{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T19:13:41Z","timestamp":1791832421384,"version":"4.3.4"},"reference-count":35,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T00:00:00Z","timestamp":1566950400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"College of Health Sciences, University of KwaZulu-Natal","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties available in virtual libraries. Therefore, we opted to divide an existing covalent Nedd4-1 inhibitor into two parts: a non-covalent binding group and a pre-selected \u03b1, \u03b2-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on molecular interactions at the binding site. The pharmacophore was then subjected to virtual screening to identify structurally similar hit compounds. Multiple filtrations were implemented prior to selecting four hits, which were validated with a covalent conjugation and later assessed by molecular dynamic simulations. The results showed that, of the four hit molecules, Zinc00937975 exhibited advantageous molecular groups, allowing for favourable interactions with one of the characteristic cysteine residues. Predictive pharmacokinetic analysis further justified the compound as a potential lead molecule, prompting its recommendation for confirmatory biological evaluation. Our inhouse, refined, pharmacophore model approach serves as a robust method that will encourage screening for novel covalent inhibitors in drug discovery.<\/jats:p>","DOI":"10.3390\/molecules24173125","type":"journal-article","created":{"date-parts":[[2019,8,28]],"date-time":"2019-08-28T11:23:18Z","timestamp":1566991398000},"page":"3125","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling"],"prefix":"10.3390","volume":"24","author":[{"given":"Imane","family":"Bjij","sequence":"first","affiliation":[{"name":"Molecular Bio-Computation &amp; Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa"},{"name":"D\u00e9partement de Chimie, Facult\u00e9 des Sciences Semlalia, Universit\u00e9 Cadi Ayyad, Av. My Abdellah, BP2390 Marrakech, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pritika","family":"Ramharack","sequence":"additional","affiliation":[{"name":"Molecular Bio-Computation &amp; Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shama","family":"Khan","sequence":"additional","affiliation":[{"name":"Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg 2193, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Driss","family":"Cherqaoui","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Chimie, Facult\u00e9 des Sciences Semlalia, Universit\u00e9 Cadi Ayyad, Av. My Abdellah, BP2390 Marrakech, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahmoud E. S.","family":"Soliman","sequence":"additional","affiliation":[{"name":"Molecular Bio-Computation &amp; Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,8,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/nrm2690","article-title":"Physiological functions of the HECT family of ubiquitin ligases","volume":"10","author":"Rotin","year":"2009","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1039\/C3MB70572B","article-title":"Crosstalk between kinases and Nedd4 family ubiquitin ligases","volume":"10","author":"An","year":"2014","journal-title":"Mol. BioSyst."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1146\/annurev.biochem.78.082307.091526","article-title":"Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes","volume":"78","author":"Ventii","year":"2009","journal-title":"Annu. Rev. Biochem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature17888","article-title":"Ubiquitination without E1 and E2 enzymes","volume":"533","author":"Bhogaraju","year":"2016","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1074\/jbc.M109.030882","article-title":"HECT Domain-containing E3 Ubiquitin Ligase Nedd4 Interacts with and Ubiquitinates Sprouty2","volume":"285","author":"Edwin","year":"2010","journal-title":"J. Biol Chem."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1038\/sj.onc.1207436","article-title":"The Nedd4 family of E3 ubiquitin ligases: Functional diversity within a common modular architecture","volume":"23","author":"Ingham","year":"2004","journal-title":"Oncogene"},{"key":"ref_7","first-page":"91","article-title":"Biochimica et Biophysica Acta Molecular functions of NEDD4 E3 ubiquitin ligases in cancer","volume":"1856","author":"Zou","year":"2015","journal-title":"BBA - Rev. Cancer"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"549","DOI":"10.2174\/1568009614666140725092430","article-title":"NEDD4: A promising target for cancer therapy","volume":"14","author":"Ye","year":"2014","journal-title":"Curr. Cancer Drug Targets"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"12442","DOI":"10.1021\/jacs.5b06839","article-title":"A Small Molecule That Switches a Ubiquitin Ligase from a Processive to a Distributive Enzymatic Mechanism","volume":"137","author":"Kathman","year":"2015","journal-title":"J. Am. Chem. Soc."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"D129","DOI":"10.1093\/nar\/gkh028","article-title":"The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data","volume":"32","author":"Porter","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"149","DOI":"10.2174\/157015907781695973","article-title":"Allosteric theory: Taking therapeutic advantage of the malleable nature of GPCRs","volume":"5","author":"Kenakin","year":"2007","journal-title":"Curr. Neuropharmacol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/S0022-2836(65)80285-6","article-title":"On the Nature of Allosteric Transitions: A Plausible Model","volume":"12","author":"Monod","year":"1965","journal-title":"J. Mol. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1007\/s10930-018-9795-5","article-title":"Exploring the Structural Mechanism of Covalently Bound E3 Ubiquitin Ligase: Catalytic or Allosteric Inhibition?","volume":"37","author":"Bjij","year":"2018","journal-title":"Protein J."},{"key":"ref_14","first-page":"47","article-title":"The molecular docking of 1,4-naphthoquinone derivatives as inhibitors of Polo-like kinase 1 using Molegro Virtual Docker","volume":"4","author":"Kusumaningrum","year":"2014","journal-title":"J. Appl. Pharm. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"O\u2019Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., and Hutchison, G.R. (2011). Open Babel: An Open chemical toolbox. J. Cheminform.","DOI":"10.1186\/1758-2946-3-33"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Dallakyan, S., and Olson, A.J. (2015). Small-molecule library screening by docking with PyRx. Methods Mol. Biol.","DOI":"10.1007\/978-1-4939-2269-7_19"},{"key":"ref_17","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_18","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"J. Comput. Chem."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10822-013-9644-8","article-title":"Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments","volume":"27","author":"Adzhigirey","year":"2013","journal-title":"J. Comput. Aided Mol. Des."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.jmgm.2005.12.005","article-title":"Automatic atom type and bond type perception in molecular mechanical calculations","volume":"25","author":"Wang","year":"2006","journal-title":"J. Mol. Graph. Model."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1002\/wcms.1121","article-title":"An overview of the Amber biomolecular simulation package","volume":"3","author":"Case","year":"2013","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"key":"ref_23","unstructured":"Betz, R. (2017, August 01). Dabble. Available online: https:\/\/zenodo.org\/record\/836914#.XQhU49IRXIU."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1021\/ci500161d","article-title":"OriginPro 9.1: Scientific Data Analysis and Graphing Software\u2014Software Review","volume":"54","author":"Seifert","year":"2014","journal-title":"J. Chem. Inf. Model."},{"key":"ref_27","first-page":"945","article-title":"G3BP: A promising target for cancer therapy","volume":"45","author":"Zhang","year":"2010","journal-title":"Curr. Cancer Drug Targets"},{"key":"ref_28","unstructured":"Bethesda (MD): National Library of Medicine (US) (2018, March 11). National Center for Biotechnology Information (NCBI), Available online: https:\/\/www.ncbi.nlm.nih.gov\/."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/ijms17020144","article-title":"Insights into Protein\u2014Ligand Interactions: Mechanisms, Models, and Methods","volume":"17","author":"Du","year":"2016","journal-title":"Int. J. Mol. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1517\/17460441.2015.1032936","article-title":"The MM\/PBSA and MM\/GBSA methods to estimate ligand-binding affinities","volume":"10","author":"Genheden","year":"2015","journal-title":"Expert Opin. Drug Discov."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Daina, A., Michielin, O., and Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci. Rep., 7.","DOI":"10.1038\/srep42717"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/21688370.2015.1129476","article-title":"Blood brain barrier: An overview on strategies in drug delivery, realistic in vitro modeling and in vivo live tracking","volume":"4","author":"Pandey","year":"2016","journal-title":"Tissue Barriers"},{"key":"ref_34","first-page":"233","article-title":"Nedd4 and Nedd4-2: Closely related ubiquitin-protein ligases with distinct physiological functions","volume":"71","author":"Yang","year":"2013","journal-title":"Cell Death Differ."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.tibs.2018.06.004","article-title":"Physiological Functions of Nedd4-2: Lessons from Knockout Mouse Models","volume":"43","author":"Manning","year":"2018","journal-title":"Trends Biochem. Sci."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/24\/17\/3125\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T13:14:36Z","timestamp":1760188476000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/24\/17\/3125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,28]]},"references-count":35,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2019,9]]}},"alternative-id":["molecules24173125"],"URL":"https:\/\/doi.org\/10.3390\/molecules24173125","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,28]]}}}