Bits In Bio Weekly - October 29th 2024
Updates From and Around the Bits in Bio Community
📢 Highlights
ScGenePT fuses biology's words and data to predict cellular behavior
Aliada's blood-brain barrier breakthrough earns AbbVie's $1.4B bet
Alpha-9 $175M Series C shows radiopharma may be biotech's new hot ticket
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ScGenePT: Is language all you need for modeling single-cell perturbations?
In a new preprint, researchers from the Chan Zuckerberg Initiative have introduced scGenePT, a new model that combines experimental and language-based gene representations to predict single-cell perturbations. As an extension of scGPT foundation model, scGenePT integrates text-derived embeddings from sources like NCBI gene cards, UniProt, and Gene Ontology annotations, blending traditional experimental data with textual gene representations which offer valuable prior information to understanding perturbations. ScGenePT’s multimodal approach surpasses single-modality models, underscoring the potential of a holistic approach to computational biology models. The team mentionnes that while the scGPT architecture has been retrieved directly from the scGPT github repository, they plan to release the code that includes the gene-embeddings upon publication.
AbbVie Adds Alzheimer’s Platform to CNS Pipeline in $1.4B Aliada Deal
AbbVie announced its $1.4 billion acquisition of Aliada Therapeutics, a Phase 1 biotech focused on Alzheimer’s and CNS therapies. Aliada’s lead asset, ALIA-1758, targets Alzheimer’s by improving drug delivery across the blood-brain barrier. The acquisition complements AbbVie’s CNS portfolio, which includes treatments for Parkinson’s, schizophrenia, and epilepsy. This follows a trend of large pharma acquiring smaller biotechs for under $2 billion, a strategy that, while expanding pipelines, raises concerns about innovation dependency on smaller companies.
Behind the Deal: Alpha-9 $175M Series C to Capitalize on Radiopharma Momentum
Alpha-9’s $175 million Series C with top-tier investors, including Lightspeed Venture Partners and Ascenta Capital reflects rising investor interest in radiopharmaceuticals - a field poised for exponential growth, driven by clinical breakthroughs and market potential. Alpha-9 has recently achieved promising preclinical results, enhancing confidence in its pipeline’s ability to treat traditionally resistant cancers, with proceeds from the raise fueling clinical trials. Moreover, Alpha-9's refined approach has the potential to expand into diverse oncology targets, justifying the investment. Radiopharmaceuticals are emerging as a hotbed of investment because they offer a competitive edge through targeted radiation delivery. This modality reduces systemic toxicity and integrates well with combination therapies, positioning firms for success in oncology’s high-margin market. With large players like Eli Lilly and Novartis aggressively acquiring radiopharmaceutical assets, Alpha-9 is strategically placed to attract future partnerships or acquisition interest as the field matures. Furthermore, growing investments in radiopharmaceutical manufacturing infrastructure mitigate prior supply bottlenecks, allowing Alpha-9 to scale more efficiently for market entry.
A NextFlow pipeline for the classification of protein kinases - KiNext
KiNext is a NextFlow pipeline designed for the identification and classification of protein kinases in annotated eukaryotic genomes. The pipeline addresses a significant challenge: identifying eukaryotic protein kinases based on amino acid sequence, which is complex due to divergence outside of the catalytic domain. Operating in three main steps—kinome identification, protein kinase classification, and phylogenetic tree construction for both eukaryotic and atypical protein kinases—KiNext utilizes Hidden Markov Models for sequence analysis and classification. The researchers selected NextFlow as their framework to "simplify the development of the KiNext pipeline, optimize the use of its resources, manage the installation and versions of the software with the capabilities of operating on a personal computer as well as on a computing cluster." A key motivation behind KiNext's development was adherence to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, which the developers note are not consistently followed by many existing tools in the field. Access and learn more about KiNext here.
Monte Rosa Therapeutics and Novartis $150M Partnership for Protein Degraders
Boston-based Monte Rosa Therapeutics has entered a $150 million partnership with Novartis to advance molecular glue degraders for autoimmune and inflammatory diseases. The collaboration focuses on leveraging Monte Rosa's small molecule protein degradation technology to selectively degrade harmful proteins driving disease progression. Novartis will provide milestone payments based on clinical, regulatory, and commercial achievements, with the potential for Monte Rosa to receive up to $1.5 billion. The deal emphasizes Novartis' growing interest in protein degradation as a frontier for autoimmune treatment innovation. [URL:]
Computational Design Boosts Enzyme Activity for Parkinson's Drug Synthesis
Researchers at Tianjin University and the Hangzhou Institute of Medicine have published their innovative computational approach for engineering tyrosine phenol-lyase for efficient L-DOPA synthesis, a medicine for Parkinson’s disease. The researchers developed a "computational approach that integrates structure-based analysis of conformational flexibility with in silico screening for stabilizing mutants.” Their approach integrates structural analysis with computational design and addresses the “stability-activity tradeoff” of enzymes by “rigidifying flexible regions distant from active sites.” Their work highlights the potential of computational techniques for understanding the structure-function relationship in enzymes and may guide future work in rational enzyme design.
Agomab Raises $89M to Advance Inflammatory Bowel Disease Therapies
Backed by Sanofi, Agomab Therapeutics has raised $89 million in a Series C funding round to accelerate its pipeline of therapies targeting inflammatory bowel disease (IBD) and fibrotic conditions. The funding will support the development of Agomab's novel small molecules aimed at inhibiting fibroblast growth factor receptor signaling pathways. The company's lead candidate, AGMB-001, is set to enter Phase 2 trials in 2024, with early preclinical results showing significant promise in reducing intestinal inflammation. The raise marks another significant investment in the IBD treatment landscape, which is projected to grow to $5.2 billion by 2030. [URL:
Benchling Acquires PipeBio to Boost AI-Powered Antibody Discovery
In its latest move to expand its AI-driven capabilities, Benchling has acquired PipeBio, a Danish bioinformatics company specializing in antibody discovery. The acquisition will allow Benchling to incorporate PipeBio’s platform, which uses AI and machine learning for faster and more precise antibody development. By adding PipeBio’s tools, Benchling aims to streamline drug discovery workflows and improve collaboration among researchers in the biopharma space. The integration of AI-powered platforms like PipeBio signifies a growing trend toward automating and optimizing therapeutic discovery.
Multi-state modeling of Kinases using AlphaFold2
A recent study in Scientific Reports introduces a multi-state modeling (MSM) approach using AlphaFold2 to improve structure-based virtual screening for kinases, which are subject to conformational changes. These changes make traditional docking methods challenging as they generally focus on a single kinase state, usually the DFGin conformation. The introduced MSM protocol addresses this by generating diverse structural models, including DFGin, DFGinter, and DFGout states, with state-specific templates in AF2. This approach provides more accurate binding predictions and enhances the identification of a diverse set of kinase inhibitors, as compared to AlphaFold2 and AlphaFold3. By reflecting the range of kinase binding site conformations, the MSM protocol supports broader screening possibilities in kinase-targeted drug discovery.
Rancho Biosciences and Sapitent team up for NextGen Human Biology Database
Sapient has partnered with Rancho Biosciences to enhance its human biology data integration and analysis capabilities. This collaboration aims to build a next-gen database focusing on multi-omics data to accelerate drug discovery and development. By integrating Sapient’s expertise in human biology with Rancho's data science services, the partnership will enable faster data processing and more sophisticated insights. The partnership further underscores the need for robust data solutions as the biotech industry increasingly depends on comprehensive, scalable data platforms to drive precision medicine.
Seagen’s David Epstein Joins Ottimo Pharma for Immunotherapy Breakthroughs
Veteran biotech executive David Epstein, who previously led Seagen, has joined Ottimo Pharma to spearhead its efforts in developing next-gen cancer immunotherapies. Ottimo Pharma is focusing on combining PD-1 and VEGF inhibition to develop dual-action treatments, aiming to enhance immune responses while cutting off tumor blood supplies. Epstein stated that Ottimo's approach could transform cancer treatment, with several clinical programs set to launch by 2025. With backing from top industry figures, Ottimo aims to challenge existing immunotherapy paradigms.
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