Anamika Singh Gaur
Articles written in Journal of Chemical Sciences
Volume 129 Issue 5 May 2017 pp 515-531 Regular Article
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
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.
Volume 133 All articles Published: 8 September 2021 Article ID 0097
A perspective on the nature of cation-p interactions
NANDAN KUMAR ANAMIKA SINGH GAUR G NARAHARI SASTRY
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.
Volume 134 All articles Published: 22 April 2022 Article ID 0057 Regular Article
Applying polypharmacology approach for drug repurposing for SARS-CoV2
Esther Jamir Himakshi Sarma Lipsa Priyadarsinee Selvaraman Nagamani Kikrusenuo Kiewhuo Anamika Singh Gaur Ravindra K Rawal Natarajan Arul Murugan Venkatesan Subramanian G Narahari Sastry
Exploring the new therapeutic indications of known drugs for treating COVID-19, popularly known as drug repurposing, is emerging as a pragmatic approach especially owing to the mounting pressure to control the pandemic. Targeting multiple targets with a single drug by employing drug repurposing known as the polypharmacology approach may be an optimised strategy for the development of effective therapeutics. In this study, virtual screening has been carried out on seven popular SARS-CoV-2 targets (3CLpro,PLpro, RdRp (NSP12), NSP13, NSP14, NSP15, and NSP16). A total of 4015 approved drugs were screened against these targets. Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected based on the docking score, ability to interact with four or more targets and having a reasonably good number of interactions with key residues in the targets. The MD simulations and MM-PBSA studies showed reasonable stability of protein-drug complexes and sustainability of key interactions between the drugs with their respective targets throughout the course of MD simulations. The identified four drug molecules were also compared with the known drugs namely elbasvir and nafamostat. While the study has provided a detailed account of the chosen protein-drug complexes, it has explored the nature of seven important targets of SARSCoV-2 by evaluating the protein-drug complexation process in great detail.
Drug repurposing strategy against SARS-CoV2 drug targets. Computational analysis was performed to identify repurposable approved drug candidates against SARS-CoV2 using approaches such as virtual screening, molecular dynamics simulation and MM-PBSA calculations. Four drugs namely venetoclax, tirilazad, acetyldigitoxin, and ledipasvir have been selected as potential candidates.
Volume 135, 2023
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