PT - JOURNAL ARTICLE AU - Charis Georgiou AU - Iain McNae AU - Martin Wear AU - Harris Ioannidis AU - Julien Michel AU - Malcolm Walkinshaw TI - Pushing the limits of detection of weak binding using fragment based drug discovery: identification of new cyclophilin binders AID - 10.1101/136101 DP - 2017 Jan 01 TA - bioRxiv PG - 136101 4099 - http://biorxiv.org/content/early/2017/06/15/136101.short 4100 - http://biorxiv.org/content/early/2017/06/15/136101.full AB - Fragment Based Drug Discovery (FBDD) is an increasingly popular 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.Research Highlights FBDD 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 identifiedCypsCyclophilinsCypAcyclophilin APPIasespeptidyl-prolyl isomerasesCsAcyclosporin AHIV-1human immunodeficiency virus 1HCVhepatitis C virusSBDDstructure-based drug designFBDDfragment based drug discoveryMDmolecular dynamicsSPRsurface plasmon resonanceHBDhydrogen bond donorHBAhydrogen bond acceptorDMSOdimethyl sulfoxidePBSphosphate buffered saline