Therapeutic protein degradation by design?
The old problem and the new paradigm Classical small molecule drug paradigms generally involve intervention at a ligand protein binding ...
One of the advantages of working for Cresset Discovery Service is that I have access to software that is under development. I’ve therefore been working successfully with Flare, our newly-released structure-based modeling application, on client discovery projects for some time and I’m delighted that it is now available to a wider market.
So, what does Flare offer Cresset Discovery Services that it didn’t have before? Forge is the comprehensive workbench for ligand-centric workflows and I use it as the main workhouse for ligand work. However, more and more drug discovery projects are now structure enabled.
In fact, the increasingly routine use of X-rays and Cryo-EM means that projects generally have access to lots of structures, not just one. Processing these in order to extract useful information is often a key step for us on client projects. For this structure enabled work, Flare has become my Forge equivalent – my main workbench for structure-based work.
The Flare GUI is intuitive and easy to navigate, yet already has significant, powerful and unique functionality. From a practical point of view, Flare is stable on loading 20 or more X-ray structures, and doesn’t slow down (unlike some other tools) or glitch. These structures can be automatically aligned by sequence (Cobalt) and superimposed at the click of button.
Protein preparation is automated. Water analysis via 3D-RISM allows exploration of key water molecules around ligands and binding pockets. Of course, Cresset’s own electrostatic fields can now be visualized on selected protein surfaces, in addition to ligands.
Lead Finder is a Flare plug-in that gives the capability to dock ligands and ultimately conduct high throughput structure-based virtual screening as a complementary addition to Cresset’s state of the art ligand centric-virtual screening service using Blaze.
Zika virus protease PDB : 5H6V and a covalent inhibitor. Protein positive fields (left), negative fields (middle) and ligand fields (right).
The addition of Flare to the Cresset Discovery Services toolbox enhances our client offering with a new degree of confidence for structure-based work. Flare has been developed based on input from scientists in industry and academia so that it is relevant to real discovery workflows. My own work on client projects also contributed to the design of Flare, and I know from personal experience that it is ideally suited to the needs of computational chemists.
The upshot of this is that Flare has been created with ligand design as a central task. This means that even the most computationally intensive tasks are tailored to the effect that they have on the molecules that you make. This really is the great power of computational chemistry; informing and enhancing the discovery of the molecules that matter to your project, using the best computational methods at our disposal. Flare greatly eases that task and is a great addition to our toolbox.
However, what really puts Flare apart from other structure-based methods is the seamless use of the XED forcefield between ligands and proteins. This means that I can make calculations on structure-ligand interactions based on a continuous force field, and make meaningful comparisons at all stages of work.
Ever since I joined Cresset in 2012, customers have been asking me, ‘Why not apply the XED force field to proteins?’ I’m delighted that this question has finally been answered with the release of Flare.
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