• G NARAHARI SASTRY

      Articles written in Journal of Chemical Sciences

    • Dynamic ligand-based pharmacophore modeling and virtual screening to identify mycobacterial cyclopropane synthase inhibitors

      CHINMAYEE CHOUDHURY U DEVA PRIYAKUMAR G NARAHARI SASTRY

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      Multidrug resistance in Mycobacterium tuberculosis (M. Tb) and its coexistence with HIV arethe biggest therapeutic challenges in anti-M. Tb drug discovery. The current study reports a Virtual Screening(VS) strategy to identify potential inhibitors of Mycobacterial cyclopropane synthase (CmaA1), an importantM. Tb target considering the above challenges. Five ligand-based pharmacophore models were generatedfrom 40 different conformations of the cofactors of CmaA1 taken from molecular dynamics (MD) simulationstrajectories of CmaA1. The screening abilities of these models were validated by screening 23 inhibitors and1398 non-inhibitors of CmaA1. A VS protocol was designed with four levels of screening i.e., ligand-basedpharmacophore screening, structure-based pharmacophore screening, docking and absorption, distribution,metabolism, excretion and the toxicity (ADMET) filters. In an attempt towards repurposing the existing drugsto inhibit CmaA1, 6,429 drugs reported in DrugBank were considered for screening. To find compounds thatinhibit multiple targets of M. Tb as well as HIV, we also chose 701 and 11,109 compounds showing activitybelow 1 μM range on M. Tb and HIV cell lines, respectively, collected from ChEMBL database. Thus, a totalof 18,239 compounds were screened against CmaA1, and 12 compounds were identified as potential hits forCmaA1 at the end of the fourth step. Detailed analysis of the structures revealed these compounds to interactwith key active site residues of CmaA1.

    • Anomalous Lithium Adsorption Propensity of Monolayer Carbonaceous Materials: A Density Functional Study

      SWATI PANIGRAHI DEIVASIGAMANI UMADEVI G NARAHARI SASTRY

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      Interaction between lithium and carbonaceous materials has gained a lot of importance in lithium battery industry as an important source of energy and storage. The size, dimension, curvature and chirality of the carbonaceous materials are found to be very important factors in controlling the sequential binding oflithium. The propensity of lithium binding to the monolayer carbonaceous materials has been studied using Density functional theory (DFT). Structural and energetical parameters of the complexes have been analyzed through interaction energy, sequential energy, Mulliken population analysis and spin density distribution. Spindensity of odd Li doped systems reveals the preferences for addition of further lithium atoms on the surface. Upon analyzing the interaction energy in armchair carbon nanotubes (A-CNTs) and zigzag carbon nanotubes (Z-CNTs), it has been observed that external and internal surfaces of CNTs have contrasting binding preferences for sequential addition of Li atoms. Internal surface is found to be more feasible site for lithium adsorption than the external surface. This current study provides fundamental understanding of the mechanism of lithium adsorption in lithium battery.

    • Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis (MPDSTB)

      ANAMIKA SINGH GAUR ANSHU BHARDWAJ ARUN SHARMA LIJO JOHN M RAM VIVEK NEHA TRIPATHI PRASAD V BHARATAM RAKESH KUMAR SRIDHARA JANARDHAN ABHAYSINH MORI ANIRBAN BANERJI ANDREW M LYNN ANMOL J HEMROM ANURAG PASSI APARNA SINGH ASHEESH KUMAR CHARUVAKA MUVVA CHINMAI MADHURI CHINMAYEE CHOUDHURY D ARUN KUMAR DEEPAK PANDIT DEEPAK R BHARTI DEVESH KUMAR ER AZHAGIYA SINGAM GAJENDRA PS RAGHAVA HARI SAILAJA HARISH JANGRA KAAMINI RAITHATHA KARUNAKAR TANNEERU KUMARDEEP CHAUDHARY M KARTHIKEYAN M PRASANTHI NANDAN KUMAR N YEDUKONDALU NEERAJ K RAJPUT P SRI SARANYA PANKAJ NARANG PRASUN DUTTA R VENKATA KRISHNAN REETU SHARMA R SRINITHI RUCHI MISHRA S HEMASRI SANDEEP SINGH SUBRAMANIAN VENKATESAN SURESH KUMAR UCA JALEEL VIJAY KHEDKAR YOGESH JOSHI G NARAHARI SASTRY

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      Molecular Property Diagnostic Suite (MPDSTB) is a web tool (http://mpds.osdd.net) designed to assist the in silico drug discovery attempts towards Mycobacterium tuberculosis (Mtb). (MPDSTB) tool has nine modules which are classified into data library (1–3), data processing (4–5) and data analysis (6–9). Module 1 is a repository of literature and related information available on the Mtb. Module 2 deals with the protein targetanalysis of the chosen disease area. Module 3 is the compound library consisting of 110.31 million unique molecules generated from public domain databases and custom designed search tools. Module 4 contains toolsfor chemical file format conversions and 2D to 3D coordinate conversions. Module 5 helps in calculating the molecular descriptors. Module 6 specifically handles QSAR model development tools using descriptors generated in the Module 5. Module 7 integrates the AutoDock Vina algorithm for docking, while module 8 provides screening filters. Module 9 provides the necessary visualization tools for both small and large molecules. The workflow-based open source web portal,(MPDSTB) 1.0.1 can be a potential enabler for scientists engaged in drug discovery in general and in anti-TB research in particular.

    • On the origin of spurious errors in many-body expansion for water cluster

      SOUMEN SAHA M RAM VIVEK G NARAHARI SASTRY

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      Many-body expansion (MBE) has been carried out to investigate two- to five-body energy terms and their contributions to the interaction energy (IE) of (H₂O)₁₅ cluster. We have observed that the erroneous contribution of many-body terms on IE originated from cheaper convergence thresholds set as default in popular quantum mechanics packages. The propagation of errors from smaller to higher-body terms, due to the combinatorial nature of MBE, is also observed.

    • A perspective on the nature of cation-p interactions

      NANDAN KUMAR ANAMIKA SINGH GAUR G NARAHARI SASTRY

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      Recent years have witnessed a remarkable surge in the study of noncovalent interactions andtheir role in diverse areas of chemistry, biology, material science and allied fields. Among all, hydrogenbonding is quite extensively studied. Several other noncovalent interactions continue to attract wide attention.Notably, cation-π interactions play a crucial role in the function of several binding sites, reaction mechanisms,self-assemblies, catalytic mechanisms, adhesion and cohesion properties in many biological andchemical systems. The current review focuses on the character of cation-π interactions, its range and itsoccurrence from a conceptual point of view. The range and nature of cation-π interactions depend on the typeof π-system and cation involved, besides solvent and environment. The size and polarizability of the psystemsand the effective nuclear charge on cation and its multiplicity and spin dictate the structural andenergetic aspects of cation-π interaction. Further, factors affecting the modulation of strength and nature arebrought out in the review. The interplay between the cation-π interaction and the other noncovalent interactions,solvent and counter-ion effects are analysed, and the cooperativity of these forces in organizingsupramolecular architectures are discussed.

      How strong is cation-π interaction depends on various factors: It may be weak, medium or strong depending on the nature of cation, π system and environment. The strength of the interaction was shown to alternate a few orders of magnitude depending on the environment.

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