{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:45:04Z","timestamp":1789191904713,"version":"build-2803163510"},"reference-count":64,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2022,6,25]],"date-time":"2022-06-25T00:00:00Z","timestamp":1656115200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002383","name":"King Saud University, Riyadh Saudi Arabia","doi-asserted-by":"publisher","award":["RSP-2021\/357"],"award-info":[{"award-number":["RSP-2021\/357"]}],"id":[{"id":"10.13039\/501100002383","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>NIMA-related kinase7 (NEK7) plays a multifunctional role in cell division and NLRP3 inflammasone activation. A typical expression or any mutation in the genetic makeup of NEK7 leads to the development of cancer malignancies and fatal inflammatory disease, i.e., breast cancer, non-small cell lung cancer, gout, rheumatoid arthritis, and liver cirrhosis. Therefore, NEK7 is a promising target for drug development against various cancer malignancies. The combination of drug repurposing and structure-based virtual screening of large libraries of compounds has dramatically improved the development of anticancer drugs. The current study focused on the virtual screening of 1200 benzene sulphonamide derivatives retrieved from the PubChem database by selecting and docking validation of the crystal structure of NEK7 protein (PDB ID: 2WQN). The compounds library was subjected to virtual screening using Auto Dock Vina. The binding energies of screened compounds were compared to standard Dabrafenib. In particular, compound 762 exhibited excellent binding energy of \u221242.67 kJ\/mol, better than Dabrafenib (\u221233.89 kJ\/mol). Selected drug candidates showed a reactive profile that was comparable to standard Dabrafenib. To characterize the stability of protein\u2013ligand complexes, molecular dynamic simulations were performed, providing insight into the molecular interactions. The NEK7\u2013Dabrafenib complex showed stability throughout the simulated trajectory. In addition, binding affinities, pIC50, and ADMET profiles of drug candidates were predicted using deep learning models. Deep learning models predicted the binding affinity of compound 762 best among all derivatives, which supports the findings of virtual screening. These findings suggest that top hits can serve as potential inhibitors of NEK7. Moreover, it is recommended to explore the inhibitory potential of identified hits compounds through in-vitro and in-vivo approaches.<\/jats:p>","DOI":"10.3390\/molecules27134098","type":"journal-article","created":{"date-parts":[[2022,6,26]],"date-time":"2022-06-26T21:01:41Z","timestamp":1656277301000},"page":"4098","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":78,"title":["Deep Learning and Structure-Based Virtual Screening for Drug Discovery against NEK7: A Novel Target for the Treatment of Cancer"],"prefix":"10.3390","volume":"27","author":[{"given":"Mubashir","family":"Aziz","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8935-2242","authenticated-orcid":false,"given":"Syeda Abida","family":"Ejaz","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seema","family":"Zargar","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, College of Science, King Saud University, P.O. Box 22452, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naveed","family":"Akhtar","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2516-5920","authenticated-orcid":false,"given":"Abdullahi Tunde","family":"Aborode","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Mississippi State University, Starkville, MS 39759, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5623-2685","authenticated-orcid":false,"given":"Tanveer","family":"A. Wani","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7817-425X","authenticated-orcid":false,"given":"Gaber El-Saber","family":"Batiha","sequence":"additional","affiliation":[{"name":"Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheira, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4358-5259","authenticated-orcid":false,"given":"Farhan","family":"Siddique","sequence":"additional","affiliation":[{"name":"Laboratory of Organic Electronics, Department of Science and Technology, Link\u00f6ping University, SE-60174 Norrk\u00f6ping, Sweden"},{"name":"Department of Pharmacy, Royal Institute of Medical Sciences (RIMS), Multan 60000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4192-1653","authenticated-orcid":false,"given":"Mohammed","family":"Alqarni","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8171-0439","authenticated-orcid":false,"given":"Ashraf Akintayo","family":"Akintola","sequence":"additional","affiliation":[{"name":"Department of Biomedical Convergence Science and Technology, Kyungpook National University, Daegu 41566, Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1002\/1878-0261.12152","article-title":"Dabrafenib inhibits the growth of BRAF-WT cancers through CDK16 and NEK9 inhibition","volume":"12","author":"Phadke","year":"2018","journal-title":"Mol. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.3389\/fphys.2020.606996","article-title":"Physiological and pathological roles of mammalian NEK7","volume":"11","author":"Sun","year":"2020","journal-title":"Front. Physiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/ncb1694","article-title":"Control of daughter centriole formation by the pericentriolar material","volume":"10","author":"Loncarek","year":"2008","journal-title":"Nat. Cell Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1016\/j.molcel.2017.01.015","article-title":"Nek7 protects telomeres from oxidative DNA damage by phosphorylation and stabilization of TRF1","volume":"65","author":"Tan","year":"2017","journal-title":"Mol. Cell"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"8771","DOI":"10.1038\/ncomms9771","article-title":"Mechanistic basis of Nek7 activation through Nek9 binding and induced dimerization","volume":"6","author":"Haq","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"102","DOI":"10.3389\/fcell.2017.00102","article-title":"Mitotic regulation by NEK kinase networks","volume":"5","author":"Fry","year":"2017","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/ni.3391","article-title":"The NEK-sus of the NLRP3 inflammasome","volume":"17","author":"Hauwermeiren","year":"2016","journal-title":"Nat. Immunol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1093\/abbs\/gmw080","article-title":"NEK7: A novel promising therapy target for NLRP3-related inflammatory diseases","volume":"48","author":"Xu","year":"2016","journal-title":"Acta Biochim. Biophys. Sin."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1091\/mbc.e16-09-0643","article-title":"NEK7 is required for G1 progression and procentriole formation","volume":"28","author":"Gupta","year":"2017","journal-title":"Mol. Biol. Cell"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"74","DOI":"10.5582\/bst.2020.01029","article-title":"NEK7: A potential therapy target for NLRP3-related diseases","volume":"14","author":"Liu","year":"2020","journal-title":"BioScience Trends"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1016\/j.trac.2008.10.001","article-title":"Identification and determination of metabolites and degradation products of sulfonamide antibiotics","volume":"27","year":"2008","journal-title":"Trends Anal. Chem."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1002\/med.10047","article-title":"Protease inhibitors of the sulfonamide type: Anticancer, antiinflammatory, and antiviral agents","volume":"23","author":"Supuran","year":"2003","journal-title":"Med. Res. Rev."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"925","DOI":"10.2174\/0929867033457647","article-title":"Anticancer and antiviral sulfonamides","volume":"10","author":"Scozzafava","year":"2003","journal-title":"Curr. Med. Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4093","DOI":"10.1016\/j.bmcl.2004.05.016","article-title":"Synthesis of new coumarin 3-(N-aryl) sulfonamides and their anticancer activity","volume":"14","author":"Reddy","year":"2004","journal-title":"Bioorganic Med. Chem. Lett."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.parint.2012.05.015","article-title":"Nuclease activity and ultrastructural effects of new sulfonamides with anti-leishmanial and trypanocidal activities","volume":"61","author":"Vega","year":"2012","journal-title":"Parasitol. Int."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.tetlet.2003.10.139","article-title":"Unprecedented observation of sulfonamides in the transesterification of N-unsubstituted carbamates with sulfonyl chlorides","volume":"45","author":"Dauvergne","year":"2004","journal-title":"Tetrahedron Lett."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1248\/cpb.47.809","article-title":"Selective monodesulfonylation of N, N-disulfonylarylamines with tetrabutylammonium fluoride","volume":"47","author":"Yasuhara","year":"1999","journal-title":"Chem. Pharm. Bull."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"4775","DOI":"10.1021\/jo00043a046","article-title":"1-Benzenesulfonyl-and 1-p-toluenesulfonyl-3-methylimidazolium triflates: Efficient reagents for the preparation of arylsulfonamides and arylsulfonates","volume":"57","author":"Rapoport","year":"1992","journal-title":"J. Org. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/S0040-4039(97)10638-4","article-title":"Neighbouring group assisted sulfonamide cleavage of Sharpless aminols under acetonation conditions","volume":"39","author":"Chandrasekhar","year":"1998","journal-title":"Tetrahedron Lett."},{"key":"ref_20","first-page":"893","article-title":"Drug therapy reviews: Trimethoprim-sulfamethoxazole","volume":"36","author":"Gleckman","year":"1979","journal-title":"Am. J. Hosp. Pharm."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1111\/j.1476-5381.1968.tb00475.x","article-title":"Trimethoprim, a sulphonamide potentiator","volume":"33","author":"Bushby","year":"1968","journal-title":"Br. J. Pharmacol. Chemother."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1093\/bib\/bbp023","article-title":"Recent advances in computer-aided drug design","volume":"10","author":"Song","year":"2009","journal-title":"Briefings Bioinform."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.1007\/s12272-015-0640-5","article-title":"Role of computer-aided drug design in modern drug discovery","volume":"38","author":"Macalino","year":"2015","journal-title":"Arch. Pharmacal Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1878","DOI":"10.1093\/bib\/bby061","article-title":"Recent applications of deep learning and machine intelligence on in silico drug discovery: Methods, tools and databases","volume":"20","author":"Rifaioglu","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1038\/nature03197","article-title":"Virtual screening of chemical libraries","volume":"432","author":"Shoichet","year":"2004","journal-title":"Nature"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy","volume":"47","author":"Friesner","year":"2004","journal-title":"J. Med. Chem."},{"key":"ref_28","first-page":"1","article-title":"High-throughput parallel blind virtual screening using BINDSURF","volume":"13","author":"Cecilia","year":"2012","journal-title":"BMC Bioinform."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1177\/1094342017697471","article-title":"METADOCK: A parallel metaheuristic schema for virtual screening methods","volume":"32","author":"Cecilia","year":"2018","journal-title":"Int. J. High Perform. Comput. Appl."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"335","DOI":"10.31887\/DCNS.2006.8.3\/tban","article-title":"The role of serendipity in drug discovery","volume":"8","author":"Ban","year":"2022","journal-title":"Dialogues Clin. Neurosci."},{"key":"ref_31","unstructured":"Huang, K., Fu, T., Khan, D., Abid, A., Abdalla, A., Abid, A., Glass, L.M., Zitnik, M., Xiao, C., and Sun, J. (2020). Moldesigner: Interactive design of efficacious drugs with deep learning. arXiv."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5545","DOI":"10.1093\/bioinformatics\/btaa1005","article-title":"DeepPurpose: A deep learning library for drug\u2013target interaction prediction","volume":"36","author":"Huang","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"B864","DOI":"10.1103\/PhysRev.136.B864","article-title":"Inhomogeneous electron gas","volume":"136","author":"Hohenberg","year":"1964","journal-title":"Phys. Rev."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1002\/qua.560280857","article-title":"Orthonormalization and symmetry adaptation of crystal orbitals","volume":"28","author":"Calais","year":"1985","journal-title":"Int. J. Quantum Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"021101","DOI":"10.1063\/1.3160670","article-title":"Virial theorem in the Kohn\u2013Sham density-functional theory formalism: Accurate calculation of the atomic quantum theory of atoms in molecules energies","volume":"131","author":"Ayers","year":"2009","journal-title":"J. Chem. Phys."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1021\/cr00005a001","article-title":"Approximate density functional theory as a practical tool in molecular energetics and dynamics","volume":"91","author":"Ziegler","year":"1991","journal-title":"Chem. Rev."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/9780470125847.ch4","article-title":"An introduction to density functional theory","volume":"7","author":"Bartolotti","year":"1996","journal-title":"Rev. Comput. Chem."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"6404","DOI":"10.1038\/s41598-022-10253-5","article-title":"Identification of potent inhibitors of NEK7 protein using a comprehensive computational approach","volume":"12","author":"Aziz","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"10705","DOI":"10.1021\/j100027a005","article-title":"Properties of Hydrogen-Bonded Complexes Obtained from the B3LYP Functional with 6-31G (d, p) and 6-31+ G (d, p) Basis Sets: Comparison with MP2\/6-31+ G (d, p) Results and Experimental Data","volume":"99","author":"Person","year":"1995","journal-title":"J. Phys. Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1758-2946-4-17","article-title":"Avogadro: An advanced semantic chemical editor, visualization, and analysis platform","volume":"4","author":"Hanwell","year":"2012","journal-title":"J. Chemin."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"516","DOI":"10.2174\/1570178612666150529205707","article-title":"DFT study and NBO analysis of conformational properties of 2-Substituted 2-Oxo-1, 3, 2-dioxaphosphorinanes and their dithia and diselena analogs","volume":"12","author":"Azarakhshi","year":"2015","journal-title":"Lett. Org. Chem."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Aziz, M., Ejaz, S.A., Rehman, H.M., Al-Buriahi, M.S., Siddique, F., Somaily, H.H., and Alrowaili, Z.A. (2022). Identification of NEK7 Inhibitors: Structure based Virtual Screening, Molecular Docking, Density functional theory calculations and Molecular Dynamics Simulations. Res. Sq., preprint.","DOI":"10.21203\/rs.3.rs-1445619\/v1"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"13384","DOI":"10.3390\/molecules200713384","article-title":"Molecular Docking and Structure-Based Drug Design Strategies","volume":"20","author":"Ferreira","year":"2015","journal-title":"Molecules"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1016\/j.tibs.2019.06.004","article-title":"Bringing Molecular Dynamics Simulation Data into View","volume":"44","author":"Hildebrand","year":"2019","journal-title":"Trends Biochem. Sci."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Rasheed, M.A., Iqbal, M.N., Saddick, S., Ali, I., Khan, F.S., Kanwal, S., Ahmed, D., Ibrahim, M., Afzal, U., and Awais, M. (2021). Identification of lead compounds against Scm (fms10) in Enterococcus faecium using computer aided drug designing. Life, 11.","DOI":"10.3390\/life11020077"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1021\/ct900587b","article-title":"Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field","volume":"6","author":"Shivakumar","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1063\/1.467468","article-title":"Constant pressure molecular dynamics algorithms","volume":"101","author":"Martyna","year":"1994","journal-title":"J. Chem. Phys."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","article-title":"Canonical dynamics: Equilibrium phase-space distributions","volume":"31","author":"Hoover","year":"1985","journal-title":"Phys. Rev. A"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1080\/08927029408022004","article-title":"A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems","volume":"14","author":"Luty","year":"1994","journal-title":"Mol. Simul."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Zhang, Y., Zhang, T.J., Tu, S., Zhang, Z.H., and Meng, F.H. (2020). Identification of Novel Src Inhibitors: Pharmacophore-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations. Molecules, 25.","DOI":"10.3390\/molecules25184094"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"6885","DOI":"10.1021\/j100078a035","article-title":"A Multiple-Time-Step Molecular Dynamics Algorithm for Macromolecules","volume":"98","author":"Humphreys","year":"1994","journal-title":"J. Phys. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/prot.10613","article-title":"A hierarchical approach to all-atom protein loop prediction","volume":"55","author":"Jacobson","year":"2004","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0022-2836(02)00470-9","article-title":"On the role of the crystal environment in determining protein side-chain conformations","volume":"320","author":"Jacobson","year":"2002","journal-title":"J. Mol. Biol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Bowers, K.J., Chow, D.E., Xu, H., Dror, R.O., Eastwood, M.P., Gregersen, B.A., Klepeis, J.L., Kolossvary, I., Moraes, M.A., and Sacerdoti, F.D. (2006, January 11\u201317). Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM\/IEEE Conference on Supercomputing, Tampa, FL, USA.","DOI":"10.1145\/1188455.1188544"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/1758-2946-5-34","article-title":"A big data approach to the ultra-fast prediction of DFT-calculated bond energies","volume":"5","author":"Qu","year":"2013","journal-title":"J. Chemin."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1021\/cr200107z","article-title":"Challenges for Density Functional Theory","volume":"112","author":"Cohen","year":"2011","journal-title":"Chem. Rev."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"3499","DOI":"10.1093\/bioinformatics\/btz062","article-title":"Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions","volume":"35","author":"Ribeiro","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1080\/07391102.2017.1338164","article-title":"NSAIDs as potential treatment option for preventing amyloid \u03b2 toxicity in Alzheimer\u2019s disease: An investigation by docking, molecular dynamics, and DFT studies","volume":"36","author":"Azam","year":"2018","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_59","first-page":"37","article-title":"Molecular dynamics simulations: Advances and applications","volume":"8","author":"Hospital","year":"2015","journal-title":"Adv. Appl. Bioinform. Chem. AABC"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Choudhary, M.I., Shaikh, M., tul-Wahab, A., and ur-Rahman, A. (2020). In silico identification of potential inhibitors of key SARS-CoV-2 3CL hydrolase (Mpro) via molecular docking, MMGBSA predictive binding energy calculations, and molecular dynamics simulation. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0235030"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"558","DOI":"10.3109\/10799893.2016.1141955","article-title":"Inhibitor design against JNK1 through e-pharmacophore modeling docking and molecular dynamics simulations","volume":"36","author":"Katari","year":"2016","journal-title":"J. Recept. Signal Transduct."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"David, C.C., and Jacobs, D.J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Protein Dynamics, Humana Press.","DOI":"10.1007\/978-1-62703-658-0_11"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"S639","DOI":"10.4103\/0973-1296.139809","article-title":"Identification of natural inhibitors against angiotensin I converting enzyme for cardiac safety using induced fit docking and MM-GBSA studies","volume":"10","author":"Vijayakumar","year":"2014","journal-title":"Pharmacogn. Mag."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"4805","DOI":"10.1021\/jm060522a","article-title":"Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring","volume":"49","author":"Lyne","year":"2006","journal-title":"J. Med. Chem."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/13\/4098\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:38:24Z","timestamp":1760139504000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/27\/13\/4098"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,25]]},"references-count":64,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2022,7]]}},"alternative-id":["molecules27134098"],"URL":"https:\/\/doi.org\/10.3390\/molecules27134098","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,25]]}}}