Target Gallery

Beryllium announces the signing of a structural biology collaboration with Deciphera Pharmaceuticals.  Under the terms of the agreement, Beryllium will provide gene-to-structure research information on multiple kinase targets and deliver high-resolution crystal structures to support Deciphera’s kinase inhibitor discovery activities.

“Deciphera’s collaboration with Beryllium exemplifies our commitment to advancing improved treatment options for patients with cancer,” said Daniel Flynn, Ph.D., Chief Scientific Officer at Deciphera Pharmaceuticals.  “Beryllium’s expertise in structure-directed drug discovery coupled with Deciphera’s proprietary switch control kinase inhibitor platform offers the potential to accelerate the delivery of tumor-targeted therapies and immuno-targeted therapies to improve human health.”

“At Beryllium we are very excited to partner with Deciphera, an industry leading oncology therapeutics company,” said Johan Pontin, Chief Executive Officer at Beryllium Discovery.  “Deciphera’s cutting edge research in kinase inhibitors dovetails with Beryllium’s gene to structure expertise and together we will unlock the therapeutic potential of new oncology targets.”


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Using a biology-first, target-centric approach and established platforms, Beryllium provides research services and engages in collaborations with commercial and academic partners.  Beryllium’s teams of experienced scientists work closely with drug discovery clients to help manage and advance their goals by complementing their capabilities and resources.


Media Contact: Mark Schmeizl, Beryllium Discovery,


Recorded on: Tuesday, January 24, 2017
Duration: 60 minutes
Featured Speaker: Douglas R. Davies, Senior Manager of Structural Biology, Beryllium Discovery Corp.

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This webinar will discuss the use of ligand-observe NMR techniques for rapid and efficient fragment screening of viral targets. Fragment screening was performed on two different viral proteins, an H1N1 Influenza A virus polymerase acid protein C-terminal domain (PA-CTD) and the Ebola virus matrix protein VP30 as part of a structural genomics consortium which targets infectious diseases. The influenza virus PA-CTD is part of the heterotrimeric viral RNA-dependent RNA polymerase involved in genome replication, whereas the Ebola virus VP30 protein is a phosphoprotein which associates with the nucleocapsid protein and is essential for viral transcription initiation.

In each case, the strategy was to target a protein-protein interface rather than an enzymatic active site. Interestingly, the majority of hits for the influenza A virus PA-CTD screen bind to a surface exposed site located near the viral RNA loading site rather than the expected PB1 N-terminus binding site which is a computational hot spot. Crystal structures of initial hits and follow on analogue-by-catalogue compounds were obtained. For the Ebola virus VP30 screen, VP30 was screened from both the 2013-2015 Zaire outbreak as well as the related Marburg virus VP30 in an effort to identify fragments which can target divergent viral VP30 strains. All of this work has been done as part of the Seattle Structural Genomics Center for Infectious Disease (SSGCID), a structural genomics consortium funded by the National Institute for Allergy and Infectious Diseases (NIAID).

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Doug Davies Senior Manager Structural BiologyAbout Douglas R. Davies, Senior Manager of Structural Biology, Beryllium Discovery Corp.
Over the past twenty years, some of Douglas’ work has focused on structural studies of functional nucleic acids and nucleic-acid modifying enzymes. His graduate thesis work at the University of Wisconsin-Madison involved the first structures of Tn5transposase. As a postdoctoral fellow at the University of Washington, Douglas studied the DNA repair enzyme Tyrosyl DNA Phosphodiersterase (Tdp1), elucidating the first crystal structures and verifying the proposed mechanism of action. During the past 10 years at Beryllium, he has applied these experiences to a number of DNA aptamer diagnostics and potential therapeutics (SOMAmers) as well as DNA Polymerase C from Geobacillus kaustophilus. Douglas is the lead crystallographer for 77 crystal structures in the Protein Data Bank and has published 28 peer-reviewed journal articles.



Ebolaviruses can cause severe haemorrhagic fever and was responsible for the 2013-2015 epidemic in West Africa, that resulted in over 11,000 deaths. Utilizing our fragments library, we employed saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy to identify fragments that bound Filoviridae family members, Ebolavirus Zaire or Marburgvirus Lake Victoria nucleoprotein transcriptional cofactor VP30. Due to the adaptive tendencies of viral proteins, we identified fragments that bound one or both strains. To further interrogate the potential relationship of fragments with Ebola, additional STD NMR screening of Ebolavirus Zaire mutants was performed, determining the difference signal of select fragments with the active “unphosphorylated” and inactive “phosphorylated” mutants. A greater difference signal was observed with the active mutant which also included the Marburgvirus specific fragments. We believe that our findings and strategy lead towards a structure guided drug design path for more successful viral therapies in Ebola and can be applied to other pathogens.

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Probing Filoviridae: Identifying fragments that bind Ebolavirus and Marburgvirus

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