School Of Basic And Applied Sciences

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    Nucleation and Growth of Iron (II) Oxide Nanoparticles in Thermal Arc Plasma and Their Interaction Study with SARS-CoV-2: A Computational Approach
    (Institute of Electrical and Electronics Engineers Inc., 2021-07-01T00:00:00) Mitra, Rahul; Patel, Shivkumar; Ghorui, S.; Mahapatra, S.K.; Banerjee, I.
    A computational model for nucleation and growth of iron (II) oxide nanoparticle (IONP) in thermal plasma has been developed. A nondimensional form of the aerosol general dynamic equations (GDEs) along with a discrete volume sectional model assumption is used to numerically solve the coupled system of GDEs. The variation in supersaturation ratio and the mean particle diameter of IONPs with respect to temperature across the plasma reactor has been presented. The scatter plot showing the distribution of particle number density of certain size across the reactor chamber is shown. In silico molecular docking study was performed to reveal the putative interaction of the IONPs with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus. The results revealed significant binding affinity of IONPs with 6LZG (spike receptor-binding domain complexed with its receptor ACE2) and 5RH4 (main protease) of SARS-COV-2 by forming hydrogen and hydrophobic bonds with nearby amino acid residues. The interactions of IONPs are associated with the conformational changes in the protein which could be used to treat and control SARS-CoV-2 infection. � 1973-2012 IEEE.
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    Homology modeling and molecular docking study of biogenic Muga silk nanoparticles as putative drug-binding system
    (John Wiley and Sons Inc, 2020-12-22T00:00:00) Asapur, Prithvi C.; Sahare, Purushottam D.; Mahapatra, Santosh Kumar; Banerjee, Indrani
    The recent emergence of natural biopolymers as drug delivery vehicles is attributed to their biodegradability and less systemic toxicity. Muga silk nanoparticles were prepared using microwave radiolysis method and were characterized by Fourier transform infrared spectroscopy, circular dichroism, X-ray diffraction and transmission electron microscopy. To find the applicability in the drug delivery system of these nanoparticle and to know the binding site(s), a computational study was carried out. The structure of the Muga protein is predicted using homology modeling, which is further used for molecular docking. The in silico molecular docking between the Muga silk nanoparticles and three United States Food and Drug Administration-approved model drugs of doxorubicin, remdesivir and dexamethasone was performed. The binding capabilities and binding energy of the Muga silk proteins with these drugs are determined. The basic idea of the active site and the residues involved in the binding of the drugs/ligands is also studied. Doxorubicin showed the highest binding affinity of ?8.7�kcal/mol and that of the remdesivir and dexamethasone are found to be ?7.2 and ?7.9 kcal/mol, respectively. Such high binding affinity(ies) would help for slow drug release kinetics and the other two drugs can be loaded when the requirement is for sustained drug release. The data were also validated using the UV�vis. spectroscopy. � 2020 International Union of Biochemistry and Molecular Biology, Inc.
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    Oxazoline/amide derivatives against M. tuberculosis: experimental, biological and computational investigations
    (Taylor and Francis Ltd., 2023-11-10T00:00:00) Bajpai, Priyanka; Singh, Ankit Kumar; Kandagalla, Shivanada; Chandra, Phool; Kumar Sah, Vimlendu; Kumar, Pradeep; Grishina, Maria; Verma, Om Prakash; Pathak, Prateek
    Tuberculosis (TB) is a treatable contagious disease that continuously kills approximately 2 million people yearly. Different oxazoline/amide derivatives were synthesized, and their anti-tuberculosis activity was performed against different strains of Mtb. This study designed the anti-Mtb compounds based on amide and oxazoline, two different structural moieties. The compounds were further synthesized and characterized by spectral techniques. Their anti-Tb activity was evaluated against strain (M. tuberculosis: H37Rv). Selectivity and binding affinity of all synthesized compounds (2a�2e, 3a�3e) against PanK in Mtb were investigated through molecular docking. Molecular dynamics simulation studies for the promising compounds 2d and 3e were performed for 100 ns. The stability of these complexes was assessed by calculating the root mean square deviation, solvent-accessible surface area, and gyration radius relative to their parent structures. Additionally, free energy of binding calculations were performed. Among all synthesized compounds, 2d and 3e had comparable antitubercular activity against standard drug, validated by their computational and biological study. � 2023 Informa UK Limited, trading as Taylor & Francis Group.
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    Phytochemical Profiling and Pharmacological Evaluation of Leaf Extracts of Ruellia tuberosa L.: An In Vitro and In Silico Approach
    (John Wiley and Sons Inc, 2023-08-04T00:00:00) Sharma, Akanksha; Kumar, Adarsh; Singh, Ankit Kumar; Singh, Harshwardhan; Kumar, K. Jayaram; Kumar, Pradeep
    The present study was designed to appraise the photoprotective, antioxidant, and antibacterial bioactivities of Ruellia tuberosa leaves extracts (RtPE, RtChl, RtEA, RtAc, RtMe, and RtHMe). The results showed that, RtHMe extracts of R. tuberosa was rich in total phenolic content, i. e., 1.60 mgGAE/g dry extract, while highest total flavonoid content was found in RtAc extract, i. e., 0.40 mgQE/g. RtMe showed effective antioxidant activity (%RSA: 58.16) at the concentration of 120 ?L. RtMe, RtEA and RtHMe exhibited effective in vitro antibacterial activity against Gram-negative bacteria (E. coli). In silico docking studies revealed that paucifloside (?11.743 kcal/mol), indole-3-carboxaldehyde (?7.519 kcal/mol), nuomioside (?7.275 kcal/mol), isocassifolioside (?6.992 kcal/mol) showed best docking score against PDB ID 2EX8 [penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-G], PDB ID 6CQA (E. coli dihydrofolate reductase protein complexed with inhibitor AMPQD), PDB ID 2Y2I [Penicillin-binding protein 1B in complex with an alkyl boronate (ZA3)] and PDB ID 2OLV (from S. aureus), respectively. Docked phytochemicals also showed good drug likeness properties. � 2023 Wiley-VHCA AG, Zurich, Switzerland.
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    In Silico Studies of Indole Derivatives as Antibacterial Agents
    (Korean Pharmacopuncture Institute, 2023-06-30T00:00:00) Shah, Mridul; Kumar, Adarsh; Singh, Ankit Kumar; Singh, Harshwardhan; Narasimhan, Balasubramanian; Kumar, Pradeep
    Objectives: Molecular docking and QSAR studies of indole derivatives as antibacterial agents. Methods: In this study, we used a multiple linear regressions (MLR) approach to construct a 2D quantitative structure activity relationship of 14 reported indole derivatives. It was performed on the reported antibacterial activity data of 14 compounds based on theoretical chemical descriptors to construct statistical models that link structural properties of indole derivatives to antibacterial activity. We have also performed molecular docking studies of same compounds by using Maestro module of Schrodinger. A set the molecular descriptors like hydrophobic, geometric, electronic and topological characters were calculated to represent the structural features of compounds. The conventional antibiotics sultamicillin and ampicillin were not used in the model development since their structures are different from those of the created compounds. Biological activity data was first translated into pMIC values (i.e. -log MIC) and used as a dependent variable in QSAR investigation. Results: Compounds with high electronic energy and dipole moment were effective antibacterial agents against S. aureus, indole derivatives with lower ?2 values were excellent antibacterial agents against MRSA standard strain, and compounds with lower R value and a high 2?v value were effective antibacterial agents against MRSA isolate. Conclusion: Compounds 12 and 2 showed better binding score against penicillin binding protein 2 and penicillin binding protein 2a respectively. Copyright � Korean Pharmacopuncture Institute
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    Synthesis and in-silico Studies of 4-phenyl Thiazol-2-amine Derivatives as Putative Anti-breast Cancer Agents
    (Bentham Science Publishers, 2023-03-22T00:00:00) Lavanya, Kanamarlapudi Joshna; Kaur, Kamalpreet; Jaitak, Vikas
    Background: Breast cancer (BC) is the second-leading cause of cancer-related fatalities in women after lung cancer worldwide. The development of BC is significantly influenced by estrogen receptors (ERs). The problem with current cancer treatments is selectivity, target specificity, cytotoxicity, and developing resistance. Thiazole scaffolds are gaining popularity in drug discovery due to their broad range of biological activity. It has the extraordinary capacity to control a variety of cellular pathways, and its potential for selective anticancer activity can be explored. Objective: Synthesis and in-silico studies of 4-Phenyl thiazol-2-amine derivatives as anti-breast cancer agents and molecular docking was used to assess the compounds� capacity to bind ER-? protein target. Methods: In this study, 4-Phenylthiazol-2-amine derivatives (3a-j) have been synthesized, and using Schrodinger software, molecular docking and ADME studies of the compounds were conducted. Results: Most of the synthesized compounds have shown dock scores ranging from-6.658 to 8.911 kcal/mol, which is better than the standard drug tamoxifen (-6.821 kcal/mol). According to molecular docking, all compounds fit in the protein�s active site and have the same hydrophobic pocket as the standard drug tamoxifen. Further, all of the compounds� ADME properties are below acceptable limits. Conclusion: Compound 3e showed the best docking score of-8.911. All compounds� ADME properties are within acceptable limits, and their p/o coefficients fall within a range, suggesting they will all have sufficient absorption at the site of action. These compounds can be evaluated invitro and in-vivo in the future. � 2024 Bentham Science Publishers.
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    Flavonoids as promising anticancer agents: an in silico investigation of ADMET, binding affinity by molecular docking and molecular dynamics simulations
    (Taylor and Francis Ltd., 2022-09-27T00:00:00) Biharee, Avadh; Yadav, Arpita; Jangid, Kailash; Singh, Yogesh; Kulkarni, Swanand; Sawant, Devesh M.; Kumar, Pradeep; Thareja, Suresh; Jain, Akhlesh Kumar
    Cancer is one of the most concerning diseases to humankind. Various treatment strategies are being employed for its treatment, out of which use of natural products is an essential one. Flavonoids have proven to be promising anticancer targets since decades. Also, tubulin is a significant biological target for the development of anticancer agents due to its crucial role in mitosis and abundance throughout the body. In the current study, in silico ADMET parameters of 104 flavonoids were examined, followed by molecular docking with the colchicine binding site of Tubulin protein (PDB; Id 4O2B). The best conformation from each flavonoid subcategory with the best docking score (MolDock score) was further subjected to 100 ns of molecular dynamics to investigate the protein-ligand complex�s stability. Different parameters such as RMSD, RMSF, rGy and SASA were calculated for the six flavonoids using molecular dynamic studies. The top most compound from all the six subcategories of flavonoids elicited best behavior in the colchicine binding site of Tubulin protein. This in silico study employing molecular docking and molecular dynamics simulation provides strong evidence for flavonoids to be excellent anti-tubulin agents for the treatment of cancer. Communicated by Ramaswamy H. Sarma. � 2022 Informa UK Limited, trading as Taylor & Francis Group.
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    A Review of Pyridine and Pyrimidine Derivatives as Anti-MRSA Agents
    (Bentham Science Publishers, 2022-07-06T00:00:00) Kumar, Adarsh; Singh, Ankit Kumar; Thareja, Suresh; Kumar, Pradeep
    Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a Gram-positive strain whose resistance against existing antibiotics is a significant concern for researchers across the globe. Gram-positive infections, particularly methicillin-resistant Staphylococcus aureus spreading among S. aureus isolates, increased exponentially from 29% in 2009 to 47% in 2014. Literature reviews revealed that about 13-74% of S. aureus strains are Methicillin-resistant world-wide. Objective: In this article, we have summarized the mechanism of bacterium resistance, molecular targets to treat MRSA, and the activity of reported pyridine and pyrimidine derivatives against methicillin-resistant Staphylococcus aureus. Results: The data collected for this study from online peer-reviewed research articles and the Molecular-docking study of reported anti-MRSA agents performed using the Maestro Module of Schrodinger software. In silico studies showed that some pyridine derivatives have better binding interactions than standard anti-MRSA agents. Conclusion: Molecular docking studies of reported pyridine derivatives resulted in excellent hits for developing novel anti-MRSA agents. Overall, this study will be of immense importance for researchers designing and developing target-based anti-MRSA agents. � 2023 Bentham Science Publishers.
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    The medicinal perspective of 2,4-thiazolidinediones based ligands as antimicrobial, antitumor and antidiabetic agents: A review
    (John Wiley and Sons Inc, 2022-06-18T00:00:00) Kajal, Kumari; Singh, Gurpreet; Pradhan, Tathagata; Bhurta, Deendyal; Monga, Vikramdeep
    2,4-Thiazolidinedione (2,4-TZD), commonly known as glitazone, is a ubiquitous heterocyclic pharmacophore possessing a plethora of pharmacological activities and offering a vast opportunity for structural modification. The diverse range of biological activities endowed with a novel mode of action, low cost, and easy synthesis has attracted the attention of medicinal chemists. Several researchers have integrated the TZD core with different structural fragments to develop a wide range of lead molecules against various clinical disorders. The most common sites for structural modifications at the 2,4-TZD nucleus are the N-3 and the active methylene at C-5. The review covers the recent development of TZD derivatives such as antimicrobial, anticancer, and antidiabetic agents. Various 2,4-TZD based agents or drugs, which are either under clinical development or in the market, are discussed in the study. Different synthetic methodologies for synthesizing the 2,4-TZD core are also included in the manuscript. The importance of various substitutions at N-3 and C-5 and the mechanisms of action and structure�activity relationships are also discussed. We hope this study will serve as a valuable tool for the scientific community engaged in the structural exploitation of the 2,4-TZD core for developing novel drug m\olecules for life-threatening ailments. � 2022 Deutsche Pharmazeutische Gesellschaft.
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    In silico identification of potential ?-secretase inhibitor of marine-algal origin: an anticancer intervention
    (Taylor and Francis Ltd., 2022-12-28T00:00:00) Singh, Atul Kumar; Choudhary, Princy; Singh, Sangeeta; Kumar, Shashank
    Gamma secretase (GS) activates notch signalling pathway (NSP) by liberating the truncated notch intracellular domain (NICD). The NSP is associated with the cancer development and progression, which makes GS a potential therapeutic target. Now day�s marine compounds emerged as a major source of bioactive entity. The NSP inhibition potential of marine-algal compounds has not yet been studied. Thus, in the present study, we have used molecular docking, molecular dynamics (MD) simulations, principal component analysis (PCA) and free energy and binding energy calculations to identify the potential GS inhibitors of marine-algal origin. Laminarin showed better docking score (?12.72) compared to the known GS inhibitor DAPT (?9.2). Laminarin formed H-Bond interaction with the Asp257 and Asp385 required for the catalytic cleavage activity of gamma-secretase. It potentially stabilised the structural parameters (RMSD, RMSF, Rg and SASA) of GS catalytic subunit compared to DAPT during the MD simulation. The PCA and free energy calculation revealed conformationally and energetically stable Laminarin�GS complex formation. Laminarin showed lower binding energy (?44.75 kcal/mol) with GS catalytic subunit than DAPT (?20.92 kcal/mol). In conclusion, the present study provides a marine-algal compound as a novel potential GS inhibitor, which requires further validation in experimental model. � 2022 Informa UK Limited, trading as Taylor & Francis Group.