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Sygnature Discovery announces collaboration with software firm SilcsBio

Tuesday, April 23, 2019

Nottingham, UK – 17th April 2019 – Sygnature Discovery, a leading independent integrated drug discovery and pre-clinical services company, has today announced a collaboration with SilcsBio, a scientific software company focused on high-throughput fully atomistic simulations of protein targets and protein-ligand structures.

SilcsBio has provided Sygnature with access to its SILCS (Site Identification by Ligand Competitive Saturation) and SSFEP (Single Step Free Energy Perturbation) software. Sygnature’s researchers are now able to offer clients the benefits of these powerful techniques in their drug discovery projects.

The SILCS software identifies binding site hot spots on a protein’s surface. This could, potentially, include ‘cryptic pockets’ – binding sites for which little structural information is available. SILCS methodology involves performing molecular dynamics simulations on a protein in an aqueous solution of chemically diverse small molecules. This generates probability distributions of fragment types, termed FragMaps. These FragMaps can be used rapidly and with minimal computational expense to predict or refine ligand binding poses, quantitatively score ligands in the binding pocket, and generate multiple receptor-based pharmacophore models for use in virtual screening campaigns. This has been shown to be a more effective technique than standard docking studies or receptor-based pharmacophore modelling.

In a complementary manner, the SSFEP software has demonstrated success in ranking compound binding affinities to target proteins. In particular, the SSFEP approach is about 1000-fold faster than the more widely used FEP methodology. It achieves this speed by post-processing molecular dynamics simulation data of a ligand, and using it to estimate the alchemical free energy change of chemically modifying that ligand.

Such a rapid assessment of the drug design team’s ideas could be advantageous in speeding up the design-test-optimise cycle. Being able to evaluate and prioritise design ideas in just a few days can have a significant impact in structure-based design projects.

In the past six months, Sygnature has applied the SilcsBio software suite successfully in various hit-to-lead and lead optimisation projects. The company believes these new software tools will offer substantial benefits to its customers, not least because of the time savings the software can provide.


  • Cryptic/transient binding pocket detection in GPCRs, Nuclear receptors & other transmembrane proteins
  • Revealed previously unknown binding pockets, allowing customers to design of more potent ligands
  • Predicted crystallographic binding modes of customers’ newly designed inhibitors
  • Provided crucial insights to drive medicinal chemistry refinement of BCL6 inhibitors
  • 2019 NIH award to fund expansion of SILCS software to enable its use with biological therapeutics, especially for excipient design

“We’re delighted to be collaborating with Sygnature Discovery to bring the advantages of our drug design software to Sygnature’s projects and customers. This collaboration is very meaningful to us as Sygnature continues to be a great partner and it opens the door to new markets for SilcsBio”, says Ken Malone, Chief Executive Officer of SilcsBio.

“SilcsBio software suite, with its robust physics-based algorithms and user-friendly interface, provides great leverage in the structure-based drug design area and enables us to rapidly validate new ideas/hypothesis” commented Bill Tatsis, Computational Chemist at Sygnature Discovery.

About Sygnature Discovery
Sygnature Discovery is a leading independent integrated drug discovery and pre-clinical services company. Private equity-backed since 2017, we operate fully-enabled research facilities in Nottingham and Alderley Park, UK, housing more than 200 research scientists (more than 80% of whom have PhD) and have an office presence in Cambridge, Massachusetts, US. Our experienced drug-hunters possess all the professional skills and know-how required to undertake the most demanding of research programmes, and drive them from target validation through hit identification, hit-to-lead and lead optimisation to pre-clinical development candidate. Since 2011, we have delivered 14 drug candidates to our clients that have subsequently entered the clinic (Phases I, II and III). In 2017, Sygnature Discovery received the prestigious Queen’s Award for Enterprise for International Trade.

For further information, visit: or email: [email protected]

About SilcsBio
SilcsBio started operations in April 2013 based on licensed intellectual property developed by Dr. MacKerell at the University of Maryland, Baltimore where he is the Grollman-Glick Professor of Pharmaceutical Sciences and Director of the Computer-Aided Drug Design Center. SilcsBio offers commercial software and services based on their software tools for structure-based drug design and has customers in the US, UK, Japan, and Europe. The company is headquartered at Spark-Baltimore located at 8 Market Place, Suite 300, Baltimore, MD 21202.

For further information, visit: or email: [email protected]