no study has addressed the relation between enzyme dynamics and substrate promiscuity for more than three CYPs. Here, we show by constraint dilution simulations with the Constraint Network Analysis for the 12 isoforms that structural rigidity of the F/G region is significantly inversely correlated to the enzymes' substrate promiscuity. This highlights the functional importance of structural dynamics of the substrate tunnel.

3D QSAR studies on amphiphilic indoles for antimycobacterial activity.

A persistent infection prolongs treatment duration and also enhances the chance of resistance development against antibiotics. Recently, a class of amphiphilic indole derivatives was discovered exhibiting bactericidal activity against both growing and nongrowing Mycobacterium bovis BCG (M. bovis BCG). These antibacterials are suggested to disturb the integrity and functioning of the cell membrane, a property that can help eradicate persistent organisms. This study article describes field-based three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of 79 amphiphilic indole derivatives. The aim of this QSAR study is to optimize this class of compounds for the development of more potent antimycobacterial agents. The results obtained indicate that steric interactions are crucial for antimycobacterial activity, while hydrogen bond donor groups participate negligibly in activity. The derived 3D-QSAR models showed acceptable r2 (0.91) and q2 (0.91) with a root mean squared error (RMSE) of 0.08. The models were cross-validated using the leave-one-out method. Applying the same QSAR model to another congeneric series of amphiphilic indoles externally validated the QSAR model. The model could appreciably predict the activity (pMIC50 ) of this congeneric series of amphiphilic indoles, with an RMSE of 0.49, indicating the robustness of the model and its efficiency in predicting the potentially active compounds.

Synthesis of 1,4-dihydropyrazolo[4,3-b]indoles via intramolecular C(sp2)-N bond formation involving nitrene insertion, DFT study and their anticancer assessment.

We herein report a new synthetic route for a series of unreported 1,4-dihydropyrazolo[4,3-b]indoles (6-8) via deoxygenation of o-nitrophenyl-substituted N-aryl pyrazoles and subsequent intramolecular (sp2)-N bond formation under microwave irradiation expedite modified Cadogan condition. This method allows access to NH-free as well as N-substituted fused indoles. DFT study and controlled experiments highlighted the role of nitrene insertion as one of the plausible reaction mechanisms. Furthermore, the target compounds exhibited cytotoxicity at low micromolar concentration against lung (A549), colon (HCT-116), and breast (MDA-MB-231, and MCF-7) cancer cell lines, induced the ROS generation and altered the mitochondrial membrane potential of highly aggressive MDA-MB-231 cells. Further investigations revealed that these compounds were selective Topo I (6h) or Topo II (7a, 7b) inhibitors.

Mechanistic studies on the drug metabolism and toxicity originating from cytochromes P450.

Cytochromes P450 are oxidizing enzymes; a few families of cytochromes P450 are implicated in drug metabolism. These enzymatic reactions involve many processes including (i) prodrug to drug conversion, (ii) easy excretion of drug, (iii) generation of reactive metabolites, many of which cause toxicity. In this review, the fundamental biochemical mechanisms associated with the conversion of drugs into the useful or toxic metabolites have been discussed. The mechanisms can be established with the help of many experimental methods like mass spectral analysis, NMR and in vitro analysis etc. Computational methods provide detailed atomic level information, which is generally not available from experimental studies. Thus, the in silico efforts in elucidating the molecular mechanisms are complementary to the known experimental methods and are often clearer (especially in providing 3D information about the metabolites and their reactions). Quantum chemical methods and molecular docking become especially very useful. This review includes five case studies, which explain how the atomic level details were obtained to explore the reaction mechanisms of drug metabolism by cytochromes P450.

Divalent NI Compounds: Identifying new Carbocyclic Carbenes to Design Nitreones using Quantum Chemical Methods.

Nitreones are compounds with oxidation state 1 at the nitrogen, these compounds carry formal positive charge as well as two lone pairs of electrons at nitrogen center. These compounds are also known as divalent NI compounds and can be represented with the general formula L → N+ ← L, where L is an electron donating ligand. In the recent past, several divalent NI compounds have been reported with L = N-heterocyclic carbene (NHC), remote N-heterocyclic carbene (rNHC), carbocyclic carbene (CCC) and diaminocarbene. Recently, our group reported that a novel six-membered CCC (cyclohexa-2,5-diene-4-[diaminomethynyl]-1-ylidene) can stabilize N+ center in nitreones. As an independent carbene, this species is very unstable. In this work, modulation of this CCC using (a) annulation, (b) heterocyclic ring modification, (c) substitutions adjacent to the carbenic carbon, (d) exocyclic double bond insertion and (e) ring contraction, has been reported. These modulations and quantum chemical analyses helped in the identification of five new six-membered CCCs which carry improved donation and stability properties. Further, these CCCs were employed in the design of new divalent NI compounds (nitreones) which carry coordination bonds between ligands and N+ center. The molecular and electronic structure properties, and the donor→acceptor coordination interactions present in the resultant low oxidation state divalent NI compounds have been explored.

Oxone-DMSO Triggered Methylene Insertion and C(sp2)-C(sp3)-H-C(sp2) Bond Formation to Access Functional Bis-Heterocycles.

Metal-free insertion of a methylene group was achieved for the construction of a new C(sp2)-C(sp3)-H-C(sp2) bond in order to prepare novel bis-heterocyclic scaffolds. The complete mechanistic investigations included experimental study and DFT calculations, and various symmetric and unsymmetric bis-pyrazoles as well as other pyrazole-based bis-heterocyclic molecules were prepared in moderate to high yields. Further modification of the bridged methylene group in the unsymmetric pyrazoles generated a chiral center to extend the scope of this method.

NL2+ Systems as New-Generation Phase-Transfer Catalysts.

Phase-transfer catalysts (PTCs), currently, are one of the most important tools of chemists for performing organic reactions. PTCs accelerate several types of reactions in biphasic systems, giving excellent yields of the desired product. Most of the PTCs belong to the general formula NR4+X-. In the recent past, several compounds possessing a novel scaffold with the general formula NL2+X- have been reported as PTCs. In the NL2+ species, a nitrogen atom with a formal positive charge accepts electron density from electron-donating ligands. Electronic structure studies reported in the literature confirmed the possibility of L → N coordination (donor-acceptor) interactions in these species, and thus, this class of compounds are known as divalent NI compounds. These species are reported to exhibit better catalytic potential in comparison to the traditional NR4+ systems. Some of the NL2+ systems are found to be useful in asymmetric phase-transfer catalysis. Thus, these systems offer extensive opportunities for exploring the catalytic properties and novel mechanistic aspects associated with their unique electronic structure. In this paper, the synthesis, electronic, and structural properties and the applications in catalysis of the NL2+-based PTCs are reviewed with their bright future scope in catalytic organic chemistry.

Synthesis of N-substituted indole derivatives as potential antimicrobial and antileishmanial agents.

Leishmaniasis and microbial infections are two of the major contributors to global mortality and morbidity rates. Hence, development of novel, effective and safer antileishmanial and antimicrobial agents having reduced side effects are major priority for researchers. Two series of N-substituted indole derivatives i.e. N-substituted indole based chalcones (12a-g) and N-substituted indole based hydrazide-hydrazones (18a-g, 19a-f, 21 a-g) were synthesized. The synthesized compounds were characterized by 1H NMR, 13C NMR, Mass and FT-IR spectral data. Further these derivatives were evaluated for their antimicrobial potential against Escherichia coli, Bacillus subtilis, Pseudomonas putida and Candida viswanathii, and antileishmanial potential against promastigotes of Leishmania donovani. Compounds 18b, 18d and 19d exhibited significant activity with an IC50 of 0.19 ± 0.03 µM, 0.14 ± 0.02 µM and 0.16 ± 0.06 µM against B. subtilis which was comparable to chloramphenicol (IC50 of 0.25 ± 0.03 µM). Compounds 12b and 12c exhibited an IC50 of 24.2 ± 3.5 µM and 21.5 ± 2.1 µM in the antileishmanial assay. Binding interactions of indole based hydrazide-hydrazones were studied with nitric oxide synthase in silico in order to understand the structural features responsible for activity.