Science Pool

With game changer therapies and unprecedented clinical successs for patients, Immunotherapy has becomes an essential pillar for cancer treatment. During this webinar, Michael Esquerre, our VP, In Vitro Biology, discusses how the team at Evotec are pusing Immuno-Oncology drug discovery, playing with multi-therapeutic modalities. Stream it on demand now!

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How to knock down proteins driving disease processes in a cell

Many diseases are caused by the overproduction of certain proteins. The traditional approach to interfere with these proteins is based on small molecules or antibodies blocking these proteins or their corresponding target, e.g., receptors. Thanks to the recent progress of nucleic acid research, there are several new approaches today which intervene at different stages, from gene regulation to transcription to translation: CRISPR-Cas9 methods to target the DNA, zinc finger repressors targeting gene transcription, or RNA-molecules (antisense oligonucleotides, RNA interference, micro RNAs, etc.) to inactivate the mRNA or to suppress the translation. All approaches come with advantages and disadvantages. The main problem with DNA- and RNA-based medicine is delivery, followed by off-target-effects.

There are, however other new knockdown strategies as well, e.g., enhancing the protein clearance pathways to speed up the degradation of unwanted proteins, such as the autophagy-lysosome pathway and the ubiquitin-proteasome system (UPS).

Transcriptomics, data analysis, and AI/ML platforms as basis for partnership with BMS in targeted protein degradation

Since 2018, the latter technology of targeted protein degradation is also being used in a cooperation with Bristol Myers Squibb (BMS) to identify first-in-class drug candidates in oncology to treat solid tumors. For this collaboration, Evotec uses its PanOmics platform, EVOpanOmics, which combines enhanced throughput proteomics, high-throughput transcriptomics, and cell imaging with the integrated data analysis platform EVOpanHunter and Evotec’s AI/ML-based drug discovery and development platforms.

This research has led to the discovery of novel first-in-class molecular glue degraders. These small, drug-like compounds induce interactions between an E3 ubiquitin ligase and a molecular target, leading to ubiquitination and subsequent degradation of the recruited protein. The resulting therapeutic effect is long-lasting as the molecular glue degraders themselves are not degraded in the process and can initiate the degradation process through several iterations. BMS is a leader in this field based in particular on its unique library of cereblon E3 ligase modulators (CELMoD®) with specific protein-binding properties. Based on the needs of this project, Evotec focused on the development of dedicated and innovative software solutions that greatly helped to accelerate not only the project’s progress but also contributed to the overall progression of Evotec’s PanHunter platform.

The approach has generated a pipeline of novel first-in-class programs, two of which have transitioned successfully into lead optimization after completing respective validation processes on Evotec’s platforms. In this context, Evotec´s integrated data analysis platform panHunter and the Company’s AI and machine learning tools are used to quickly screen, share, and validate results – not only by Evotec, but also by BMS scientists. In May 2022, the partnership was expanded even further for an additional 8 years with the goal to once again broaden and deepen the strategic alliance.

Targeted protein degradation is not only useful in oncology - a number of other diseases, e.g. Alzheimer’s, bacterial and viral infections lead to the presence of unwanted proteins inside cells that may be marked for destruction by this powerful technology. Evotec therefore is welcoming partners interested in exploring this approach in collaborations.

To learn more about the BMS collaboration and the use of targeted protein degradation technology read the official press release.

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Autotaxin (ATX) is a secreted glycoprotein that hydrolyzes lysophosphatidylcholine (LPC) to lysophosphatidic acid (LPA). LPA signalling directly modulates tumour cell function and contributes to the development of the fibrotic tumour microenvironment, resulting in reduced host immunity and impaired response to therapy.

iOnctura, a clinical-stage oncology company, based in Switzerland (Genève), targeting core resistance and relapse mechanisms at the tumor-stroma-immune interface, has developed a potent and orally available autotaxin inhibitor, IOA-289, as a novel treatment for pancreatic cancer and other highly fibrotic tumours.

The first Phase I clinical study in healthy volunteers has been successfully completed. Evotec is very proud to have actively contributed in conducting the trial and analyzing the results that led to the achievement of this exciting goal.

Read the poster presented by iOnctura at the ESMO Immuno-Oncology Congress held in December 2021 to learn more about IOA-289 and its activity as autotaxin inhibitor. IOA-289 was also presented by iOnctura at the recently held AACR Annual Meeting in New Orleans.

 

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In this work, published in collaboration with Boston Children's Hospital, Evotec actively contributed to the identification of DW0254 and small molecule analogs capable of inhibiting RAC activation in acute lymphoblastic leukemia cell lines. Photoaffinity labelling mass spectrometry (PALMS) approach was successfully applied to identify PDE6D as the molecular target of DW0254. PALMS and biophysical methods were also used to identify the binding site of DW0254 in PDE6D. Our study provides evidence that PDE6D-dependent RAS trafficking with downstream activation of PI3K/AKT and RAC constitutes a novel potential therapeutic target in high risk leukemias.

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In this poster we focus on:

• Development of robust feeder-free 3D differentiation protocol to reduce iNK cells
• Transnational validation of iNK functionality with freshly isolated CLL patient tumor cells
• Enhances CLL patient tumor cell killing with CAR19 iNK
• EVOcells Oncology programs

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While the public has taken note of RNA-based medicine only with the advent of mRNA-based Corona virus vaccines, biopharmaceutical research and development has been working on mRNA-based medicine for almost two decades. Evotec also expanded the druggable target space to RNA and in the last years added considerable know-how in RNA-based medicine.

RNA is used by cells in multiple ways: mRNA is conveying genetic information from DNA to the ribosomes which also are made from RNA (ribosomal RNA), where another RNA species (tRNA) is transporting amino acids to the ribosomal apparatus so that a protein can be synthesized. In addition to mRNA, there are also shorter RNA molecules being used in the cell for the regulation of genes and entire genetic cascades.

This provides for plenty of potential interventions: antisense (ASO) and short interfering RNA (siRNA) can up or down regulate an RNA target, e.g., to block the translation of an unwanted or diseased protein or to suppress or stimulate the expression of genes. RNA can be targeted with (complementary) RNA, but it is also possible to alter or block the translation, re-locate or initiate RNA, degradation, etc. by small molecules interfering with the three-dimensional structure of RNAs or protein-RNA-complexes.

During our recent Innovation Week, Evotec experts Steffen Grimm, Group Leader, Hit ID & Biophysics, and Hilary Brooks, Senior Research Scientist, In Vitro Pharmacology, hosted a session called "The early bird catches the helix: Expanding the druggable target space to RNA".

In the session, they discussed how to:

• Expand the potential for drugs targeting RNA to offer alternative solutions for diseases with otherwise undrugged targets
• Target RNA providing highly specific solutions for protein removal, alternative splicing or pathway regulation via noncoding RNA
• Use the small molecule RNA targeting platform to contribute to new opportunities for target identification and validation

RNA as Therapeutics
Using RNA as therapeutics is not trivial. Nucleic acids introduced from outside may trigger adverse reactions by the innate immune system. A lot of knowledge is necessary to ensure delivery, avoid degradation and inflammation and to fine-tune the stability and function of the molecules. RNA may also have off-target effects. To ensure efficacy and safety, monitoring these early on needs to be incorporated into the developmental workflow. High quality synthetic RNA is costly to make, therefore a scaleable process and the relevant analytics must be established early in the process to accompany both the discovery and development stages of research with quality test material; Eventually producing GMP grade RNA at a commercial scale (several hundred grams) for human administration.

Evotec already has integrated all capabilities under one roof, allowing for the complete preclinical data set, reduced transition times and efficient communication to the regulators. For antisense oligonucleotide therapy, efficient hit sequences that knock down target expression can be selected in a matter of weeks. Toxicity profiling is a priority to establishing final leads and, subsequently, project-specific dose, duration and delivery will be established using optimized backbone chemistry. Using its in-silico capabilities as well as iPSCs, animal models, transcriptomics, etc. Evotec is able to predict toxicity and efficacy, and de-risk unwanted immune stimulation as well as off-target effects. For manufacturing, Evotec is discovery-capable and already building medium-scale capacity (up to 50g) which will be ready by 2023.

For inhibiting the translational machinery, Evotec has established an RNA small molecule targeting platform and established in various case studies, molecules binding to RNA, and demonstrating a significant effect in vitro without affecting cell viability. Evotec’s capabilities also allow the creation of a representation of the 3-dimensional structure of the target complex and its interaction with the compounds.

Evotec’s experienced team of scientists with proven drug discovery and development expertise already have a track record of driving RNA targeting projects forward. Its integrated medicinal and computational chemistry capabilities, combined with bioinformatics, structural biology, pharmacology, and drug safety expertise allows for the identification and characterization of RNA target species and their modulation by different modalities. Partner projects can be driven all the way from target identification to IND and beyond. Evotec therefore is a low-risk outsourcing partner and a company continually investing in its platform to the benefit of the customer.

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This article published in Nature describes a first-in-class METTL3 inhibitor for the treatment of acute Myeloid Leukaemia.

The publication covers:

• Development of STM2457 following high-throughput screen
• Selectivity screening across the panel of 45 human methyltransferases
• Crystal structure of METTL3-14 complex with STM2457, part of structure-based drug design strategy for this target
• Compound validation in cellular assays and in vivo efficacy

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Molecular profiling of cancer patients is a great success story: A single test can analyse a patient’s genome to identify genetic alterations from the four main classes that are known to drive cancer growth: base mutations, gene insertions and deletions, copy number alterations, and rearrangements or fusions. In addition to retrieving information on these common oncogenic drivers, it is also possible to obtain new information on complex or rare biomarkers from the same test. Based on this knowledge, oncologists can select the most suitable cancer therapy, often a combination of increasingly targeted drugs that address a specific cancer mechanism. As a result, molecular profiling approaches have been integrated to mainstream clinical oncology, and targeted therapies have become standard of care for patients known to express certain mutations in their tumours.

Molecular profiling – suitable for many indications

This success has fueled interest in the molecular profiling of other complex indications as well and has also expanded the profiling process: not only the sequence is analysed, but also methylation and expression patterns. The profiling toolbox also includes proteomics to analyse the proteins expressed in a cell or tissue and metabolomics to study the metabolism of diseased cells, tissue, organs, and patients.

The wealth of data generated by these approaches is now being analysed by artificial intelligence linking these data to individual patient information to identify biomarkers that provide insights into the genesis and course of the disease and that may help to stratify patients, predict outcome, and select therapies. The goal of these efforts is the development of precision medicines for complex diseases not only in cancer, but also in autoimmune or other chronic diseases – a clear departure from the old paradigm of “one-drug-fits-all.”

By systematically integrating data science across its discovery and development platform, Evotec aims to lead this paradigm change towards highly effective personalised medicine of the future. It has industrialised the generation of genomics, transcriptomics, proteomics and metabolomics data with its EVOpanOmics platform and has built a strong complementary data analytics platform driven by artificial intelligence and machine learning with EVOpanHunter. This platform makes use of molecular patient databases, bioinformatics and the data generated by EVOpanOmics.

Integrated approach

The company is in a unique position as these platforms are complemented by Evotec’s multimodality expertise spanning from small molecules and chemistry to biologicals, antisense molecules to cell and gene therapy. Moreover, with its iPSC platform Evotec’s scientists can design and test patient-derived disease models for comprehensive compound profiling in the treatment development process, focusing on disease relevance throughout the entire pre-clinical and clinical steps.

Already, Evotec has closed a number of collaborations in this field. In 2020, it joined forces with Indivumed GmbH for the discovery and development of first-in-class therapeutics for the treatment of non-small cell lung cancer (NSCLC). The collaboration combines Evotec’s bioinformatics, advanced analytics and AI capabilities as well as its small molecule and antibody discovery platforms, with the NSCLC cohort of Indivumed’s multi-omics cancer database “IndivuType.”

In the same year, Evotec closed a partnership with the University of Oxford, gaining access to biospecimens from the biobank Quality in Organ Donation (QUOD), an initiative of the university’s Nuffield Department of Surgical Sciences (NDS) in close collaboration with the National Health Service Blood and Transplant (NHSBT) organisation in the UK. QUOD is providing blood, urine and tissue samples from heart, lung, liver and kidney from consented organ donors for researchers with anonymised integrated medical records. Evotec at present is investigating first samples from 1,000 individuals using a comprehensive multi-omics approach (genomics, transcriptomics, proteomics, metabolomics) to complement its existing patient database. The goal is to enable a better understanding of disease mechanisms across indications, i.e. cardiovascular, kidney, and liver diseases.

A particular focus of Evotec is chronic kidney disease (CKD). CKD is an impending public healthcare challenge, and the traditional diagnostic biomarkers, e.g. creatinine, have low sensitivity and specificity. Therefore, novel diagnostic and prognostic biomarkers for patients at high risk of early-stage progression are urgently needed. They may not only provide information about the etiology and mechanisms underlying CKD progression, but may also enable early diagnosis and the selection of appropriate therapies, thereby personalising therapy. Evotec closed a strategic partnership with the University Hospital of Erlangen for the molecular analysis of biospecimens from the German Chronic Kidney Disease (GCKD) cohort study initiated by the university. GCKD is the world’s largest cohort study on chronic kidney disease, enabled by scientists from eleven universities and more than 150 practicing nephrologists that monitor more than 5,000 patients with CKD. The study comprises sampling of biospecimens, clinical data and multiple interviews. The collaboration aims to better understand the various kidney disease etiologies, their respective disease mechanisms, progression, and potential complications. Together with Evotec’s existing molecular patient database, this systematic integrated exploitation of the GCKD biobank is expected to provide novel starting points for drug discovery and the identification of biomarkers, enabling precision medicine approaches for highly effective treatment options for clearly defined patient populations.

Also in kidney disease, Evotec is collaborating with Novo Nordisk to jointly identify and develop novel targets based on comprehensive medical and molecular data sets of thousands of chronic kidney disease patients, and with Chinook Therapeutics to identify, characterise and validate novel mechanisms and discover and develop precision medicines.

All collaborations leverage the EVOpanOmics and EVOpanHunter platforms with the overarching goal to develop disease-modifying therapies for the targeted treatment of patients with unmet medical needs.

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Mass spectrometry (MS)-based ubiquitinomics allows a system-level understanding of ubiquitin signalling. 

In this publication, we focus on:

• a background to ubiquitinome profiling
• presentation of a scalable and robust workflow for deep and precise in vivo ubiquitinome profiling using DIA-MS (data-independent acquisition mass spectrometry) and neural network based data processing
• comprehensive mapping of substrates of deubiquitinase USP7, an anticancer drug target known to regulate tumour suppressor p53
• application of the method including rapid mode of action profiling of candidate drugs targeting deubiquitinases or ubiquitin ligases 

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Dendritic Cells (DCs) are very efficient antigen-presenting cells and have long been considered as attractive candidates for cancer immunotherapy. They are obtained from the patient and loaded in vitro with tumour antigens and additional maturation stimuli and subsequently, infused back into the patient. However, after more than 200 clinical trials involving thousands of patients, clinical responses have been disappointing so far.

While the treatment is safe and well-tolerated and often elicits anti-tumour immunity in both patients with advanced stages of disease and those with minimal residual disease following tumour resection, only a minority of patients demonstrates objective response rates. There are several reasons why the results are disappointing, and while scientists have been able to address problems such as active immune suppression and evasion mechanisms of the tumour, some DC therapy-related aspects contributing to the limited clinical efficacy of DC therapy remain to be solved: the choice of the antigen, the method of loading, and, above all, the type of DCs used. Access to the full spectrum of DCs is limited and many subsets known to be very effective simply are not accessible as they can be derived from the patients only in very low quantities.

As a result, sentiment has switched to approaches viewed as more promising, such as checkpoint inhibitors or chimeric antigen receptor (CAR)-T cells.

Exciting advances with iPSCs

However, thanks to the recent advances made with induced pluripotent stem cells (iPSCs) interest in these vaccines has been renewed. iPSCs can be induced to produce dendritic cells and this provides an opportunity for the rational design of DC vaccines displaying additional functionality via genetic engineering technologies. As iPSCs also open up the possibility for the mass production of large numbers of high-quality iPSC-derived DCs, it is now possible to design next generation DC vaccines from engineered DCs.

Moreover, iPSCs also allow for the production of DC subsets that are not accessible as yet for therapeutic development because sufficient quantities could not be obtained. Examples are DCs facilitating anti-viral responses and a certain subset called CD141+ specialised on cross-presentation of antigens. The CD141+ subset, which is found in very low abundance in vivo, is of particular interest for cancer therapy as it induces optimal cytotoxic T lymphocyte (CTL) responses. Thanks to iPSC, these subsets now can be produced under cGMP conditions in bulk quantities.

Off-the-shelf cancer vaccines?

All in all, these advances may provide the opportunity to design off-the-shelf DC products suitable for cancer vaccines.

Evotec therefore has invested in British immune oncology company OXvax Ltd., a spin-out from the University of Oxford focused on the development of an advanced next-generation dendritic cell vaccine platform for the treatment of solid cancers. The company is pioneering the use of iPSCs as a novel source of CD141+ dendritic cells (DC) and is based on intellectual property from the Fairchild laboratory at the Sir William Dunn School of Pathology. OXvax’s technology addresses, among others, the low cross-presentation and the T-cell activation problems of past DC-based cancer treatments. The platform enables the manufacture at scale of an off-the-shelf, highly potent vaccine which addresses the major limitations that have frustrated cancer vaccine development in the past. If the approach is successful in oncology, it can also be expanded to other therapeutic areas, e.g. viral infections.

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