Model molecules to classify CHO hydrogen-bonds.

We developed a set of conformationally locked molecules each of which makes a single CHO H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CHO H-bond varied from 0.93-1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CHO H-bond strengths quantified using a computational method.

Structural and Functional Diversities of the Hexadecahydro-1H-cyclopenta[a]phenanthrene Framework, a Ubiquitous Scaffold in Steroidal Hormones.

Hexadecahydro-1H-cyclopenta[a]phenanthrene framework (HHCPF) has been considered as one of the privileged scaffolds due to its versatile presence in many biologically essential molecules. In our quest to unravel the privileged nature of this framework, we undertook a systematic analysis of target binding and Absorption, Distribution, Metabolism, Elimination, Toxicity (ADMET)/physicochemical properties of 110 drugs containing HHCPF reported in DrugBank. Effect of number and positions of double bonds in the framework and substitutions at each carbon position on the target selectivity as well as drug like properties of these drugs were studied. Fifteen different scaffolds based on the numbers and positions of double bonds in the HHCPF were identified among these drugs. The optimum number of double bonds present in the HHCPF scaffolds was observed to be one to three, and one particular positional isomer is predominant among many scaffolds with same numbers of double bonds. Docking studies reveal the role of substituents at different positions to make specific interactions with their respective targets. Based on the docking interactions, we proposed structure based e-Pharmacophore models for seven important targets of HHCPF drugs. Good correlations were observed between the substitutions carbon positions 3 and 17 of the scaffolds and ADMET properties of the HHCPF drugs. This work enables preliminary prediction of the target selectivity and ADMET properties of a new HHCPF molecule based on the scaffold, substituents and the pharmacophoric features.

Nucleobases tagged to gold nanoclusters cause a mechanistic crossover in the oxidation of CO.

DNA is considered as a programmable building block for the assembly of nanomaterials that play a significant role in modern day nanotechnology and catalysis. In this work, density functional theory (DFT) is used to explore the possible application of complexes of DNA bases (adenine (A), thymine (T), guanine (G), and cytosine (C)) and their size expanded (x) counterparts with Au3 gold clusters as a model catalyst system for oxidation of CO to CO2. We investigate how the catalytic potential of the Au3 cluster is modulated on being tagged with the nuclebases. The CO oxidation can take place via the ER or the LH mechanism. On a pristine cluster, the LH pathway is thermodynamically favored. However, the CO oxidation reaction on the nucleobase tagged gold cluster is found to be more facile following the ER mechanism, with a significant reduction in the barrier height. The reduction in barrier height is attributed to the formation of additional hydrogen bonds between O2 and the polar sites of the attached base in the transition state. This indicates an interesting implication of tagging the cluster to a nucleobase resulting in a mechanistic crossover which is responsible for making nucleobase tagged gold clusters a better catalyst in comparison to pristine Au3 clusters. Our results indicate that nucleobase-gold cluster complexes open new avenues as efficient catalytic models having a wider range of technological applications.

Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process.

Mycobacterial cyclopropane synthase 1 (CmaA1) is one of the most important drug targets in anti tuberculosis drug discovery as it is responsible for cis-cyclopropanation at the distal position of unsaturated mycolates, which is an essential step for the pathogenicity, persistence and drug resistance. Five representative models of CmaA1 which correspond to different stages in the cyclopropanation process have been studied using molecular dynamics (MD) simulations. The MD simulations and structural analyses provide a detailed account of the structural changes in the active sites of CmaA1. CmaA1 has two distinct binding sites, i.e., cofactor binding site (CBS) and acyl substrate binding site (ASBS). The apo state of CmaA1 corresponds to a closed conformation where the CBS is inaccessible due to the existence of H-bond between Pro202 of loop10 (L10) and Asn11 of N-terminal α1 helix. However, cofactor binding leads to the breaking of this H-bond and thus the H-bond is absent in the holo form. The hydrophobic side chains orient towards the inner side of the ASBS upon cofactor binding to create a hydrophobic environment for the substrate. The cofactor and substrate tend to come close to each other facilitated by opening of L10 to exchange the methyl group from the cofactor to the substrate. The MD study also revealed that the system tends to regain the apo conformation within 40ns after releasing the product.