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Isoform specific inhibition by transient protein state stabilization

Periodic Reporting for period 1 - ISOTRAPSS (Isoform specific inhibition by transient protein state stabilization)

Reporting period: 2015-09-15 to 2017-09-14

The project focussed on the development of a novel approach to small molecules drug design. A major problem for pharmaceutical R&D is that many small molecules fail to bind selectively to a disease-involved protein. Frequently a protein implicated in disease looks very similar to other proteins that should not be targeted by a small molecule.

It is important for society to research new approaches to small molecule drug design that can contribute small molecules with greater binding selectivity, as this is associated with fewer side effects and greater likelihood that the small molecules may become viable drugs to treat diseases.

The overall objectives of the project were to validate a drug design strategy that uses information about the dynamics of proteins (’molecular movies’). This differs from traditional strategies that leverage information about the structure of a protein (‘molecular pictures’). The approach pursued in ISOTRAPSS used the Cyclophilin family of proteins as a model system and had three main objectives.

The first objective was to generate models of protein dynamics for selected Cyclophilin proteins starting from experimental data, and a novel methodology (aMD/MSM) that was developed for that purpose.

The second objective was to validate a computational model that can rationalise structure-activity relationships for literature Cyclophilin ligands. This was pursued using software and methodologies developed for that purpose.

The third objective was to combine the findings from the first two objectives to discover new Cyclophilin ligands. The work involved a combination of computational modelling, biophysical experiments, and organic syntheses.
In relation to the first work package, a detailed atomistic model of Cyclophilin A dynamics was produced via a novel combination of two molecular simulation methodologies, accelerated Molecular Dynamics (aMD) and Markov State Modelling (MSM). The results generated with this algorithm provided a clear rationale for millisecond loop motions in Cyclophilin A that link the major state with a transient state. Such transient state was predicted to be stabilised by a single amino-acid mutation. Thus a Cyclophilin A mutant was prepared to validate the computational prediction, and subjected to a battery of biophysical measurements (Including NMR, X-ray, ITC). Overall the findings validate the transient state computed by the molecular modelling protocol. Along these lines, a preliminary similar model for the related isoform CypD was generated, but delays in production of samples have prevented experimental validation over the timescale of the reporting period. Preliminary results have been presented at several public meetings, and a paper is being written up.

In relation to the second work package, work published since the proposal submission indicated that a number of literature compounds were in fact artefacts. Attention focussed on another class of literature Cyclophilin ligands, but co-workers were unable to establish that these compounds do in fact, bind to Cyclophilins. Thus there was relatively little scope to pursue structure-activity relationship studies, and efforts focussed on the third work package. Instead the fellow has pursued collaborative work with co-workers to validate computational protocols for predictions of binding affinities. This has led to a number of publications.

In relation to the third work package, a combination of computational modelling with experiments carried out by co-workers has led to the discovery of a structurally novel class of Cyclophilin ligands that engage with Cyclophilins in a novel way. These compounds are under evaluation for possible patent filing, and a publication will report our findings in due course.
This project has significantly progressed the state of the art of protein dynamics. To our knowledge this is the first time that proteins have been rationally designed by molecular dynamics simulations to modulate conformational changes that occur on millisecond timescales. The work has pushed the limits of biomolecular simulations, and challenged protein NMR measurements, in order for theory and experiments to ‘meet in the middle’. This should impact research activities worldwide across a broad range of disciplines.

The project has also validated the use of alchemical free energy (AFE) methods for drug discovery. There is currently significant interest from industry in these methods. The protocols we tested and reported are currently being adopted by a number of pharmaceutical companies, thus the work done is already having an impact on industrial R&D processes.

The project has also generated novel classes of Cyclophilin ligands. While further developments are necessary before these compounds could become useful therapeutics, the strategy we used and the chemical structures obtained will influence ongoing and future Cyclophilin R&D programs worldwide one the work is published.
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