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SAR and QSAR in Environmental Research Volume 30, 2019 - Issue 1
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Combining molecular docking and molecular dynamics studies for modelling Staphylococcus aureus MurD inhibitory activity

M.A. AzamDepartment of Pharmaceutical Chemistry, JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru), IndiaCorrespondence[email protected] [email protected]
ORCID Iconhttp://orcid.org/0000-0001-9770-9371View further author information
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S. JupudiDepartment of Pharmaceutical Chemistry, JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru), IndiaORCID Iconhttp://orcid.org/0000-0001-8005-1905View further author information
ORCID Icon,
N. SahaDepartment of Pharmaceutical Chemistry, JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru), IndiaView further author information
&
R.K. PaulDepartment of Pharmaceutical Chemistry, JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru), IndiaView further author information
Pages 1-20 | Received 27 Jun 2018, Published online: 08 Nov 2018

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A. Arwansyah, A.R. Arif, I. Ramli, I. Kurniawan, S. Sukarti, M. Nur Alam, I. Illing, A. Farid Lewa & B. Manguntungi. (2021) Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations. SAR and QSAR in Environmental Research 32:9, pages 699-718.
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S.L. Wu, J. Zhao, H.B. Sun, H.Y. Li, Y.Y. Yin & L.L. Zhang. (2021) Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. SAR and QSAR in Environmental Research 32:3, pages 221-246.
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S.L. Wu, L.F. Wang, H.B. Sun, W. Wang & Y.X. Yu. (2020) Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis. SAR and QSAR in Environmental Research 31:7, pages 547-570.
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L.F. Wang, Y. Wang, Z.Y. Yang, J. Zhao, H.B. Sun & S.L. Wu. (2020) Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses. SAR and QSAR in Environmental Research 31:5, pages 373-398.
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Y. Wang, L.F. Wang, L.L. Zhang, H.B. Sun & J. Zhao. (2020) Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies. SAR and QSAR in Environmental Research 31:2, pages 149-170.
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Srikanth Jupudi, Mohammed Afzal Azam & Ashish Wadhwani. (2019) Synthesis, molecular docking, binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors. Journal of Receptors and Signal Transduction 39:3, pages 283-293.
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Articles from other publishers (8)

Dharmendra Kumar, Nandan Sarkar, Kuldeep K. Roy, Dheeraj Bisht, Deepak Kumar, Bitasta Mandal, Mogana Rajagopal & Yadu Nandan Dey. (2023) The Potential of Mur Enzymes as Targets for Antimicrobial Drug Discovery. Current Drug Targets 24:8, pages 627-647.
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Shashank Shekher Mishra, Neeraj Kumar, Bidhu Bhusan Karkara, C. S. Sharma & Sourav Kalra. (2022) Identification of potential inhibitors of Zika virus targeting NS3 helicase using molecular dynamics simulations and DFT studies. Molecular Diversity 27:4, pages 1689-1701.
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Vinita Gaur & Surojit Bera. (2022) Recent developments on UDP-N-acetylmuramoyl-L-alanine-D-gutamate ligase (Mur D) enzyme for antimicrobial drug development: An emphasis on in-silico approaches. Current Research in Pharmacology and Drug Discovery, pages 100137.
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Yingli Jin, Panpan Yang, Li Wang, Zeyuan Gao, Jia Lv, Zheyu Cui, Tiedong Wang, Dacheng Wang & Lin Wang. (2021) Galangin as a direct inhibitor of vWbp protects mice from Staphylococcus aureus ‐induced pneumonia . Journal of Cellular and Molecular Medicine 26:3, pages 828-839.
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Shahrukh Qureshi, Ravina Khandelwal, Maddala Madhavi, Naveesha Khurana, Neha Gupta, Saurav K. Choudhary, Revathy A. Suresh, Lima Hazarika, Chillamcherla D. Srija, Khushboo Sharma, Mali R. Hindala, Tajamul Hussain, Anuraj Nayarisseri & Sanjeev K. Singh. (2021) A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Current Topics in Medicinal Chemistry 21:9, pages 790-818.
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Srikanth Jupudi, Mohammed Afzal Azam & Ashish Wadhwani. (2020) Design, synthesis and molecular modelling of phenoxyacetohydrazide derivatives as Staphylococcus aureus MurD inhibitors. Chemical Papers 75:3, pages 1221-1235.
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Mohammed Afzal Azam & Srikanth Jupudi. (2020) MurD inhibitors as antibacterial agents: a review. Chemical Papers 74:6, pages 1697-1708.
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Mohammed Afzal Azam & Srikanth Jupudi. (2019) Structure-based virtual screening to identify inhibitors against Staphylococcus aureus MurD enzyme. Structural Chemistry 30:6, pages 2123-2133.
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