Dr Fayne has published >40 papers, a book chapter and two patents, the vast majority of which describe computational design approaches for discovering novel small molecules targeting proteins involved in human disease.
Dr Fayne and Ms Kandwal have recently published a paper using pharmacophore queries to propose the mechanism of action and possible repurposing opportunities of approved drugs showing in vitro efficacy against SARS-CoV-2.
Kandwal S. Fayne D. Repurposing drugs for treatment of SARS-CoV-2 infection: computational design insights into mechanisms of action, J Biomol Struct Dyn, 2022, 40(3):1316-1330. Published online Sept 2020. doi: 10.1080/07391102.2020.1825232
Ms Kandwal started her PhD with Dr Fayne in Sept 2021 on designing small molecule inhibitors of conserved regions of SARS-CoV-2 nsps.
The MoPBS software is described in this recently published paper:
Braun J, Fayne D. Mapping of Protein Binding Sites using clustering algorithms - Development of a pharmacophore based drug discovery tool. J Mol Graph Model. 2022 Sep;115:108228
A paper describing DataPype is currently under preparation for submission.
Tiered-screening approaches previously developed by the research group are described in the following papers. All of these published approaches have successfully identified hit compounds from commercial vendor databases, primarily by only screening the SPECS library. The proposed work in this study represented a significant increase in complexity and scale from these previous works but we have the expertise, infrastructure and software to ensure a successful completion of the described project.
Nevin, DK, Peters, MB, Carta, G, Fayne, D, Lloyd, DG, Integrated virtual screening for the identification of novel and selective Peroxisome Proliferating Activated Receptor (PPAR) modulators. J. Med. Chem. 2012 55(11):4978-89
McKay, PB, Fayne, D*, Horn, HW, James, T, Peters, MB, Carta, G, Caboni, L, Nevin, DK, Price, T, Bradley, G, Williams, DC, Rice, JE, Lloyd, DG. Consensus computational ligand-based design for the identification of novel modulators of human Estrogen Receptor alpha. Mol Inf. 2012 31(3-4) 246–258. *Corresponding author
Caboni L, Kinsella GK, Blanco F, Fayne D, Jagoe WN, Carr M, Williams DC, Meegan MJ, Lloyd DG. “True” antiandrogens-selective non-ligand-binding pocket disruptors of androgen receptor-coactivator interactions: novel tools for prostate cancer, J Med Chem. 2012 55(4):1635-44
McKay PB, Peters MB, Carta G, Flood CT, Dempsey E, Bell A, Berry C, Lloyd DG, Fayne D. Identification of plasmepsin inhibitors as selective anti-malarial agents using ligand based drug design. Bioorg Med Chem Lett. 2011 1;21(11):3335-41
Yang Y, Carta G, Peters MB, Price T, O’Boyle N, Knox AJS, Fayne D, Williams DC, Meegan MJ, Lloyd DG. tieredScreen – layered virtual screening tool for the identification of novel Estrogen Receptor Alpha modulators. Mol Inf. 2010, 29, 421 – 430