Discovery on Target Virtual

Online

As in the previous years ZoBio participated as a sponsor in Discovery on Target, the industry’s preeminent event on novel drug targets and technologies for drug discovery professionals. The conference highlighted advances in current and emerging “hot” targets and technologies, as well as target validation strategies for the discovery and development of novel therapeutic agents, ranging from biologics to small molecules.

Gregg Siegal presented the lecture: ‘Targeting RNA Readers’ on Wednesday September 16. In his presentation Gregg has shared insights of a developing inhibitors of YTHDF2,  a protein that selectively recognized 6 methyl-adenosine in mRNA thereby regulates protein expression. Results from fragment screening and hit evolution campaign were presented.

Drug Discovery Chemistry Virtual

Online

Focused on discovery and optimization challenges of small molecule drug candidates, Drug Discovery Chemistry is a dynamic virtual event for medicinal and biophysical chemists working in pharma and biotech.

Gregg Siegal has presented the lecture: ‘Biophysics-Based Drug Discovery for Epitranscriptomics‘ during Fragment-Based Drug Discovery session. Afterwards, together with other speakers he participated in interesting and educational Q&A session.

Axxam and ZoBio Form a Strategic Alliance Integrating their Drug Discovery Services Platforms

Axxam and ZoBio Form a Strategic Alliance Integrating their Drug Discovery Services Platforms

MILAN, IT, AND LEIDEN, NL

Axxam and ZoBio have initiated a strategic alliance to provide a combination of integrated discovery services spanning all phases from gene to fully optimized leads.

This alliance provides access to a synergistic, industry-leading, integrated toolbox of protein production and engineering technologies and screening methods using cellular, biochemical, high content and biophysical assays. These capabilities are used to probe our innovative small molecule and fragment libraries for ideally behaved hits. The hits can subsequently be evolved with our focused medicinal chemistry expertise supported by NMR and X-ray crystallography-based structural biology, all under a single, seamless contractual arrangement. The Axxam and ZoBio collaboration brings together decades of experience with unbeatable technology to help you to overcome your greatest drug discovery challenges.

Stefan Lohmer, co-founder and Chief Executive Officer of Axxam, commented, “We are very pleased to announce this strategic alliance with ZoBio. Both Axxam and ZoBio share a common philosophy based on excellence and creativity in biology. Axxam is a biology-driven company with a deep understanding of targets, assay development and high throughput screening, with a culture of scientific excellence and the attention to delivering the quality results our clients need and expect.

The complementary technical skillsets between Axxam and ZoBio provide a seamless suite of options to our clients looking to interrogate pharmacologically challenging drug targets with a variety of complementary platforms.”

Gregg Siegal, Chief Executive Officer of ZoBio added, “Fundamentally, HTS and fragments offer tremendous complementarity with the result being a far more robust drug discovery campaign. Our biophysical approach allows us to select for molecules with the desired mode of action whereas Axxam’s cellular and biochemical expertise selects molecules with the desired biological activity. While the science of our two companies is orthogonal, we share a deep commitment to excellence, which is why this is the perfect collaboration.”

2nd Alpine Winter Conference on Medicinal and Synthetic Chemistry

St. Anton, Austria

Gregg Siegal presented the poster ‘The ZoBio Biophysics Toolbox for Fragment Screening and Hit Validation in Epitranscriptomics’ in this scenic environment that stimulated networking and scientific exchange between the participants. This was a small, but focused event that enabled intensive contact in the lecture hall and on the ski slopes of the Arlberg region.

YTHDF2 – An unprecedented epitranscriptomic reader protein

YTHDF2 – A unprecedented epitranscriptomic reader protein

Challenge
The epitranscriptomic YTHDF2 reader is a member of a family of proteins that selectively binds to a modified base (m6A) in mRNA.  Our client tasked us with setting up a complete “gene to lead” fragment-based drug discovery campaign. Since the entire family is unprecedented, there were no “tool compounds” typically required to set up assays. As we progressed, further challenges presented themselves.

Solution
Once we determined that we could immobilize YTHDF2 while retaining its selective m6A binding, we could use our proprietary TINS fragment screening technology, which does not require tool compounds to setup. TINS generated a list of primary hits from the ZoBio fragment library. Using a nearly identical immobilization approach, we observed binding of many of these raw hits in SPR. The binding response could be used to optimize the assay for fragment screening.

We subsequently confirmed that hits from both TINS and SPR targeted the desired binding site on YTHDF2 using protein observed NMR experiments. This information rich assay revealed that buffer components were also selectively binding to the desired site and effectively competing against the fragment hits. With this knowledge we could further optimize our assays and structural biology approaches.

Inverse SPR assay
The classic “forward” SPR assay identified compounds that selectively bind to YTHDF2 with ideal behavior. However, this assay does not provide insight into the biological activity of compounds, that is whether or not they prevent binding of m6A containing RNA. In order to do so, we developed an inverse SPR assay (iSPR©) in which RNA carrying the relevant chemical modification, is immobilized. This allows us to directly probe the ability of test compounds to interfere with the binding of YTHDF2 to the immobilized RNA, in other words, a biophysics-based biological assay. We further refined the assay to quantify the level of competition based on the affinity of the ligand to discriminate and prioritize chemotypes.

The assay cascade
We efficiently guided medicinal chemistry efforts by focusing on functionally active chemotypes, as determined by iSPR. These compounds were further characterized by biochemical assays (trFRET). Chemotypes exhibiting good correlation in the different assays were prioritized. From the start of the project, NMR played a crucial role in obtaining structural information about the way selected chemotypes bound the target. Initially we could rapidly map the binding sites of 10’s of compounds at low resolution. Subsequently, when it was not possible to obtain liganded structures do to crystal packing issues, we elucidated the solution structure of ligand-protein complexes that were then used to guide medicinal chemistry.

Achievements
By capitalizing on our unique expertise in developing customized biophysical assays, we created a biologically relevant compound screening cascade in the absence of tool compounds. The cascade delivered chemically diverse sets of validated fragments that we successfully elaborated towards lead compounds using structural information that could only be gleaned through NMR.

Mettl3/Mettl14 – An epitranscriptomic writer complex

Mettl3/Mettl14 – An epitranscriptomic writer complex

Challenge
Mettl3/Mettl14 is a large (90 kDa) heterodimeric “writer” complex that uses S-adenosyl methionine (SAM) as a cofactor.  Identifying low affinity, validated fragment hits in the large amount of electron density derived from X-ray diffraction data was extremely difficult.

Achievements
X-ray crystallography provides the necessary high resolution structural data needed to efficiently elaborate hits from fragment or HTS campaigns. However, even highly validated fragment hits typically exhibit low affinity (100s to 1000s of µM). As a result, the occupancy of ligand binding sites in the crystal may be substantially less than 100%, which degrades the quality of the electron density of the fragment. Moreover, fragments are small and overall somewhat symmetric, further reducing identifiable features of their electron density.

We set up a solution competition binding experiment using NMR as a readout to focus on fragments that bind at the SAM site. We quickly found a fragment containing a CF3 moiety that bound at the SAM site. We could then use 19F NMR studies as a clean, sensitive and fast approach to reveal other ligands that bound at the same site. Once we were certain of the binding site, we were readily able to identify electron density at the SAM site and confidently assign it to the ligand.

Achievements
We developed a highly efficient structure pipeline capable of determining up to 10 sub 2Å structures per month which has been the basis for elaborating fragment hits to cellular activity and beyond. Multiple chemotypes are promising, allowing for a robust hit-to-lead campaign.

Gotham Therapeutics and ZoBio Achieve Significant Milestone in Epitranscriptomic Drug Discovery Collaboration

Gotham Therapeutics and ZoBio Achieve Significant Milestone in Epitranscriptomic Drug Discovery Collaboration

NEW YORK, NY, USA AND LEIDEN, NL

Gotham Therapeutics has selected ZoBio to initiate a collaboration on the development of small molecules targeting epitranscriptomic targets. This collaboration has now resulted in several lead candidates for the METTL3/METTL14 complex.

With 15 years of experience, ZoBio is the proven partner for biophysics driven, fragment based drug discovery. We are dedicated to achieving the best science and highest level of transparency.

Our integrated discovery engine progresses projects from gene-to-lead. High throughput protein engineering and production, diverse, novel fragment libraries, proprietary biophysical screening technologies and complementary structural biology approaches have been tailored to provide validated data at every step of the process. The right combination of these various disciplines generates actionable medicinal chemistry hypotheses for small molecule modulators of a great variety of pharmacological targets, including those that have previously been out of reach.

‘In a sector that is still in its infancy, we have made tangible progress with our partner ZoBio to develop small molecule leads against a portfolio of epitranscriptomic targets just 14 months after initiation of the project,’ commented Dr. Lee Babiss, Chief Executive Officer of Gotham Therapeutics. ‘Today’s news is also a validation of the semi-virtual model we use and the productivity of our network with best-in-class CROs.’

‘With METTL3/METTL14 being among the more obvious approaches in epitranscriptomics, the quality of the hit matter pursued is going to be a key differentiating factor,’ added Dr, Gerhard Müller, Chief Scientific Officer of Gotham Therapeutics. ‘Together with ZoBio, we have not just successfully identified the initial candidates for Gotham’s first pipeline program but also established a robust process from gene to lead as a platform for additional projects to come.’