Insights on inhibition of Plasmodium falciparum plasmepsin I by novel epoxyazadiradione derivatives - molecular docking and comparative molecular field analysis.

In the present study, we have explored the anti-malarial potential of epoxyazadiradione, the natural entity extracted from the neem seed oil and its chemical derivatives, against Plasmodium falciparum. The Surflex dock analysis of 41 compounds against an indispensable target, plasmepsin I (PM-I) revealed that around 70% of the compounds are found to have good binding capacity with the consensus score (C-score) of 5 to 4 with few hydrogen bonds. To elucidate the major structural requirements, vital for binding with the plasmepsin enzyme and to develop the predictive models, three-dimentional quantitative structural activity relationship (3D-QSAR) - comparative molecular field analysis (CoMFA) was carried out using Sybyl X.0. Robust and predictive models were obtained with cross-validated correlation coefficient (q2) value of 0.967 and the non-cross-validated correlation coefficient (r2) value of 0.825, which were validated by an external test set with the predictive correlation coefficient r2(pred) values of 0.773. Three zones were identified for substitution with bulky groups and one zone for substitution with non-bulky groups. Three positions favouring the electronegative group substitution and one for the electropositive group substitution were identified. The physicochemical properties of ligands with the highest C-score were studied. Communicated by Ramaswamy H. Sarma.

Identification of 2-benzoxazolinone derivatives as lead against molecular targets of diabetic complications.

Diabetic complications follow multiple pathophysiological pathways involving aldose reductase (ALR2)-mediated polyol pathway, advanced glycation end products (AGEs) and reactive oxygen species formation. Literature suggests ALR2 inhibitors such as epalrestat to possess significant potential in retinopathy and neuropathy. Thus, in this study, multiple pathophysiology directed molecules targeting ALR2, AGEs and free radicals formation were designed using in silico techniques. Initially, database was screened via in silico tools to obtain hits with affinity for the catalytic domain of ALR2. Additional focus was laid on the presence of structural attributes responsible for AGE's inhibitory and anti-oxidant potential. Out of obtained hits, 2-benzoxazolinone scaffold was selected and ten derivatives were synthesized accordingly. Finally, the synthesized molecules were evaluated for their ALR2 and AGEs inhibitory activities along with free radical scavenging potency.

Computational design of new protein kinase D 1 (PKD1) inhibitors: homology-based active site prediction, energy-optimized pharmacophore, docking and database screening.

Protein kinase D 1 (PKD1) overexpression has a well-validated role in cancer progression and its inhibitors have defined a protective role-play of PKD1 for various cancers such as prostate, pancreatic and noninvasive breast cancers, and more. Therefore, the current research was aimed at designing new PKD1 inhibitors combining different ligand- and structure-based computational drug designing methodologies. Initially, the three-dimensional structure of PKD1's active site was computationally modeled, corrected using molecular dynamic simulations and validated for docking experiments. The highest active PKD1 inhibitor was used to develop a structure-based energetic pharmacophore (e-pharmacophore) model, and a final model was selected with five structural features (Pmodel_AADHR). Pmodel_AADHR was validated and used for database screening to obtain new hits against PKD1. These newly retrieved hits were docked against our PKD1 protein model, and those displaying essential interactions are reported herein as new hits, which could serve as new leads for cancer research, especially pancreatic cancer.

Molecular dynamics and integrated pharmacophore-based identification of dual [Formula: see text] inhibitors.

Despite increase in the understanding of the pathogenesis of rheumatoid arthritis (RA), it remains a tough challenge. The advent of kinases involved in key intracellular pathways in pathogenesis of RA may provide a new phase of drug discovery for RA. The present study is aimed to identify dual JAK3/[Formula: see text] inhibitors by developing an optimum pharmacophore model integrating the information revealed by ligand-based pharmacophore models and structure-based pharmacophore models (SBPMs). For JAK3 inhibitors, the addition of an aromatic ring feature and for [Formula: see text] the addition of a hydrophobic feature proposed by SBPMs lead to five-point pharmacophore (i.e., AADHR.54 (JAK3)) and six-point pharmacophore (i.e., AAAHRR.45 ([Formula: see text])). The obtained pharmacophores were validated and used for virtual screening and then for docking-based screening. Molecules were further evaluated for ADME properties, and their docked protein complexes were subjected to MM-GBSA energy calculations and molecular dynamic simulations. The top two hit compounds with novel scaffolds 2-oxo-1,2-dihydroquinoline and benzo[d]oxazole showed inhibitory activity for JAK3 and [Formula: see text].

Investigations on the role of CH O interactions and its impact on stability and specificity of penicillin binding proteins.

Penicillin binding proteins are recognized as important antibacterial targets because of their crucial role in the cell wall synthesis of bacteria. Alteration in the binding site of penicillin binding proteins is one of the major problems for beta lactam antibiotics to exert its effect. In the present study the influence of CH…O interactions in the conformational stability of penicillin binding proteins were analyzed in both Gram positive and Gram negative bacteria. CH…O interactions constitute about 20 to 25% of total hydrogen bonds and act as an important driving force in ligand selectivity. From our analysis we observed a total of 13,398 CH…O interactions in Gram positive bacteria and 10,855 CH…O interactions in Gram negative bacteria. It was interesting to observe that CH…O interactions were higher in Gram positive bacteria than in Gram negative bacteria, which augurs well for the discrepancy in cell wall of the bacteria. CH…O interactions are classified into four types depending on the interaction of acceptor residues with the back bone or side chain of CH groups. From our results we observed that major contribution to penicillin binding proteins was observed from side chain atoms of donor residues and back bone atoms of acceptor residues [SM CH…O] in both Gram positive and Gram negative bacteria. Conformational preference of Gram positive bacteria indicated that amino acids lacking side chain and the cyclized amino acids preferred to be in turn regions, whereas aromatic amino acids dominated in Gram negative bacteria. Our analysis gives detailed information about the principles involved in the conformational stability of penicillin binding proteins and the results will be useful for researchers exploring penicillin binding proteins.