Computational Sciences - Research Publications
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Item Caesium carbonate promoted regioselective O-functionalization of 4,6-diphenylpyrimidin-2(1H)-ones under mild conditions and mechanistic insight(Royal Society of Chemistry, 2023-06-05T00:00:00) Kumar, Vijay; Singh, Praval Pratap; Dwivedi, Ashish Ranjan; Kumar, Naveen; Rakesh kumar, None; Chandra Sahoo, Subash; Chakraborty, Sudip; Kumar, VinodA facile one-step catalyst free methodology has been developed for the regioselective functionalization of 4,6-diphenylpyrimidin-2(1H)-ones under mild conditions. Selectivity towards the O-regioisomer was achieved by using Cs2CO3 in DMF without use of any coupling reagents. A total of 14 regioselective O-alkylated 4,6-diphenylpyrimidines were synthesized in 81-91% yield. In the DFT studies it was observed that the transition state for the formation of the O-regioisomer is more favourable with Cs2CO3 as compared to K2CO3. Furthermore, this methodology was extended to increase the O/N ratio for the alkylation of 2-phenylquinazolin-4(3H)-one derivatives. � 2023 The Royal Society of Chemistry.Item Discovery of plant-based phytochemical�as effective antivirals that target the non-structural protein C of the Nipah virus through computational methods(Taylor and Francis Ltd., 2023-05-24T00:00:00) Sureshan, Muthusamy; Prabhu, Dhamodharan; Joshua, Sharon Nissi; Sasikumar, Shruti Vardhini; Rajamanikandan, Sundarraj; Govindhapriya, Muthukumar; Umadevi, Venkatachalam; Kadhirvel, SarabojiNipah Virus (NiV) belongs to the Paramyxoviridae family and was first identified during an outbreak in Malaysia. Some initial symptoms include mild fever, headache and sore throat, which could escalate to respiratory illness and brain inflammation. The mortality rate of NiV infection can range from 40% to 75%, which is quite high. This is mainly due to the lack of efficient drugs and vaccines. In most instances, NiV is transmitted from animals to humans. Non-Structural Proteins (C, V and W) of the Nipah virus impede the host immune response by obstructive the JAK/STAT pathway. However, Non-Structural Proteins�C (NSP-C) plays a vital role in NiV pathogenesis, which includes IFN antagonist activity and viral RNA production. In the present study, the full-length structure of NiV-NSP-C was predicted using computational modelling, and the stability of the structure was analysed using 200 ns molecular dynamic (MD) simulation. Further, the structure-based virtual screening identified five potent phytochemicals (PubChem CID: 9896047, 5885, 117678, 14887603 and 5461026) with better binding affinity against NiV-NSP-C. DFT studies clearly showed that the phytochemicals had higher chemical reactivity, and the complex MD simulation depicted that the identified inhibitors exhibited stable binding with NiV-NSP-C. Furthermore, experimental validation of these identified phytochemicals would likely control the infection of NiV. Communicated by Ramaswamy H. Sarma. � 2023 Informa UK Limited, trading as Taylor & Francis Group.Item Tinospora cordifolia: a potential neuroprotective agent against various neurodegenerative diseases(Elsevier GmbH, 2023-09-19T00:00:00) Singh, Randeep; Bhattacharyya, Chinmoyee; Prashar, Vikash; Arora, Tania; Sharma, Arti; Changotra, Harish; Parkash, JyotiIntroduction: Neurodegenerative diseases negatively affect the various neuronal populations of the central nervous system (CNS). Moreover, conventional treatment strategies are inefficient and have considerable side effects. Since Ayurveda has always been considered an effective alternative to synthetic drugs, Tinospora cordifolia, an age-old renowned herb in Ayurveda with great medicinal importance, is drawing the attention of researchers. The effect of the crude extract of T. cordifolia and its constituents in alleviating neurodegenerative diseases has been reported previously and recently. Methods: This study followed thorough research on scientific databases like PubMed, Google Scholar, and ScienceDirect regarding the practical implications of T. cordifolia extracts and compounds in alleviating neurodegeneration. Various search terms like �neurodegenerative diseases�, �T. cordifolia and neurodegeneration�, �signalling mechanisms of neurodegeneration�, and �neuroprotective effect of T. cordifolia� have been used. Results: Several in vitro studies have suggested that T. cordifolia extracts and compounds can improve memory, cognition, and learning deteriorated by various neurodegenerative diseases. They also enhance the potential of the antioxidant system by restoring Glutathione (GSH) and Superoxide dismutase (SOD) levels and scavenging the free radicals that cause neuronal oxidative stress and neurodegeneration. Conclusion: This review article summarises the various aspects of T. cordifolia against different neurodegenerative diseases and its future potential therapeutic values. It also emphasises the need to investigate other compounds present in T. cordifolia. Limitations and future prospects: Exploring anti-oxidative, anti-inflammatory, and neuroprotective properties proved T. cordifolia to be a life saviour. Despite this, extensive clinical and pharmacological studies are required to evaluate the precise dosage and formulation of its constituents. � 2023 Elsevier GmbHItem Pd/C-Catalyzed Carbonylative Amidation for the Synthesis of 2-Carboxamidocyclohexane-1,3-diones(American Chemical Society, 2023-10-05T00:00:00) Sheetal, None; Chauhan, Arvind Singh; Sharma, Ajay Kumar; Sharma, Navneet; Giri, Kousik; Das, PralayHerein, a first-ever heterogeneous Pd/C-catalyzed single-step tandem approach for the synthesis of 2-carboxamidocyclohexane-1,3-diones via direct carbonylative C-H amidation of cyclohexane-1,3-diones is reported. The reaction progressed under base-, oxidant-, and ligand-free conditions employing oxalic acid as a CO surrogate and sodium azide as a nitrogen precursor in a double-layer vial system. � 2023 American Chemical Society.Item Recent advances and challenges of carbon nano onions (CNOs) for application in supercapacitor devices (SCDs)(Elsevier Ltd, 2023-06-26T00:00:00) Kaur, Simran; Krishnan, Abhinand; Chakraborty, SudipSince the discovery of CNOs, the number of publications and citations related to these carbon nanostructures research are still growing, indicating their strange behavior attracting the attention of the scientific community. As far as, the reviews published on CNOs have paid attention to the synthesis, characterization, surface functionalization and biomedical applications. However, very few works have summarized the advances and challenges of CNOs for application in SCDs. In this review, our objective is to summarize the recent advancement and challenges of the synthetic strategy, morphology, and electrochemical performance of different CNOs based materials along with their application in SCDs. The review commence with a short description of CNOs history and its structure, followed by the CNOs based supercapacitors and its recent advancement for the capacitance value augmentation. Then emphasized the synthetic procedure of Doped CNOs and its applications. After a critical analysis of the literature, we have discussed the molecular mechanism behind the improved electrochemical behavior of doped CNOs as compared with the pristine CNOs. A common guidance for selecting dopants based on their specific applications in supercapacitors have been explored. Further, the physico-chemical and electrochemical properties of CNO-composites are also discussed. We summarized the DFT based studies for CNOs based materials, and the advantages of Molecular Modeling/ReaxFF based simulation techniques for modeling of CNOs based electrodes and task specific electrolyte design for SCDs. The CNOs based materials are very good candidates for supercapacitor electrode design, with various challenges, more specifically the structural ordering of CNOs, electrochemical performance and condition of supercapacitor health. The Artificial Intelligence (AI)/Machine Learning (ML) based literatures are discussed and recommended several AI/ML based algorithms in the field of supercapacitors and energy storage devices (ESDs) to predict the specific capacitance value and the supercapacitors condition of health. We have outlined the current challenges and opportunities in this field. To the best of our knowledge, the review will be useful to provide a systematic framework for CNOs based research in the field of supercapacitor devices. � 2023 Elsevier LtdItem The Comparative Genomics and Network Analysis of eNOS by Using Different Bioinformatics Approaches(Bentham Science Publishers, 2023-01-27T00:00:00) Banerjee, Arpita; Singh, Randeep; Arora, Nymphaea; Arora, Tania; Prashar, Vikash; Godara, Priya; Sharma, Arti; Changotra, Harish; Parkash, JyotiBackground: Nitric oxide synthase (NOS) is an enzyme that catalyzes the synthesis of nitric oxide (NO) from L-arginine. It has three isoforms-(i) neuronal NOS (nNOS or NOS1), which participates in neural transmission; (ii) inducible NOS (iNOS or NOS2), which produces NO in macrophages; and (iii) endothelial NOS (eNOS or NOS3) that regulates blood pressure. The eNOS is mainly expressed in blood vessels and is a crucial regulator of endothelial homeostasis. Objective: The present study aimed to unravel the role of eNOS in different signaling pathways and its involvement as a therapeutic target in various neurodegenerative disorders. Methods: This study used various in silico methods for comprehensive genomic analysis of eNOS in 16 organisms from 7 different phyla. Prediction of conserved domains and evolutionary relationship for eNOS among 16 organisms was made. Various physical and chemical parameters, signal peptides, and transmembrane regions that helped understand its functional relevance were also studied. Results: Three transcription factor binding sites (TFBS), i.e., CP2, AR, and LDSPOLYA, were identified in human eNOS, while ATF1, T3R, and STAT1 were predicted in mouse eNOS. Transcription factors were identified for each regulatory region in human as well as mouse eNOS. eNOS protein was predicted to harbor 14 different post-translational modification (PTM) sites, most of which have phosphorylation (serine followed by threonine and tyrosine phosphorylation) followed by sumoylation and palmitoylation among all the organisms used in the current study. However, human eNOS has a relatively lower number of PTM sites for tyrosine phosphorylation. Conclusion: Structures of eNOS isoform, consistent with available biochemical and structural data, provide substantial insight into the NOS conformational changes, which give in-depth knowledge of the mechanism of eNOS, and will be helpful for better understanding the role of eNOS in pathophysiology. � 2023 Bentham Science Publishers.Item Spin-polarized linear dispersions, lattice dynamics and transport properties of quaternary Heusler alloys (LiMgXSb)(Elsevier Ltd, 2023-01-16T00:00:00) Nag, Abhinav; Gupta, Yuhit; Kumar, JagdishIn this study, we are predicting a new class of materials obtained by substituting a magnetic transition metal ion in quaternary Heusler alloys with the formula LiMgXSb (X = Co, Cr, Fe, Mn). We found that all the studied alloys exhibit a ferromagnetic ground state except LiMgCoSb. The phonon dispersions of the studied alloys computed within spin-polarized density functional perturbation theory (DFPT) do not exhibit any imaginary frequencies indicating that the proposed alloys are dynamically stable. The band structure calculations show that the studied alloys are metallic and exhibit the states near Fermi level for both spins. The fixed spin moment (FSM) calculations have been employed to exclude the possibility of other ferromagnetic ground states. One of the most interesting aspects of the band structure of these compounds is the existence of multiple band crossings leading to multiple Weyl points in the Brillouin zone. We have also computed the spin-polarized transport properties of these alloys. Our results find that doping charge carriers in the unit cell can significantly enhance the power factor and ZT. Electron doping is more effective for improving the power factor. Our findings show that among all the alloys LiMgFeSb has the highest ZT value with electron doping. Our studied materials constitute a new family of three-dimensional materials exhibiting band degeneracies that lead to Weyl points. � 2023 Elsevier B.V.Item Rotational state-changes in C5N? by collisions with He and H2(Oxford University Press, 2023-04-28T00:00:00) Biswas, R.; Giri, K.; Gonz�lez-S�nchez, L.; Gianturco, F.A.; Lourderaj, U.; Sathyamurthy, N.; Veselinova, A.; Yurtsever, E.; Wester, R.The anion C5N? is one of the largest linear (C, N)-bearing chains detected in the interstellar medium. Here we present and discuss the general features of new ab initio potential energy surfaces describing the interaction of this linear anion with He and H2. We employ a Legendre Polynomials expansion representation for the former and an artificial neural network fit for the latter. We then carry out quantum scattering calculations to yield rotationally inelastic cross-sections for collisions with He and H2, using relative translational energy values in the range of 0.1-300 cm?1. We then obtained the corresponding inelastic rate coefficients as a function of temperature covering the range from 1 to 100 K. The results for these two systems are compared with each other, as well as with the earlier results on the C3N? colliding with the same partners. We found that the final inelastic rate coefficients for this anion are all fairly large, those from collisions with H2 being the largest. The consequences of such findings on their non-equilibrium rotational populations in interstellar environments are discussed in our conclusions. � 2023 The Author(s) Published by Oxford University Press on behalf of Royal Astronomical Society.Item Advances in the computational methods to understand protein folding and stability(Inderscience Publishers, 2022-11-09T00:00:00) Srikanth, Srimari; Srinivasan, Thamarai Selvi; Prabhu, Dhamodharan; Kadhirvel, SarabojiUnderstanding the molecular basis of life is important for advances in fundamental and applied biological research. Numerous and complex biological activities occur simultaneously in all living cells in a controlled manner to execute an optimal equilibrium and function. Specifically, life depends on the regular functioning of the protein molecules, which depends upon the attainment of the correct three-dimensional structure and its stability. Therefore, deducing a fundamental understanding of how proteins fold and stabilise in the native states is of great intellectual and technological significance. Similar to all natural events, protein folding is a physicochemical process that is much more complex in-vivo, with the association of chaperones and/or other co-factors. Perturbations in protein�s stability results in misfolded proteins and their aggregated forms associated with protein misfolding disorders. Interestingly, researchers are involved in developing computational methods to predict the folded state of the protein and its stabilising mechanisms, which are essential in designing biotechnologically and medicinally important protein molecules. The present review aims to explore developments in the computational procedures which aid in understanding protein folding and stability and its applications. Copyright � 2021 Inderscience Enterprises Ltd.Item Discovery of potent inhibitors targeting Glutathione S-transferase of Wuchereria bancrofti: a step toward the development of effective anti-filariasis drugs(Institute for Ionics, 2023-02-16T00:00:00) Sureshan, Muthusamy; Prabhu, Dhamodharan; Rajamanikandan, Sundarraj; Saraboji, KadhirvelLymphatic filariasis (LF) is one of the major health problems for the human kind in developing countries including India. LF is caused by three major nematodes namely Wuchereria bancrofti, Brugia malayi, and Brugia timori. The recent statistics of World Health Organization (WHO) showed that 51 million people were affected and 863 million people from 47 countries around worldwide remain threatened by LF. Among them, 90% of the filarial infection was caused by the nematode W. bancrofti. Approved drugs were available for the treatment of LF but many of them developed drug resistance and no longer effective in all stages of the infection. In the current research work, we explored the Glutathione S-transferase (GST) of W. bancrofti, the key enzyme responsible for detoxification that catalyzes the conjugation of reduced GSH (glutathione) to xenobiotic compounds. Initially, we analyzed the stability of the WbGST through 200 ns MD simulation and further structure-based virtual screening approach was applied by targeting the substrate binding site to identify the potential leads from small molecule collection. The in silico ADMET profiles for the top-ranked hits were predicted and the predicted non-toxic lead molecules showed the highest docking score in the range of ?�12.72 kcal/mol to ?�11.97 kcal/mol. The cross docking of the identified hits with human GST revealed the potential binding specificity of the hits toward WbGST. Through WbGST�lead complex simulation, the lead molecules were observed to be stable and also intactly bound within the binding site of WbGST. Based on the computational results, the five predicted non-toxic molecules were selected for the in vitro assay. The molecules showed significant percentage of inhibition against the filarial worm Setaria digitata which is the commonly used model organism to evaluate the filarial activity. In addition, the molecules also showed better IC50 than the standard drug ivermectin. The identified lead molecules will lay a significant insight for the development of new drugs with higher specificity and lesser toxicity to control and treat filarial infections. Graphical abstract: [Figure not available: see fulltext.] � 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.