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Abstract: In this work, we introduce the development and application of a three-step scoring and filtering procedure for the design of type II p38 MAP kinase leads using allosteric fragments extracted from virtual screening hits. The design of the virtual screening filters is based on a thorough evaluation of docking methods, DFG-loop conformation, binding interactions and chemotype specificity of the 138 p38 MAP kinase inhibitors from Protein Data Bank bound to DFG-in and DFG-out conformations using Glide, GOLD and CDOCKER. A 40ns molecular dynamics simulation with the apo, type I with DFG-in and type II with DFG-out forms was carried out to delineate the effects of structural variations on inhibitor binding. The designed docking-score and sub-structure filters were first tested on a dataset of 249 potent p38 MAP kinase inhibitors from seven diverse series and 18,842 kinase inhibitors from PDB, to gauge their capacity to discriminate between kinase and non-kinase inhibitors and likewise to selectively filter-in target-specific inhibitors. The designed filters were then applied in the virtual screening of a database of ten million (107) compounds resulting in the identification of 100 hits. Based on their binding modes, 98 allosteric fragments were extracted from the hits and a fragment library was generated. New type II p38 MAP kinase leads were designed by tailoring the existing type I ATP site binders with allosteric fragments using a common urea linker. Target specific virtual screening filters can thus be easily developed for other kinases based on this strategy to retrieve target selective compounds. [Copyright &y& Elsevier]

Abstract: Choline kinase (ChoK) is reported to involve in cell signaling pathways and cell growth by regulating the intermediate, phosphocholine (PCho), which is the first step to biosynthesis a membrane phospholipid, phosphatidylcholine. The PCho levels are overexpressed due to elevated activation of the protein under carcinogenesis conditions. ChoK has thus evolved as a novel target for various cancers and a range of compounds has been reported in this course as potent ChoK inhibitors. However, not much information is known about the binding site of the inhibitors. Therefore, we ventured to unravel the possible binding site of 39 bis-quinolinium inhibitors from which the structural requirement for better protein–ligand complex was delved. Molecular docking and 3D-QSAR studies namely comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on the series. The knowledge of the active site was obtained from the site id search and molcad surface calculations of Sybyl, which was further considered for docking studies. In 3D-QSAR, the best predictions were obtained from the model where 29 compounds were considered in the training set and remaining 10 in the test set. The best CoMFA statistics were obtained with r 2 of 0.99 and q 2 of 0.81 while, CoMSIA was resulted with r 2 of 0.98 and q 2 of 0.77. A comparative analysis was done with the resulted 3D-QSAR maps and the docked poses by overlaying the maps on the active site residues. Since, there is no reported ligand co-crystallized structure of ChoK the present study provides valuable clues on the binding conformation of the ligand and its interactions with the active site. [Copyright &y& Elsevier]

Abstract: Quantum mechanical calculations using the Hartree-Fock (HF), post-Hartree-Fock {MP2 and CCSD(T)}and gradient-corrected hybrid density functional variant, B3LYP methodology in conjugation with basis sets like 6-31G*, 6-311G** and cc-pVTZ, were employed to critically probe the right quality of basis set and the appropriate level of theory that can be applied in modeling the organo-sulfur compounds. The relative stability ordering of 1,2-dithiete and dithioglyoxal reveal the delicate basis set dependence especially on ‘S’ atom. Single point calculations at the B3LYP, MP2 and CCSD(T) levels using a series of basis set ranging from double ζ quality all the way up to the quintuple ζ quality were done to illustrate the effect of electron correlation and the basis set dependency for these compounds. Basis set requirements are much higher than affordable for medium sized molecules as very slow convergence is seen even when the calculations are carried out with basis set as high as cc-pV5Z at the B3LYP and MP2 level of theories. [Copyright &y& Elsevier]

Abstract: Hybrid density functional theory and post-SCF ab initio calculations were employed to explore the isomers of glyoxal, C2O2H2, along with the corresponding cation and anion radicals. The dependence of relative energies with respect to the methods and quality of basis set was critically analyzed, all the way up to cc-pV5Z. Bond stretch isomerism between 5a and 6 as well as 5C and 6C was clearly established. While the glyoxal isomer 1 and 1A is a global minima on neutral and anionic surfaces, 8C a ketene analog was found to be the global minima among the cation isomers. [Copyright &y& Elsevier]

Quantum chemical calculations at B3LYP/6-31G* and semiempirical levels have been performed on a series of sterically unbiased ketones, where facial differentiation during nucleophilic additions is electronically induced through distal functional groups. The face selectivity data for fifty-four substrates representing nine different skeleta were computed and compared with the available experimental data on thirty-eight of them. The predictive abilities of various computational methods such as, charge model, hydride model, LiH transition state model, Cieplak hyperconjugation effect estimated by NBO analysis and the cation complexation model have been evaluated. A comparison of the computed and experimental face-selectivity data indicates that the hydride model and the LiH transition state model at the semiempirical levels are the best choices to predict diastereoselectivity. Unexpectedly, the performance of charge, hydride and LiH transition state models are inferior at the B3LYP level compared to the semiempirical methods in predicting the facial selectivities. On the other hand, the Cieplak type hyperconjugation evaluated using the NBO analysis, and cation complexation model are less reliable despite the fact that these two involve higher (B3LYP/6-31G*) level calculations. The inadequate performance of the charge model, NBO and the cation complexation models were traced to their emphasis on only one or two factors which are responsible for stereodifferentiation and undermining of the other subtle aspects involving a combination of orbital and electrostatic effects. On the other hand, the hydride and LiH transition state models, at semiempirical levels, provide reliable results to model the face-selectivities. [Copyright &y& Elsevier]

B3LYP/6-311+G** calculations on alkali metal ion (Li+ and Na+) complexation with corannulene and sumanene indicate stronger binding compared to [5]-radialene or benzene. The dependence of binding to the convex and concave site is marginal, albeit the preference was consistent for convex binding in the range of 1–4 kcal/mol. The bowl-to-bowl inversion barriers are only marginally affected, below 2 kcal/mol, by metal ion complexation. [Copyright &y& Elsevier]

Quantum chemical calculations at the hybrid density functional, B3LYP/6-31G* and the semiempirical PM3 levels were performed on model intramolecular systems where the diene and dienophile are linked by the hydrocarbon spacer, –(CH2)n–. Six of the possible reaction pathways; namely one concerted and two stepwise each for the cis- and trans-cycloadditions are considered. All the stationary points on the potential energy surface were identified and characterized by frequency calculations at PM3 level. The study establishes that the concerted mechanism prevails over the stepwise even in the presence of the structural constrains imposed by varying intervening spacer chain lengths. [Copyright &y& Elsevier]

Human cell membranes consist of various lipids that are essential for their structure and function. It typically comprises phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), sphingomyelin (PSM), and cholesterol (CHL). Several experimental and computational techniques have been employed to characterize the composition of human cell membranes, however, CHL enriched membrane is still not clearly understood through these techniques. Molecular dynamics simulation results illustrated the biophysical properties of heterogeneous membranes based on the lipid composition as well as the concentration of lipids, exclusively for CHL and PSM. Herein, we have investigated the structure-function relationships of lipids comparatively to delineate the effect of heterogeneity on the biophysical properties of different membranes. It has been observed that the significant fraction of CHL (i.e., ~33% in ternary, ~25% in quaternary, and ~16% in senary type bilayers) in combination with other lipids introduced compactness, and increased the thickness of the membrane. The analysis of lipid mass density stated that the density of lipid head group, phosphate , and glycerol-ester in presence of CHL with or without PSM is an underlying reason for membrane ordering. Results also revealed that the presence of POPI and POPS are the reasons for an adequate drop in the ordering of lipid chain, particularly on POPE chain. The self-interaction of CHL, PSM, POPE and the interaction of CHL and POPC with POPE seem to determine the structure and function of the heterogeneous membrane. Our findings provide a qualitative understanding of the effect of membrane heterogeneity on the physiological properties of membranes. The structures inspected in this study would help to select the heterogeneous bilayer model to mimic the human cell membranes to analyse or characterize the membrane-associated phenomena. [Display omitted] • Structure-function relationship of lipids to delineate the effect of heterogeneity on the biophysical properties of membranes. • The membrane ordering depends on the density of lipid head group, phosphate, and glycerol-ester in presence of CHL with or without PSM. • Results also revealed the POPI and POPS are the reasons for an adequate drop in the ordering of lipid chain particularly of POPE chain. [ABSTRACT FROM AUTHOR]

Ab initio and density functional theory calculations indicate that a benzene dication isomer (1: C6H62=) with three contiguous planar tetracoordinate carbons is at a minimum on the potential energy surface. The remarkable preference for the planar structure for 1 is traced to the aromatic stabilization present in the three membered ring formed by the three planar tetracoordinate carbon atoms. A novel structure, C6H62=, with three contiguous planar tetracoordinate carbon atoms is proposed as a viable candidate. [Copyright &y& Elsevier]

The Vitamin D Receptor (VDR) ligand-binding domain undergoes conformation change upon the binding of VDR agonists/antagonists. Helix 12 ((H)12) is one of the important helices at VDR ligand binding and its conformational changes are controlled by the binding of agonists and antagonists molecules. Various molecular modeling studies are available to explain the agonistic and antagonistic activity of vitamin D analogs. In this work, for the first time, we attempted to generate a machine learning model with fingerprints, 2D, 3D and MD descriptors that are specific to Vitamin D analogs and VDR. Initially, 2D and 3D descriptors and fingerprints of 1003 vitamin D analogs were calculated using CDK and RDKit. The machine learning model was generated using descriptors and fingerprints. Further, 80 Vitamin D analogs (40 VDR agonists + 40 VDR antagonists) were docked in the VDR active site. 50ns MD simulation was performed for each protein-ligand complex. Different MD descriptors such as Solvent Accessible Surface Area (SASA), radius of gyration, PC1 and PC2 were calculated and considered along with CDK and RDKit descriptors as features for machine learning calculations. A few other descriptors that are related to VDR conformational changes such as conformation of the (H)12, the angle at kink were considered for machine learning model generation. It was observed that the descriptors calculated from VDR conformational changes i) were able to distinguish between agonists and antagonists ii) provide key and comprehensive information about the unique binding characteristics of agonists and antagonists iii) provide a strong basis for the machine learning model generation. Overall, this study attempts the utilization of descriptors that are specific to a protein conformation will be helpful for the generation of an efficient machine learning model. [Display omitted] • Chemical descriptors generated from MD trajectories can be able to generate target specific QSAR/machine learning models. • In this work, we generated few descriptors that are responsible for VDR agonistic/antagonistic activity. • The developed model could be effectively used as an advanced virtual screening filter. [ABSTRACT FROM AUTHOR]

Increasing the power conversion efficiency (PCE) of photovoltaic devices (PVDs) is a topic of fundamental importance not only for academia but also for industry. In this study, we systematically investigated the electronic structure of ZnX (X = O, S, Se, and Te) quantum dots (QDs)/Graphene (G) nanohybrid systems by employing the density functional method. To understand the key issues, associated with photoinduced charge generation, generated charge separation, charge transfer process, recombination probability, and variations of PCE, we have considered different combinations of hybrid nanostructures composed with ZnX QD and G. The tuning of the electronic properties of hybrid systems has been done as a function of the size of ZnX QD's, chalcogenides, and hydrogen coverage percentage on G to design a highly efficient hybrid solar cell. We have also explored the photovoltaic efficiency of ZnX/ZnX' (X/X' = O, S, Se, and Te) core/shell QDs/G to investigate the effect of core/shell QDs in composite nanomaterials. Bandgaps of ZnX QDs/G nanocomposites are very low (0.028eV–0.158 eV) which implies the probability of recombination of photo-induced separated charges at the heterojunction region is very high. After passivation with hydrogen atoms partially on the G, this unsavory circumstance is overcome. We have performed the bandgap and band alignment engineering of ZnX QDs/G hybrid nanostructures by varying the size of QD's and H-coverage percentage on G to form a type-II material which is very important to reduce the recombination rate and ultimately increase the PCE of the hybrid solar cells. Considering hydrogenated graphene (HG)-ZnX QDs nanocomposites we were achieving high PCE values (up to 30.25%), which implies our explored materials efficiency is exceptionally good and competitive with recently explored tandem/hybrid/latest perovskite solar cells. Tunning of photo conversion efficiency (PCE) of ZnX QDs (X = O, S, Se, and Te) and ZnX/ZnX' core/shell QDs/HG hybrid nanostructures. [Display omitted] • This study theoretically explored the electronic structure and photovoltaic efficiency of –NH 2 passivated ZnX (X = O. S, Se, and Te) QDs/G, ZnX QDs/HG, and ZnX/ZnX' core/shell QDs/HG hybrid nanostructures. • The tuning of the band gap and band alignment of ZnX-QDs and G in hybrid systems has been done as a function of the size of QD's, chalcogenides, and hydrogen coverage percentage on G. • ZnX QDs/HG nanohybrid systems show very high power conversation efficiency and (ZnTe) 96 QD/HG possesses the highest PCE value, 30.25%. • ZnX/ZnX' core/shell QDs/HG nanocomposites also show very good PCE and the highest PCE value has been observed for (ZnSe/ZnTe) 96 QD/HG nanocomposite, 20.72%. [ABSTRACT FROM AUTHOR]

Abstract: An antimony(V) containing α-Keggin type acidic polyoxometalate, H4PSbMo11O40, was prepared by reacting NaMoO4, H3PO4 and Sb2O3 in the presence of aqua regia to appraise its reactivity compared to the well known vanadate analog, H4PVMo11O40. Characterization was by X-ray diffraction, MALDI-TOF MS, IR, UV–vis and 31P NMR spectroscopy. Catalytic redox reactions, such as oxidative dehydrogenation using O2 and N2O as terminal oxidants were studied and showed very different reactivity of H4PSbMo11O40 versus H4PVMo11O40. It was found by DFT calculations that in contrast to analogous H4PVMo11O40 where vanadium centered catalysis is observed, in H4PSbMo11O40 catalysis is molybdenum and not antimony centered. [Copyright &y& Elsevier]

Abstract: The geometrical arrangement of the aromatic rings of phenylalanine, tyrosine, tryptophan and histidine has been analyzed at a database level using the X-ray crystal structure of proteins from PDB in order to find out the aromatic–aromatic (π–π) networks in proteins and to understand how these aromatic rings are connected with each-other in a specific π–π network. A stringent examination of the 7848 proteins indicates that close to 89% of the proteins have occurrence of at least a network of 2π or a higher π–π network. The occurrence of π–π networks in various protein superfamilies based on SCOP, CATH and EC classifiers has also been probed in the present work. In general, we find that multidomain and membrane proteins as well as lyases show a more number of these networks. Analysis of the distribution of angle between planes of two proximal aromatic rings (ϕ) distribution indicates that at a larger cutoff distance (between centroid of two aromatic rings), above 5Å, C–H⋯π interactions (T-shaped orientation) are more prevalent, while π–π interactions (stacked orientation) are more prevalent at a smaller cutoff distance. The connectivity patterns of π–π networks propose strong propensity of finding arrangement of aromatic residues as clusters rather than linear arrangement. We have also made a public domain database “Aromatic–Aromatic Interactions Database” (A2ID) comprising of all types of π–π networks and their connectivity pattern present in proteins. It can be accessed by url http://203.199.182.73/gnsmmg/databases/aidb/aidb.html. [Copyright &y& Elsevier]

A novel preference for planar tetracoordination was observed over the conventional tetrahedral arrangement in a new series of C5H2, C5H4, C5H41+/2+ and related compounds. The stability of these molecules is assessed with the ring-opening barriers, HOMO–LUMO gap, singlet–triplet energy differences and nucleus independent chemical shift values. [Copyright &y& Elsevier]

Copper bionanocomposites (CBNCS) were synthesized using Ipomoea carnea- sourced nanocellulose as support via an eco-friendly and cost-effective method. X-ray Diffractometer (XRD) pattern of CBNCS confirmed the octahedral structure of Cu 2 O, the face-centered cubic (FCC) crystal structure of Cu(0). XRD also revealed the crystal lattice of cellulose II. Surface Electron Microscope (SEM) and Transmission Electron Microscope (TEM) revealed the uniform distribution of copper nanoparticles (Cu NPs) with an average size of 10 nm due to the presence of nanocellulose. X-ray photoelectron spectroscopy (XPS) provided information about the electronic, chemical state and elemental composition of CBNCS. Thermogravimetric Analysis (TGA) showed the thermal stability of CBNCS. CBNCS catalyzed the rearrangement of oximes to primary amides in a very mild condition with a high yield of up to 92 %. CBNCS effectively inhibited the growth of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with lower minimum inhibitory concentration MIC values. Antioxidant activity and electrical conductivity of CBNCS were also determined. [Display omitted] • Synthesis of nanocellulose from Ipomoea carnea sourced cellulose. • TEMPO-mediated oxidation of nanocellulose • Synthesis of TEMPO-mediated nanocellulose/Cu/Cu2O Bionanocomposites (CBNCS). • Superior catalytic activity of CBNCS in the synthesis of amide derivatives. • Profound antibacterial, antioxidant and electrical activity of CBNCS. [ABSTRACT FROM AUTHOR]

B3LYP/6-31G* calculations indicate that annelation of three-, four-, or five-membered rings to the rim of corannulene results in lowering the bowl-to-bowl inversion barrier and flattens the bowl structure. The role of the peri hydrogen repulsion as a causative factor for such a behavior is disputed, the structure–energy relationships in this class of compounds were shown to fit with a mixed quartic–quadratic potential. [Copyright &y& Elsevier]

Breast cancer cell proliferation is promoted by a variety of mitogenic signals. Classically estrogen is considered as most predominant mitogenic signal in hormone-dependent breast cancer and progesterone is primarily considered to have protective effect. However, it is suggested that some progesterone metabolite may promote breast cancer and progesterone metabolites like 5α-pregnane and 4-pregnene could serve as regulators of estrogen-responsiveness of breast cancer cells. Here, we estimated the potential of alternate targeting of breast cancer via progesterone signalling. l -Proline derived novel 14-azasteroid compounds were screened against MCF-7 and MDA-MB-231 cell lines using MTT assay. In silico studies, cell cycle, Annexin-V-FITC/PI, JC-1 mitochondrial assay, ROS analysis were performed to analyse the impact of hit compound 3b on breast cancer cells. Further, we analysed the impact of hit 3b on the progesterone, its metabolites and enzymes responsible for the conversion of progesterone and its metabolites using ELISA. Data suggests that compound 3b binds and down regulates of 5α-reductase by specifically inhibiting production of progesterone metabolites that are capable of promoting breast cancer proliferation, epithelial mesenchymal transition and migration. This study establishes the proof of concept and generation of new leads for additional targeting of breast cancer. [ABSTRACT FROM AUTHOR]

The current study aims to develop a PAN India database of medicinal plants along with their phytochemicals and geographical availability. The database consists of 6959 unique medicinal plants belonging to 348 families which are available across 28 states and 8 union territories of India. The database sources the information on four different sections – traditional knowledge, geographical indications, phytochemicals, and chemoinformatics. The traditional knowledge reports the plant taxonomy with their vernacular names. A total of 27,440 unique phytochemicals associated with these plants were curated from various sources in this study. However, due to the non-availability of general information like IUPAC names, InChI key, etc. from reliable sources, only 22,314 phytochemicals have been currently reported in the database. Various analyses have been performed for the phytochemicals which include analysis of physicochemical and ADMET properties calculated from open-source web servers using in-house python scripts. The phytochemical data set has also been classified based on the class, superclass, and pathways respectively using NPClassifier, a deep learning framework. Additionally, the antiviral potency of the phytochemicals was also predicted using two machine learning models – Random Forest and XGBoost. The database aims to provide accurate and exhaustive data of the traditional practice of medicinal plants in India in a single platform integrating and analyzing the rich customary practices and facilitating the development and identification of plant-based therapeutics for a variety of diseases. The database can be accessed at https://neist.res.in/osadhi/. [Display omitted] • OSADHI is a PAN India database of medicinal plants and phytochemicals. • OSADHI reports highest number of medicinal plants and their phytochemicals in India. • Traditional knowledge, physiochemical properties, ADMET, classification, structures, are some major insights. • State-wise and Union Territory-wise availability of each medicinal plant has been reported. [ABSTRACT FROM AUTHOR]

The rich biodiversity of North East India is one of the recognized biodiversity hotspots of the world. This region comprises of eight states (Assam, Arunachal Pradesh, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim, and Tripura) with diverse ethnic communities having invaluable traditional knowledge/practices, passed through genesis. The medicinal plants in this region are rich in natural products/phytochemicals and have been used extensively by pharmaceutical industries. The present study is an attempt to develop a comprehensive resource of the medicinal plants with a quantitative analysis of the phytochemicals which can enhance knowledge on therapeutic indications and contribute in drug discovery and development. The database is a collection of 561 unique plants comprising of 9225 phytochemicals. The physiochemical properties of the phytochemicals were analyzed using indigenous python scripts whereas for the ADMET properties, open access servers were used. The data available in NEI-MPDB will help to connect the cutting-edge approach of various research groups and will help to translate the information into economic wealth by the pharmaceutical industries. The database is openly accessible at https://neist.res.in/neimpdb/. [Display omitted] • A database of medicinal plants integrating different ethnic communities of North East India was developed. • Repository of taxonomy, ethnobotany, phytochemicals, and ADMET properties of medicinal plants. • The extensive phytochemical data helping traditional drug discovery. • A robust knowledge base for the conservation of ethnobotanical and bio-resources of NE region of India. [ABSTRACT FROM AUTHOR]

In an attempt to develop a new class of cardiovascular drugs, a series of novel carbazolyloxy phenylquinazoline derivatives 9a – g have been synthesized and evaluated as angiotensin converting enzyme (ACE) inhibitors. Most of these compounds exhibited activity as significant ACE inhibitors and three compounds ( 9b , 9c & 9e ) showed maximum inhibitory potency in enzyme based assays. To render support to the experimental results, a series of quinazolinone derivatives were docked into active site of ACE and identified the probable binding modes compared to Lisinopril. Also we have identified common pharmacophore hypothesis (AAADDRR) among the best docked conformers of most potent compounds in a series of compounds. The most potent 9b , 9c , 9e compounds shared common active site with the Lisinopril binding site and retained the key active site residue interactions. The obtained results from pharmacological and molecular modeling studies can be utilized for further optimization of identified hits for selective inhibition of ACE. [ABSTRACT FROM AUTHOR]

A series of novel quinazolinone hybrids were synthesized by employing click chemistry and evaluated for anti-proliferative activities against MCF-7, HeLa and K562 cell lines. Among these cell lines, HeLa cells were found to respond effectively to these quinazolinone hybrids with IC 50 values ranging from 5.94 to 16.45 μM. Some of the hybrids ( 4q , 4r , 4e , 4k , 4t , 4w ) with promising anti-cancer activity were further investigated for their effects on the cell cycle distribution. FACS analysis revealed the G1 cell cycle arrest nature of these hybrids. Further to assess the senescence inducing ability of these compounds, a senescence associated β-gal assay was performed. The senescence inducing nature of these compounds was supported by the effect of hybrid ( 4q ) on p16 promoter activity, the marker for senescence. Moreover, cells treated with most effective compound ( 4q ) show up-regulation of p53, p21 and down-regulation of HDAC-1, HDAC-2, HDAC-5 and EZH2 mRNA levels. Docking results suggest that, the triazole nitrogen showed Zn +2 mediated interactions with the histidine residue of HDACs. [ABSTRACT FROM AUTHOR]

Mitogen activated protein kinases including c-Jun N-terminal kinase play an indispensable role in inflammatory diseases. Investigation of reported JNK-1 inhibitors indicated that diverse heterocyclic compounds bearing an amide group rendered potent JNK-1 inhibitory activity which prompted us to synthesize new JNK-1 inhibitors containing a pyrazole heterocyclic group. A DABCO mediated 1,3-dipolar cycloaddition reaction in neat resulted in pyrazole carboxylic acid which was converted to desired amides. Upon confirmation of the structures, all the compounds were screened for JNK-1 inhibitory activity and in vivo anti-inflammatory activity. Several synthesized analogues have exhibited JNK-1 inhibitory activity less than 10 μM, in particular compounds 9c , 10a and 10d were found to be potent among all the compounds. [ABSTRACT FROM AUTHOR]

Abstract: The generation of a bihelical (figure of 8) motif has been illustrated by trans opening of EDTAA with l-cystine-di-OMe and d-penicillamine disulfide-di-OMe. In the former case the open cyclic system, arising by cis addition, was secured as a minor product. [Copyright &y& Elsevier]

Abstract: New conceivable synthetic approach for the construction of nitrogen-rich 1,2,3-triazolo-pyrrolo[2,1-c][1,4]benzodiazepine (TPBD, 3a–c) trimers has been developed. The first example of a bis-1,2,3-triazolo-bridged unsymmetrical PBD trimer has been successfully synthesized by employing a CuAAC type ‘click’ chemistry protocol. This efficient route generates tri-imine functionality in a single molecule. It has been envisaged that such tri-imine functionalities could bring in efficient interaction with DNA in a sequence-selective manner in the minor groove of duplex DNA. One of the representative analogues 3c has shown improved DNA-binding ability (ΔT m 23.7°C) by thermal denaturation studies using CT-DNA and this data is also supported by molecular modeling (MD) studies. [Copyright &y& Elsevier]

Abstract: A series of benzothiazole and benzoxazole linked pyrrolobenzodiazepine conjugates attached through different alkane or alkylamide spacers was prepared. Their anticancer activity, DNA thermal denaturation studies, restriction endonuclease digestion assay and flow cytometric analysis in human melanoma cell line (A375) were investigated. One of the compounds of the series 17d showed significant anticancer activity with promising DNA-binding ability and apoptosis caused G0/G1 phase arrest at sub-micromolar concentrations. To ascertain the binding mode and understand the structural requirement of DNA binding interaction, molecular docking studies using gold program and more rigorous 2ns molecular dynamic simulations using Molecular Mechanics-Poisson–Boltzman Surface Area (MM-PBSA) approach including the explicit solvent were carried out. Further, the compound 17d was evaluated for in vivo efficacy studies in human colon cancer HT29 xenograft mice. [Copyright &y& Elsevier]

Abstract: A series of novel N- and O- perfluoroalkyl triazole tagged thienopyrimidines 6a–c and 7a–d was synthesized in two steps from thienopyrimidin-4-ones 2 through O- and N-propargylated regioisomers 3a–i and 4a–i respectively. Compound 2 was reacted with propargyl bromide to form O- and N-propargylated regioisomers 3 and 4 in definite proportions. Each regioisomer was separated and independently subjected to [3 + 2] cycloaddition using perfluoroalkyl azides through Click reaction under Sharpless conditions and obtained exclusively anti product in each case. The formation of two regioisomers in the first step and single anti addition product in the next step could be explained based on computational studies carried out at B3LYP/6-31G(d) level of theory. Results of Fukui function indices at the reactive centers are in accordance with the observations. On evaluation of the synthesized molecules for their binding affinities towards adenosine receptors, 4d and 4f were found to be selective to A1 over A2A receptors. [Copyright &y& Elsevier]

Abstract: The total syntheses of decarestrictines C1 and C2 have been described. The synthetic strategy involves a practical and flexible approach using esterification and ring-closing metathesis to unite the acid and alcohol fragments. The acid fragments are enantiomers of each other and have been prepared from l-(−)-malic acid via similar transformations; in Sharpless asymmetric epoxidation, (+)-DET has been used for decarestrictine C1 and (−)-DET for decarestrictine C2. The alcohol fragment is identical for both decarestrictines C1 and C2 and has been accessed from d-(+)-mannitol. Comparison of the 1H and 13C NMR data combined with the computational studies predicts the presence of two conformations without and with hydrogen bonding (conformational isomers I and II for decarestrictine C1), respectively. The 1H and 13C NMR data for decarestrictine C2 completely agreed with the analytical data reported by Kibayashi et al. [Copyright &y& Elsevier]

Abstract: C2-Fluoro substituted DC-81, and its dimers that comprise of two C2-fluoro substituted DC-81 subunits tethered to their C8-position through simple alkane spacers as well as piperazine moiety side-armed with symmetrical alkyloxy spacers have been designed and synthesized. These fluoro substituted pyrrolo[2,1-c][1,4]benzodiazepines have shown remarkable DNA-binding ability and most of them possess promising anticancer activity, having GI50 values in micromolar to nanomolar concentration range. DNA thermal denaturation studies show that some of these compounds (14a–c and 15) increase the ΔT m values in the range of 28.9–38°C, and this is further confirmed by the restriction endonuclease studies. This study illustrates the importance of introducing fluoro substitution at the C2-position apart from the incorporation of a piperazine ring in between the alkyloxy linker for enhancement of the DNA-binding ability in comparison to DSB-120 and SJG-136 (ΔT m =10.2 and 25.7°C). Moreover, the variations in the DNA-binding ability with respect to fluoro substitution in this class of dimers has been investigated by molecular modeling studies. Some representative C2-fluoro substituted dimers (8a and 14a) have also exhibited significant anticancer activity in the 60 cancer cell line assay of the National Cancer Institute (NCI). [Copyright &y& Elsevier]

Abstract: A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. It is a publicly available web-based database (via the Internet) at http://203.199.182.73/gnsmmg/databases/plid/. [Copyright &y& Elsevier]

Abstract: A new series of 10-substituted 5,5-dioxo-5,10-dihydro[1,2,4]triazolo[1,5-b]-[1,2,4]benzothiadiazine arylsulfonamide derivatives (10a–j and 13a–f) was synthesized. The structures of these compounds were confirmed on the basis of spectral data, elemental analysis, X-ray analysis, and quantum chemical calculations. These compounds were evaluated for their efficacy as antibacterial agents against various Gram-positive and Gram-negative strains of bacteria. Amongst these compounds 10f and 10i were the most active compounds against Escherichia coli and 13e against E. coli as well as Bacillus subtilis. Moreover, other compounds also showed potent inhibitory activity in comparison to the standard drugs. [Copyright &y& Elsevier]

Abstract: Two- and three-dimensional quantitative structure-activity relationship (QSAR) and docking studies were carried out on a series of pyridopurinones, to model their phosphodiesterase 5 (PDE5) inhibitory activities. 2D-QSAR was performed using the heuristic and best multi linear regression (BMLR) methods in CODESSA (comprehensive descriptors for structural and statistical analysis), which had given linear models between the inhibitory activity and five descriptors of PDE5 inhibitors, with r 2 =0.987, 0.987, q 2 =0.970, 0.970, F =166.71, 166.71 and s 2 =0.0004, 0.0176, respectively. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) have provided statistically significant models with q 2 values of 0.784, 0.742 and r 2 values of 0.975, 0.972 respectively. The predictive ability of the models was validated using a set of 6 compounds that were not included in the training set and the predictive r 2 obtained for the test set was 0.901 and 0.888 respectively. Docking studies were employed to determine the probable binding conformation of these analogues in the PDE5 active site using the programs GOLD and AutoDock whose results were found complementary with 3D-QSAR maps. Since the potency towards PDE5 and the selectivity over PDE6 is important for the successful development of new PDE5 inhibitors, a PDE6 homology model was built using Insight II and Modeller with Phi-Psi BLAST alignment. The molecules were docked in the active site of PDE6 and analyzed the probable reasons for selectivity of these molecules towards PDE5 over PDE6. Mapping the 3D-QSAR models to the active site of PDE5 provides a new insight into the protein-inhibitor interactions and helpful in designing potent and selective PDE5 inhibitors for the treatment of erectile dysfunction. [Copyright &y& Elsevier]

Abstract: Evaluation and validation of homology modeling protocols are indispensable for membrane proteins as experimental determination of their three-dimensional structure is an arduous task. The prediction ability of Modeller, MOE, InsightII-Homology and Swiss-PdbViewer (SPV) with different sequence alignments CLUSTALW, BLAST and 3D-JIGSAW have been assessed. The sequence identity of the target and template was chosen to be in the range of 25–35%. Validation protocols to assess the structure, fold and stereochemical quality, are employed by comparing with experimental structures. Two different ranking schemes are suggested to evaluate the performance of each methodology based on the validation scores. While unambiguous preference for any given procedure did not surface, statistically Modeller and the sequence alignment technique, 3D-JIGSAW, gave best results amongst the chosen protocols. The present study helps in selecting the right protocols when modeling membrane proteins, which form a major class of drug targets. [Copyright &y& Elsevier]

Abstract: Existing treatments of human cancer, which is characterized by abnormal proliferation of cells often lead to fatal outcomes. Sequence selective silencing of oncogene expression using siRNA technology is emerging as a potential solution for cancer treatment. The exclusive selectivity and easy application to virtually any therapeutic target including intracellular factors and transcription factors renders siRNA oligonucleotide applications very promising. However, synthesis of siRNA having sufficient knockdown efficiency is laborious and cost intensive. The database is designed in order to aid the synthesis of siRNAs, which target human oncogenes (OsiRNAs). It provides OsiRNAs of known efficacy from previous experiments with links to published literature and theoretically pre-generated putative target sequences. In addition, links to available theoretical tools, databases and literature corresponding to siRNAs in general are also provided. The links to literature provide information about role of siRNA in therapeutics, chemical properties and transfection methods. Statistical analysis of mono-, di- and tri- mers located in OsiRNAs of known efficacies is performed to identify positional preferences and screen specific motifs. This analysis aids the design and synthesis of effective siRNAs, which particularly target human oncogenes. The database can be accessed at http://203.199.182.73/gnsmmg/databases/dstho.html. [Copyright &y& Elsevier]

Comparative protein modeling, active site analysis and binding site specificity for the homologous series of plasmepsins (PM's), present in food vacuole of Plasmodium falciparum, are carried out. Four loops (L1, L2, L3 and L4), which show maximum structural deviations irrespective of type of inhibitor, have been identified. Comparison of the crystal structures of ligand complexes reveal that residues belonging to these loops have negligible coulomb and VDW interactions with the inhibitor but play major role in determining the openness of the binding cavity. The coulomb and VDW interactions between the PMII subsite pockets and inhibitors, which play a major role in determining the inhibition constants, are delineated. Besides small displacements, the catalytic residues D32 of PMII undergoes rotation around the Cγ–Cβ single bond to assist catalysis whereas side chain conformational deviations are not observed in D214 on plasmepsin activation. The mutant S79D of PMII (and the corresponding residues of PMI and PMIV) which helps in recognizing and cleaving substrates containing lysine at P1 position is surrounded by highly polar atmosphere stabilized by lysine. However, in PMIII significantly lower polar atmosphere around the mutant A78S/A78D is observed. Large buried side chain area of residues located at M15 and I289 of PMII (and corresponding residues of PMI and PMIV) corroborates well with increase in specificity constant for hydrophobic substrates. [Copyright &y& Elsevier]

Density functional theory (B3LYP) calculations with double and triple-ζ quality basis sets were performed on the Li+ and Na+ π-complexes of corannulene 2, sumanene 3CH2, heterosumanenes 3X, triphenylene 4 and heterotrindenes 5X. The metal ions bind to both convex and concave faces of buckybowls, with a consistent preference to bind to the convex surface by about 1–4 kcal/mol. The metal ion complexation with the π-framework of the central six-membered ring span wider range compared to benzene, indicating the control of size, curvature and electronic perturbations over the strength of cation–π interactions. Computations show that the bowl-to-bowl inversion barriers are only slightly altered upon metal complexation, indicating the continuity of bowl-to-bowl inversion despite metal complexation. We have calculated the binding energies of model systems, triphenylene (4) and heterotrindenes (5X), which indicate that the interaction energies are controlled by electronic factors. While the inversion barrier is dependent mainly on the size of the heteroatom, the extent of binding is independent of the size of the atom or the bowl depth. [Copyright &y& Elsevier]

Monosubstituted tricyclo[2.1.0.02,5]pentan-3-one derivatives have been synthesised and subjected to hydride reduction. Quite unexpectedly and in contrast to earlier observations in related systems, anti-selectivity has been encountered in these substrates. Computational studies employing various models reproduce the observed facial preference and indicate that the causative factor for the anti-preference could be the polarization of the C1&z.sbnd;C5 strained σ bond. [Copyright &y& Elsevier]

Several endo-tricyclo[5.2.1.02,6]decan-10-ones and endo-tricyclo[5.2.1.02,6]dec-8-en-10-ones with hetero atom modifications at the distal C-4 position have been subjected to hydride reduction. π-Face selectivities in these systems are largely governed by the same electronic factors that were earlier identified in the case of the norbornyl system. A computational study demonstrates good predictability at the semi-empirical level. [Copyright &y& Elsevier]

A straight forward entry into nine membered B ring of eleutherobin as oxy analog and its cyctotoxic properties on HBL cell lines is described. Molecular modeling studies were carried out to ascertain the binding of the model compound to the active site of β-tubulin. [Copyright &y& Elsevier]