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A computational perception of BBOX1-IP3R3 interaction uncovers inhibitors for dysregulated calcium signalling in triple negative breast cancer

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SAR and QSAR in Environmental Research 2025年 1-28页

作者： Sangavi, P. Shri, G.R. Singh, S.K. Langeswaran, K. Department of Bioinformatics Alagappa University Karaikudi India Center for Bioinformatics Karpagam Academy of Higher Education Coimbatore India Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi India Department of Biomedical Science Alagappa University Karaikudi India

Triple Negative Breast Cancer (TNBC) is the most aggressive type of breast cancer unveiling negative expression on oestrogen receptors, progesterone receptors, and HER2. The anomalous activation of signalling pathways and specific types of mutations characterize the progression of TNBC. Protein-protein interaction in the tumour microenvironment plays a crucial role in tumour aggressiveness. Disrupting the signalling pathways that promote cell progression, migration, and survival opens up a promising avenue for targeting the aggressive form of TNBC. The present study emphasizes the molecular interaction mechanism driving the aggressive and recalcitrant TNBC between BBOX1-IP3R3. The BBOX1-IP3R3 complex destabilization was accomplished using compounds obtained from various databases through virtual screening, molecular, and essential dynamics. The interaction study revealed that the four hits bound at the interface and facilitated better binding affinity with the highest docking score and optimal binding free energy. In addition, the molecular dynamics simulation, PCA/FEL, and MM/PBSA analysis conclusively evaluate the binding potential of the compounds and unequivocally stabilize specific conformations or deception of the complexes in high-energy states. Thus, the identified compounds lead to the disruption of BBOX1-IP3R3 interaction, which aids in the therapeutic option of TNBC. © 2025 Informa UK Limited, trading as Taylor & Francis Group.

关键词： BBOX1-IP3R3 MMGB/PBSA molecular dynamics PCA/FEL analysis structure-based virtual screening TNBC

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Novel ligand-based docking;molecular dynamic simulations;and absorption, distribution, metabolism, and excretion approach to analyzing potential acetylcholinesterase inhibitors for Alzheimer's disease

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Journal of Pharmaceutical Analysis 2018年第6期8卷 413-420页

作者： Subramaniyan Vijayakumar Palani Manogar Srinivasan Prabhu Ram Avadhar Sanjeevkumar Singh Computational Phytochemistry Laboratory PG and Research Department of Botany and Microbiology AVVM Sri Pushpam College (Autonomous) Poondi Computer Aided Drug Design and Molecular Modeling Laboratory Department of Bioinformatics Alagappa University

Acetylcholinesterase(AChE) plays an important role in Alzheimer's disease(AD). The excessive activity of AChE causes various neuronal problems, particularly dementia and neuronal cell deaths. Generally, antiAChE drugs induce some serious neuronal side effects in humans. Therefore, this study sought to identify alternative drug molecules from natural products with fewer side effects than those of conventional drugs for treating AD. To achieve this, we developed computational methods for predicting drug and target binding affinities using the Schrodinger suite. The target and ligand molecules were retrieved from established databases. The target enzyme has 539 amino acid residues in its sequence alignment. Ligand molecules of 20 bioactive molecules were obtained from different kinds of plants, after which we performed critical analyses such as molecular docking; molecular dynamic(MD) simulations; and absorption, distribution, metabolism, and excretion(ADME) analysis. In the docking studies, the natural compound rutin showed a superior docking score of à 12.335 with a good binding energy value ofà73.313 kcal/mol. Based on these findings, rutin and the target complex was used to perform MD simulations to analyze rutin stability at 30 ns. In conclusion, our study demonstrates that rutin is a superior drug candidate for AD. Therefore, we propose that this molecule is worth further investigation using in vitro studies.

关键词： Alzheimer's disease Acetylcholinesterase Phytocompounds molecular docking Free energy calculations molecular dynamic simulations

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186 molecular dynamics and ligand based studies for the validation of potential inhibitors for SrtA againstBacillus anthracis

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Journal of Biomolecular Structure and Dynamics 2013年第SUPP 1期31卷 119-120页

作者： Sanjeev Kumar Singh[a][*] & Chandrabose Selvaraj[a] [a] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi 630003 India Phone: Phone: +91-4565-230725 Fax: Phone: +91-4565-230725

SrtA enzymes cleave the sorting signals of secreted proteins to form isopeptide (amide) bonds between the secreted proteins and peptidoglycan or polypeptides to function as the principal architects of theBacillus anthracis. Inhibition of SrtA can completely eradicate the growth ofB. anthracisdue to the lack of signals and so the SrtA is universally accepted as the drug target for all gram positive pathogens. Here, with the reported compounds, the pharmacophore-based virtual screening protocol has been used to obtain similar pharmacological property that derived new compounds to inhibit the SrtA structure. New compounds on AAAHR Pharmacophore hypothesis screening were treated with four phase of docking protocols with combined Glide-QPLD docking approach and charge accuracy variations were dominated by QM/MM approach. Finally, the compounds of 19941, 14704, 121962, 20137, and 19533 from binding db, Chembridge db, and Toslab were succeeded from the screening; these compounds are having better scoring, energy parameters, ADME physio/chemical properties, tendency to transfer the electrons between the protein–ligand interactions, and these compounds also predict having cell adhesion inhibitory activity. These screened compounds have better stability at active site loop regions with strong bonding interactions and these compounds on clinical trials will definitely emerge as better SrtA inhibitor against theB. anthracis.

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Synthesis, antibacterial studies, and molecular modeling studies of 3,4-dihydropyrimidinone compounds

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Journal of Chemical Biology 2016年第1期9卷 31-40页

作者： Ramachandran, Vanitha Arumugasamy, Karthiga Singh, Sanjeev Kumar Edayadulla, Naushad Ramesh, Penugonda Kamaraj, Sathish-Kumar Department of Natural Products Chemistry School of Chemistry Madurai Kamaraj University Madurai 625021 Tamil Nadu India Department of Zoology Thiagarajar College Madurai 625009 Tamil Nadu India Computer Aided Drug Designing and Molecular Modeling Laboratory Department of Bioinformatics Alagappa University Karaikudi 630 003 Tamil Nadu India School of Chemical Engineering Yeungnam University Gyeongsan 712-749 South Korea Ingeniería en Energía Universidad Politécnica de Aguascalientes Calle Paseo San Gerardo No. 207. Fracc. San Gerardo Aguascalientes 20342 AGS Mexico

The syntheses of dihydropyrimidinones (DHPMs) using solvent-free grindstone chemistry method. All the synthesized compounds exhibited significant activity against pathogenic bacteria. The current effort has been developed to obtain new DHPM derivatives that focus on the bacterial ribosomal A site RNA as a drug target. molecular docking simulation analysis was applied to confirm the target specificity of DHPMs. The crystal structure of bacterial 16S rRNA and human 40S rRNA was taken as receptors for docking. Finally, the docking score, binding site interaction analysis revealed that DHPMs exhibit more specificity towards 16S rRNA than known antibiotic amikacin. Accordingly, targeting the bacterial ribosomal A site RNA with potential drug leads promises to overcome the bacterial drug resistance. Even though, anti-neoplastic activities of DHPMs were also predicted through prediction of activity spectra for substances (PASS) tool. Further, the results establish that the DHPMs can serve as perfect leads against bacterial drug resistance. © 2015, Springer-Verlag Berlin Heidelberg.

关键词： Bioactivity Grindstone chemistry molecular modeling Ribosomal RNA

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182 molecular recognition between active site contour maps and ligand pharmacophoric sites predicts the future leads of HTLV-PR inhibitors

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Journal of Biomolecular Structure and Dynamics 2015年第SUPP 1期33卷 120页

作者： Sanjeev Kumar Singh[a][*] Chandrabose Selvaraj[a] [a] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Science Block Alagappa University Karaikudi 630004 Tamilnadu India

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molecular characterization of Lipopeptide Biosurfactant-Producing Paenibacillus dendritiformis isolated from Brackish water and its Potential Use in Microbial Enhanced Oil Recovery and Bioremediation

Research Square

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Research Square 2021年

作者： Nayarisseri, Anuraj Bhrdwaj, Anushka Sharma, Khushboo Khan, Arshiya Singh, Sanjeev Kumar In Silico Research Laboratory Eminent Biosciences Madhya Pradesh Indore452 010 India Bioinformatics Research Laboratory LeGene Biosciences Pvt Ltd Madhya Pradesh Indore452010 India Computer Aided Drug Designing and Molecular Modeling Lab Department of Bioinformatics Alagappa University Tamil Nadu Karaikudi630 003 India Department of Data Sciences Centre of Biomedical Research SGPGIMS Campus 13 Raebareli Rd Lucknow226014 India

The biosurfactants produced by microorganisms have a high demand for microbial-enhanced oil recovery (MEOR) and they have focused on a chemical surfactant for the past few decades for degrading petro-based pollutants and oil spills due to its non-toxicity and increasing bioavailability. The study aims to identify and screen potential lipopeptide biosurfactants produced by Paenibacillus species employing a design experiment based on RSM. The bacterial culture was isolated from Chilika Lake, India. The data generated from the biosurfactant stability experiments were used to fit a regression model using the parameters such as pH, temperature, and salinity to predict the E24 index. The R-squared value 0.91 obtained from the ANOVA model explains that the regression model was significant, and the model p-value obtained was © 2021, CC BY.

关键词： Phylogenetic

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195In silicostudy on HIV-PRIs substructures to terminate proteolytic activity in HTLV

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Journal of Biomolecular Structure and Dynamics 2013年第SUPP 1期31卷 127页

作者： Poonam Singh[a][*] Sanjeev Kumar Singh[b] Chandrabose Selvaraj[b] & Rama Kant Singh[a] [a] Toxicology Division Central Drug Research Institute Lucknow 226 001 Uttar Pradesh India Phone: Phone: +91-522-2612411 Fax: Phone: +91-522-2612411 [b] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi 630003 Tamilnadu India

Human T-lymphotropic virus (HTLV) is RNA retrovirus, which causes CD3 + and CD4 + T-cell type leukemia and demyelinating diseases, like tropical spastic myelopathy. The replicative stage of the virus is one of the critical stages for the development of the disease. At present, there are no approved therapeutic agents targeting HTLV. The HTLV mechanism of malignant cell growth in adult T-cell leukemia (ATL)/lymphoma, and the HTLV-PR has been an attractive target for anticancer drug design. In comparison with other retroviruses, HTLV also encodes protease (PR) enzyme which is essential for maturation. Both the HIV and HTLV proteases show high structural similarity but known inhibitors of HIV-PR are not able to inhibit the HTLV-PR, while comparing the binding pocket of both proteases, MET37 of HTLV shows repulsive role with known HIV inhibitors. Functional analysis of M37A mutation clearly shows that MET37 is highly important for the protease function. Available inhibitors were tested against the HTLV-PR binding pocket and failed to interact with MET37. Screening of similar libraries of known compounds provides better interactions with MET37 and further validation within vivoandin vitrostudies on these screened compounds will provide more strength in discovering potent inhibitor for HTLV-PR.

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Corrigendum to “design, synthesis, biological evaluation and in silico studies of novel 1,2,3-triazole linked benzoxazine-2,4-dione conjugates as potent antimicrobial, antioxidant and anti-inflammatory agents” [Arab. J. Chem. 15(11) (2022) 104226]

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Arabian Journal of Chemistry 2023年第9期16卷

作者： Manel Ben Hammouda Iqrar Ahmad Assia Hamdi Amal Dbeibia Harun Patel Nouha Bouali Walid Sabri Hamadou Karim Hosni Siwar Ghannay Fahad Alminderej Emira Noumi Mejdi Snoussi Kaïss Aouadi Adel Kadri Laboratory of Heterocyclic Chemistry Natural Product and Reactivity/CHPNR Department of Chemistry Faculty of Science of Monastir 5000 Monastir Tunisia Division of Computer Aided Drug Design Department of Pharmaceutical Chemistry R. C. Patel Institute of Pharmaceutical Education and Research Shirpur Maharashtra 425405 India Laboratory of Analysis Treatment and Valorization of Environmental Polluants and Products Faculty of Pharmacy Monastir University Tunisia Laboratoire de développement chimique galénique et pharmacologique des médicaments/Laboratory of Chemical Pharmaceutical and Pharmacological Development of Drugs) Faculty of Pharmacy Monastir Tunisia Department of Biology University of Ha'il College of Science P.O. Box 2440 Ha’il 2440 Saudi Arabia Molecular Diagnostics and Personalized Therapeutics Unit University of Hail Hail P.O. Box 2440 Saudi Arabia Laboratoire des Substances Naturelles Institut National de Recherche et d’Analyse Physico-chimique Biotechpôle Sidi Thabet 2020 Tunisia Department of Chemistry College of Science Qassim University Buraidah 51452 Saudi Arabia Laboratory of Genetics Biodiversity and Valorisation of Bioressources High Institute of Biotechnology-University of Monastir Monastir 5000 Tunisia University of Monastir Faculty of Science of Monastir Avenue of the Environment 5019 Monastir Tunisia Department of Chemistry Faculty of Science and Arts of Baljurashi Albaha University Saudi Arabia Faculty of Science of Sfax Department of Chemistry University of Sfax B.P. 1171 3000 Sfax Tunisia

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