@article { ISI:000360934400005, title = {Protein ligand complex guided approach for virtual screening}, journal = {Combinatorial Chemistry \& High Throughput Screening}, volume = {18}, number = {6}, year = {2015}, month = {JAN}, pages = {577-590}, publisher = {BENTHAM SCIENCE PUBL LTD}, address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

The target ligand association data is a rich source of information which is not exploited enough for drug design efforts in virtual screening. A java based open-source toolkit for Protein Ligand Network Extraction (J-ProLiNE) focused on protein-ligand complex analysis with several features integrated in a distributed computing network has been developed. Sequence alignment and similarity search components have been automated to yield local, global alignment scores along with similarity and distance scores. 10000 proteins with co-crystallized ligands from pdb and MOAD databases were extracted and analyzed for revealing relationships between targets, ligands and scaffolds. Through this analysis, we could generate a protein ligand network to identify the promiscuous and selective scaffolds for multiple classes of proteins targets. Using J-ProLiNE we created a 507 x 507 matrix of protein targets and native ligands belonging to six enzyme classes and analyzed the results to elucidate the protein-protein, protein-ligand and ligand-ligand interactions. In yet another application of the J-ProLiNE software, we were able to process kinase related information stored in US patents to construct disease-gene-ligand-scaffold networks. It is hoped that the studies presented here will enable target ligand knowledge based virtual screening for inhibitor design.

}, keywords = {Complexes, ligand, protein, scaffolds, sequences, similarity score, virtual screening}, issn = {1386-2073}, doi = {10.2174/1386207318666150703112620}, author = {Karthikeyan, Muthukumarasamy and Pandit, Deepak and Vyas, Renu} } @article {43817, title = {Nature of selenium hydrogen bonding: gas phase spectroscopy and quantum chemistry calculations}, journal = {Physical chemistry Chemical physics}, volume = {19}, year = {2017}, month = {SEP}, pages = {24179-24187}, type = {Article}, abstract = {

Subsequent to the recent re-definition of hydrogen bonding by the IUPAC committee, there has been a growing search for finding the presence of this ever interesting non-covalent interaction between a hydrogen atom in an X-H group and any other atom in the periodic table. In recent gas phase experiments, it has been observed that hydrogen bonding interactions involving S and Se are of similar strength to those with an O atom. However, there is no clear explanation for the unusual strength of this interaction in the case of hydrogen bond acceptors which are not conventional electronegative atoms. In this work, we have explored the nature of Se hydrogen bonding by studying indole...dimethyl selenide (indmse) and phenol...dimethyl selenide (phdmse) complexes using gas phase IR spectroscopy and quantum chemistry calculations. We have found through various energy decomposition analysis (EDA) methods and natural bond orbital (NBO) calculations that, along with electrostatics and polarization, charge transfer interactions are important to understand Se/S hydrogen bonding and there is a delicate balance between the various interactions that plays the crucial role rather than a single component of the interaction energy. An in-depth understanding of this type of non-covalent interaction has immense significance in biology as amino acids containing S and Se are widely present in proteins and hence hydrogen bonding interactions involving S and Se atoms contribute to the folding of proteins.

}, keywords = {Center-Dot-O, Clusters, Co-Ordination, Complexes, intermolecular interactions, Proteins, Replacement, spectra, Strength, Sulfur}, issn = {1463-9076}, doi = {10.1039/c7cp05265k}, author = {Mishra, Kamal K. and Singh, Santosh K. and Ghosh, Paulami and Ghosh, Debashree and Das, Aloke} } @article {48217, title = {Synthesis and crystal structures of Mn(II) and Co(II) complexes as catalysts for oxidation of cyclohexanone}, journal = {Inorganics}, volume = {10}, year = {2022}, month = {JUL}, pages = {100}, type = {Article}, abstract = {

The global demand on adipic usage in the production of plasticizers and synthetic polyamide is increasing. In line with the search for an efficient and energy-conserving way to isolate adipic acid (AA) in good yields, this paper introduces the oxidization of cyclohexanone utilizing two new coordination compounds, [Mn(2,6-pydc)(2)](imi) (1) and [Co(H(2)pza)(2)(H2O)(2)(NO3)].NO3 (2), as catalysts. Compounds 1 and 2 were synthesized by room temperature and refluxing methods, and characterized by spectral analyses (IR and UV-Vis.), SEM, BET, TGA, elemental, and X-ray crystallography. The single crystal structure of compound 1 revealed that pyridinedicarboxylate (2,6-pydc) and imidazole (imi) moieties were coordinated to the Mn(II) atom through imine nitrogen and deprotonated oxygen atoms, to form an undistorted octahedral coordination geometry with the N2O4 donor set. The axial and equatorial planes containing O2, O4, O5, and O7 atoms were from two adjacent 2,6-pydc ligands which formed the unidendate donor ligand; imi, on the other hand, acted as a bidendate donor ligand. For compound 2, the Co(II) atom was being coordinated by two pyrazinamide (H(2)pza) moieties, which acted as an unidendate donor ligand; two water molecules occupying the axial position, and one nitrate molecule occupying the apical position, were within the coordination sphere; a nitrate molecule was disordered outside the coordination sphere. The distance, 4.658 angstrom, between the Co1 atom and the N8 atom of the uncoordinated nitrate molecule, was within the range reported elsewhere. Cyclohexanone peroxidation experiments revealed that compound 1 exhibited unique catalytic performance by giving a 72.8\% yield in adipic acid, in comparison to the 71.3\% yield obtained with compound 2. The yields in AA were maintained by way of recyclability evaluation. The reaction kinetics of compound 2 gave less activation energy, E-a 2938 J mol(-1), while the thermodynamic parameters indicated that the chemical reactivity of cyclohexanone on the active surfaces of compounds 1 and 2 was via monolayer physisorption.

}, keywords = {cobalt, Complexes, cyclohexanone, Imidazole, managanese, Oxidation, pyrazinamide, pyridinedicarboxylate}, doi = {10.3390/inorganics10070100}, author = {Tella, Adedibu C. and Isaac, Aaron Y. and Clayton, Hadley S. and Ogunlaja, Adeniyi S. and Venugopalan, Aswathy T. and Prabu, Marimuthu and Thirumalaiswamy, Raja} }