TY - JOUR T1 - Pushing the limits of detection of weak binding using fragment based drug discovery: identification of new cyclophilin binders JF - bioRxiv DO - 10.1101/136101 SP - 136101 AU - Charis Georgiou AU - Iain McNae AU - Martin Wear AU - Harris Ioannidis AU - Julien Michel AU - Malcolm Walkinshaw Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/05/09/136101.abstract N2 - Fragment Based Drug Discovery (FBDD) is an increasingly popular and successful method to identify novel small-molecule drug candidates. One of the limitations of the approach is the difficulty of accurately characterizing weak binding events. This work reports a combination of X-ray diffraction, surface plasmon resonance (SPR) experiments and molecular dynamics (MD) simulations, for the characterisation of binders to different isoforms of the cyclophilin (Cyp) protein family. Although several Cyp inhibitors have been reported in the literature, it has proven challenging to achieve high binding selectivity for different isoforms of this protein family. The present studies have led to the identification of several structurally novel fragments that bind to diverse Cyp isoforms in distinct pockets with low millimolar dissociation constants. A detailed comparison of the merits and drawbacks of the experimental and computational techniques is presented, and emerging strategies for designing ligands with enhanced isoform specificity are described.HighlightsFBDD is a popular method but weak binding is difficult to detectThere is a need for pushing the limits of weak binding detectionCombination of X-ray, SPR and MD methodologies increases successful characterization of weak binding eventsSeveral novel Cyclophilin fragment binders were identified(Cyps)Cyclophilins(CypA)cyclophilin A(PPIases)peptidyl-prolyl isomerases(CsA)cyclosporin A(HIV-1)human immunodeficiency virus 1(HCV)hepatitis C virus(SBDD)structure-based drug design(FBDD)fragment based drug discovery(MD)molecular dynamics(SPR)surface plasmon resonance(HBD)hydrogen bond donor(HBA)hydrogen bond acceptor(DMSO)dimethyl sulfoxide(PBS)phosphate buffered saline ER -