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Fields on proteins

Distinguish between protein and ligand interaction potentials to design for optimum binding
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Cresset fields and field points have been extensively validated on small molecule structures. Extending this approach to proteins is more difficult, as much more attention needs to be paid to system preparation, charge states, and solvation effects. Flare, Cresset’s ligand-based and structure-based drug design platform, solves these issues, in particular through careful protein preparation and the use of a modified dielectric function based on the work of Mehler (E. L. Mehler, The Lorentz-Debye-Sack theory and dielectric screening of electrostatic effects in proteins and nucleic acids, in Molecular Electrostatic Potentials: Concepts and Applications, Theoretical and Computational Chemistry Vol. 3, 1996).

The resulting interaction potentials (PIPs, or protein interaction potentials, to distinguish them from ligand MIPs) are extremely useful for analyzing a protein active site and determining what ligand properties might need to be altered to achieve optimum binding – For example, see the figure below for a comparison of ligand with protein electrostatics in the Btk protein.

Ligand 4L6 superimposed to the protein interaction potentials of 4Z3V. Top-left: ‘dry’ active site, not including crystallographic water molecules. Top-right: ‘wet’ active site including stable water molecules. Bottom: Ligand fields for 4L6. Protein interaction potentials shown at isolevel = 3; ligand fields shown at isolevel = 2.

What our customers say

“As a global computational chemistry team within a contract research organisation (CRO), we aimed to improve the consistency, scalability, and scientific rigor of our molecular modelling workflows across a wide range of client projects. Cresset supported a smooth transition from a previously used commercial tool and helped address key limitations around accessibility and deployment at scale. A differentiated licensing model has enabled broad access across chemistry and biology teams while reserving advanced capabilities for computational chemistry specialists. This approach has helped balance accessibility, scientific depth, and efficient use of resources, enabling wider engagement without compromising rigor. The Cresset team have been highly responsive and knowledgeable, working closely with us to support adoption across a global user base. Training was organised according to user needs, with regular office hours providing an open forum for questions and ongoing support.

Overall, Cresset has become a valuable part of our computational chemistry toolkit, strengthening consistency, productivity, and confidence in decision-making across our organisation.”

Nicola Porta, Senior Scientist, Evotec

We are pleased to be working with Cresset’s software. This provides us with intuitive molecule design, a powerful ability to understand SAR and design plus a fresh way for generating novel and diverse structures for our projects.

Dr Kristian Birchall, Medical Research Council Technology, UK

We really like the powerful combination of excellent software tools and molecular design expertise which we get from working with Cresset.

Dr Graham Sibley, Head of Chemistry, F2G, UK

We wanted to use computational methods to suggest alternative substructures which could replace part of one of our key leads. We’d looked at other tools previously, without success, then turned to the Spark™ field-based approach. We looked at the top 50 hits from Spark and selected a subset to synthesise. Whilst the synthesised compounds exhibited a broad range of activities, we were delighted to observe that a number turned out to be nanomolar hits – with several even more potent than the original lead. One of these compounds is now our key lead against this target and further analogue synthesis is underway. Spark has certainly helped direct us towards some novel and very useful SAR on this occasion.

Laurent Rigoreau, Group Leader Medicinal Chemistry, Cancer Research Technology Discovery Laboratories

Cresset Discovery’s computational experience and high standard of scientific support is ideally suited to help drive the next stage of this project.

Dr Richard Boyce, Senior Director of Research, PhoreMost

The protein interaction potential capability [in Flare] highlighted common features across the family of targets of interest that we had not been able to visualize before. We used this information to drive ligand design into a direction we have not explored before.

Dr Martin Quibell, MAQU Chemistry Consulting, UK

We sought the scientific expertise within the Cresset Discovery team to utilize their novel field and shape-based virtual screening methods in Blaze™, and their proprietary Electrostatic Complementarity™ technique to help identify a backup series for our target effectively and efficiently. Ultimately we identified 9 novel chemotypes that were clearly distinct to those arising from docking and pharmacophore virtual screening approaches, which was an exciting outcome for us.

Dr Zara Sands, Head of CADD and Informatics, Confo Therapeutics, Belgium

Working closely with the Cresset Discovery team we aimed to identify a putative binding pose for a lead series in published PDB coordinates that was not only consistent with the kinetically deduced MOA but explained the established SAR as well. The furnished results were able to satisfy these goals and then be applied prophetically for ligand design purposes.

Twentyeight-Seven Therapeutics, USA

Medicinal chemists in my team find the covalent docking feature in Flare™ very intuitive to use.

Matthias Bauer, AstraZeneca, UK