Biology subjects

Michel, J.

Publications and source records attributed to Michel, J..

4 recordsLinked to original sources

bioRxiv2018

Effect of automation on the accuracy of alchemical free energy calculation protocols

Hit-to-lead virtual screening frequently relies on a cascade of computational methods that starts with rapid calculations applied to a large number of compounds and ends with more expensive computations restricted to a subset of compounds that passed initial filters. This work focuses on set up protocols for alchemical free energy (AFE) scoring in the context of a Docking - MM/PBSA - AFE cascade. A dataset of 15 congeneric inhibitors of the ACK1 protein was used to evaluate the performance of AFE set up protocols that varied in the steps taken to prepare input files (using previously docked and best scored poses, manual selection of poses, manual placement of binding site water molecules). The main finding is that use of knowledge derived from X-ray structures to model binding modes, together with the manual placement of a bridging water molecule, improves the R2 from 0.45 {+/-} 0.06 to 0.76 {+/-} 0.02 and decreases the mean unsigned error from 2.11 {+/-} 0.08 to 1.24 {+/-} 0.04 kcal mol-1. By contrast a brute force automated protocol that increased the sampling time ten-fold lead to little improvements in accuracy. Besides, it is shown that for the present dataset hysteresis can be used to flag poses that need further attention even without prior knowledge of experimental binding affinities.

molecular biology↗

bioRxiv2017

Allosteric effects in a catalytically impaired variant of the enzyme Cyclophilin A are unrelated to millisecond time scale motions

There is much debate about the mechanisms by which molecular motions influence catalysis in enzymes. This work investigates the connection between stochastic protein dynamics and function for the enzyme cyclophilin A (CypA) in wild-type (WT) form, and three variants that features several mutations that are distal from the active site. Previous biophysical studies have suggested that conformational exchange between a major active and a minor inactive state on millisecond time scales plays a key role in catalysis for CypA. Here this hypothesis was addressed by a variety of molecular dynamic (MD) simulation techniques. The simulations reproduce X-ray crystallography derived evidence for a shift in populations of major and minor active site conformations between the wild-type and mutant forms. Strikingly, exchange between these active site conformations occurs at a rate that is 5 to 6 orders of magnitude faster than previously proposed. Further analyses indicate that the minor active site conformation is catalytically impaired, and that decreased catalytic activity of the mutants may be explained by changes in Phe113 motions on a ns-s time scale. Therefore previously described millisecond time scale motions may not be necessary to explain allosteric effects in CypA mutants.

biophysics↗

bioRxiv2017

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

The drug design data resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of FXR inhibitors with a semi-automated alchemical free energy calculations workflow featuring the FESetup and SOMD tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature SARs only, and comparable or slightly inferior, to the best submissions from other groups.

biophysics↗

bioRxiv2017

Pushing The Limits Of Detection Of Weak Binding Using Fragment Based Drug Discovery: Identification Of New Cyclophilin Binders

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.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/136101_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@5d2d48org.highwire.dtl.DTLVardef@147f922org.highwire.dtl.DTLVardef@356562org.highwire.dtl.DTLVardef@1933853_HPS_FORMAT_FIGEXP M_FIG C_FIG Research Highlights O_LIFBDD is a popular method but weak binding is difficult to detect\nC_LIO_LIThere is a need for pushing the limits of weak binding detection\nC_LIO_LICombination of X-ray, SPR and MD methodologies increases successful characterization of weak binding events\nC_LIO_LISeveral novel Cyclophilin fragment binders were identified\nC_LI

biophysics↗