• Ahmad Ebadi

      Articles written in Journal of Chemical Sciences

    • Quantum chemical analysis of potential anti-Parkinson agents

      Nima Razzaghi-Asl Sara Shahabipour Ahmad Ebadi Azam Bagheri

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      Monoamine oxidases (MAOs) are amine oxidoreductase falvoenzymes that belong to the integral proteins of the outer mitochondrial membrane. MAO exists in two distinct isoforms; MAO-A and MAO-B. Inhibition of MAO-A and MAO-B is important for developing antidepressant and antiparkinson agents, respectively. In the light of the above explanations, detailed structure binding relationship studies on the intermolecular binding components of MAO-B complexes may unravel the way toward developing novel anti-Parkinson agents. In the present contribution, intermolecular binding pattern for a series of experimentally validated 3-arylcoumarin MAO-B inhibitors (1–9) have been elucidated via molecular docking and density functional theory (DFT) calculations. Intermolecular binding energy components could not be analyzed by docking and due to this limitation, quantum mechanical (QM) calculations including functional B3LYP in association with split valence basis set (Def2-SVP) were applied to estimate the ligand-residue binding energies in the MAO-B active site. Moreover; results were interpreted in terms of calculated polarization effects that were induced by individual amino acids of the MAO-B active site. The results of the present study provide an approach to pharmacophore-based modification within the 3-arylcoumarin scaffold for potent MAO-B inhibitors.

    • Effect of substitution on the binding affinity of 5- bezylidenebarbituric acid derivatives to ctDNA: in silico and in vitro studies

      DARA DASTAN AHMAD EBADI

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      Cancer is the second leading cause of death worldwide. Drug researchers have encouraged by thegrowth of cancer incidence and low efficacy of current treatment to discover new drugs. Targeting specificregions of DNA to turn on/off genes has become an interesting research area. We evaluated the interaction of5-(benzylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione derivatives with ctDNA using in vitro and in silico studies. MD simulation indicated that selectivity switched from AT to CG-rich DNA strands whenthe chloro substitution was moved from meta to para position of the phenyl ring. 4-OH derivative showedsimilar affinity to AT and CG-rich DNA strand. Quantum mechanics calculation indicated that 4-OHderivative had the highest HOMO energy. The order in HOMO energies was compatible with the absorptiontitration result that demonstrated the order of Ka as 4-OH>4-Cl>3-Cl.

      Synopsis. 5-(benzylidene)-1,3-dimethylpyrimidine-2,4,6(1H,3H,5H)-trione derivatives could interact with ctDNA. MD simulation indicated that m- and p-chlorophenyl derivatives selectively bind to AT and CG-rich DNA strands respectively. The order in HOMO energies was compatible with absorption titration result that demonstrated the order of Ka as 4-OH > 4-Cl > 3-Cl.

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