Un-locking 🔐 Data to Transform Biology: Latest Trends on TechBio
Un-locking 🔐 Data to Transform Biology: Latest Trends on TechBio
MetaphysicalsCells: A newsletter about Science, Technology and AI Drug Discovery
Freshly baked news 👩🍳
🥯 BMS signs $674m GenAI drug discovery deal with VantAI
🥧 SCOPE: FDA facilitates AI and ML use for clinical trials and drug development
🧁 Ono Pharmaceuticals to Leverage InveniAI’s AI & ML Tools to Identify Novel Therapeutic Targets
🥖 Daewoong Pharmaceutical digitizes DB of 800 mn chemical compounds
🍞 Parse Biosciences, a leading provider of accessible and scalable single cell sequencing solutions, acquired data analysis software company Biomage
🥐 Monomer Bio has secured $5.6M in seed financing to develop its platform that combines laboratory automation with data analytics
🥞 Zetta Genomics expands second seed funding round with additional £1.8 million
Octant Bio
Octant Bio is combining advanced cell engineering, high-throughput chemistry and automation to engineer best-in-class drugs across rare disease, oncology and immunology. Their platform, Octant Navigator, is a high-throughput (HT) empirical drug discovery platform that integrates Cellular Intelligence and structure activity relationships (SAR) to guide drug design:
Cellular Intelligence is their high-throughput approach to read out on hundreds to millions of conditions to build drugs with highly desired profiles, by using RNA-barcoding technologies.
Their nano-scale automated chemistry synthesis platform (HT-SAR) screens thousands of analogs to discover which chemical modifications turn weak target binders into drug-like compounds. And
Advanced ML and automation technologies enable Cellular Intelligence and HT-SAR to iterate in a positive feedback loop.
For example, Deep Mutational Scanning (DMS) harnesses Octant’s Cellular Intelligence platform to design, build, and screen thousands to millions of cell lines, generating unique insights into a protein’s function. They engineer a distinctly barcoded cell line for every amino acid substitution of the target, mapping the functional response molecules acting on each of those cells. Precisely understanding the extent to which a residue or mutation of a protein differentially drives each of its activity pathways opens entirely new capabilities for building better drugs.
Octant was founded in 2017 in the US by Deepak Agrawal, Ramsey Homsany and Sri Kosuri and on April 28, 2022, achieved a significant milestone by securing a remarkable 🍻 $80 M in Series B funding, for a total raised capitalof $115M since the company's inception.
o2h Ventures
o2h Ventures in the UK is a specialist fund that only invests in biotech therapeutics at the intersection between biotechnology and AI/ML. o2h Ventures was co-founded by Sunil Shah and his brother Prashant Shah in the year 2018. o2h group operates from their proprietary 2.7 acre The Mill SciTech Park where they are developing a unique model for incubating small life science companies. They invest into:
Oxford Drug Design is an innovative biotechnology company spun out from Professor Graham Richards’ 👨🏫 group at the University of Oxford, developing rapid, state of-the-art virtual screening and ligand analogue searching technologies.
Building on this platform, the company is now applying ML techniques such as neural networks and topological data analysis to help further the drug discovery process. In 2023, Oxford Drug Design and PhoreMost announced a collaboration to accelerate a targeted protein degradation discovery programme for novel cancer therapeutics.
PhoreMost has developed a next-generation phenotypic screening platform called SITESEEKER® that can discern the best new targets for future therapy and crucially, how to drug them. This has the potential to significantly increase the diversity of novel therapeutics for cancer and other unmet diseases.
Based on the Company’s core proprietary ‘Protein Interference’ technology, SITESEEKER® systematically unmasks cryptic 🫥 druggable sites across the entire human genome and directly links them to useful therapeutic functions in a live-cell context.
DeepMatter Group Plc is a big data and analysis company which has built a platform DigitalGlassware™, focused on enabling reproducibility in chemistry to deliver applications resulting in new optimized chemicals, materials and formulations. DeepMatter is at the forefront of the digitization of chemistry, which will ultimately see the enabling of an autonomous synthesis engine, the Chemputer™. In 2022, DeepMatter shares drop 🪫 58% to a record low on plans to delist from AIM.
Turbine’s in silico experiments can test an almost infinite number of interventions on a Simulated Cell that accurately reflects the molecular diversity of cancer cells. Turbine takes laboratory trial and error out of drug discovery and tackles it with scalable power on their servers. In 2023, the London based Budapest University spinout Turbine AI secured €5.5M in Series A funding for a total of €25.5M.
ViaNautis (Formerly known as Somaserve) is exploiting its proprietary technology, polyNaut®, a nanovesicle platform using advanced polymer materials and ML, to direct nucleic acid therapeutics to the specific site of action with unparalleled precision. They are focused on delivery to the brain, CNS, lung, and other hard to reach areas of the body. In 2023, ViaNautis Bio announced the successful completion of its Series A funding round, raising $25M (£20M). ViaNautis was spun out of UCL in 2018 by co-founders Dr Francesca Crawford, Dr Denis Cecchin and Professor Giuseppe Battaglia, inventor of polyNaut® and honorary professor at UCL.
Kuano is an AI company using quantum computing to create molecular design solutions that is headquartered in London and was founded in 2020 by Vid Stojevic, David Wright, Parminder Ruprah and Jarryl D’Oyley. Kuano focuses on developing enzyme inhibitors using AI and quantum computing simulations for pharmaceutical, crop protection, and industrial chemistry applications. In 2023, Kuano raised a £1.8M seed funding round.
Sanome is a London-based MedTech company founded by Benedikt von Thüngen. Sanome is building a Clinical Co-Pilot 👨✈️ that supports clinicians identifying patient health change earlier, using their proprietary Foundational Multimodal Embeddings Platform. In 2023, Sanome was named Most Innovative Biomarker Platform 2023 by the Global Health & Pharma Awards, within the International Life Sciences Awards category.
💎 The NVIDIA GTC conference is back live from the San Jose Convention Center, California from March 18-21. Registration is free for virtual GTC attendance.
Creyon Bio
The US-based startup Creyon Bio, founded by Christopher Hart, Ph.D. and Swagatam Mukhopadhyay, Ph.D. in 2019 in San Diego, California, specializes in oligonucleotide-based medicines (OBMs) by combining biology, genomics, pharmacology, biophysics and chemistry with ML/AI.
Creyon’s advanced platform works by identifying the design rules and engineering principles for OBMs, including modalities ranging from single-stranded antisense oligonucleotides (ASOs) that reduce gene expression levels or change splicing events to small interfering RNA (siRNA), to DNA and RNA editing systems, to even targeting aptamers. Then it builds accurate predictive models of safety and efficacy.
Creyon Bio raised 💰 $40M.
NordicRWE
NordicRWE in Norway specializes in data-driven drug development emphasizing applications of real-world evidence (RWE). The Nordic region is uniquely positioned for high-quality RWE studies for the following reasons:
The Nordic region consists of countries with relatively small populations ranging from Iceland (approx.300,000 inhabitants) to Sweden (approx. 10.5 million inhabitants). In total, the region has 27 million inhabitants.
Nordic countries have universal, publicly funded healthcare systems that captures data from all inhabitants throughout their lives, from cradle to grave 🪦, and every event in between.
In the Nordic countries, health authorities have mandatory and complete individual-level health registries that capture births 👶, deaths, medication and vaccine usage, hospital and primary care visits, as well as a range of disease-specific registries. The registries include information about diagnoses, procedures, treatments, and for some registries, patient-reported outcomes.
The registry data can also be augmented by collecting data from electronic medical records.
In the Nordic countries there is a long tradition of setting up and maintaining consented population-based cohort studies, which provide a unique source of deeper phenotypic data.
All these data sources can be combined using the Personal Identification Number, and can be linked to sociodemographic- and immigration/emigration data to ensure a complete longitudinal follow-up.
All Nordic health data are available for researchers, following each country's approval processes, data privacy guidelines, and ethical rules.
The NordicRWE team has successfully gained approvals 👁️ from registry holders and ethics committees, and has extensive experience in using Nordic health registry data in observational research, with several real-world evidence projects that are ongoing.
NordicRWE’s R&D project focuses on two innovative applications of RWE in drug development, namely external control arms for cancer clinical trials, and drug signal detection. Their technology-driven projects focus on interactive dashboard solutions and synthetic data generation.
NordicRWE was founded in 2021 and in 2022 secured 16 million NOK (1,4 M €) by the Research Council of Norway.
Catch up with Jens Nielsen, the CEO of BioInnovation Institute. Find out from one of the top people in the field about what works best to translate academic research in bio into innovation for humanity, especially how everything is connected.
💎 ABOUT THE SPEAKER: Jens Nielsen is one of the best in this space in Europe. Not only is he the CEO of BII, he’s also a professor of systems biology at Chalmers University of Technology in Sweden, and is the most cited researcher in the field of metabolic engineering as well as industrial biotechnology. He’s the founder of the International Metabolic Engineering Society and has also founded many biotechs.
Deep Breath Intelligence
Deep Breath Intelligence in Switzerland 🧀 was founded as a spin-off of USZ/UKBB and ETH in 2018 is a healthtech company unleashing the huge potential of analyzing exhaled breath by applying ML algorithms, by combining high-resolution mass spectrometry and advanced ML techniques for breath analysis. Their first product, DBI-EPIbreath®, is a test for drug monitoring in epilepsy which is CE-certified under IVDD. The DBI-EPI breath test estimates the blood drug concentrations of valproic acid (VPA) from a simple exhale, and estimates risks of severe side effects and seizures, in order to evaluate epilepsy treatment decisions. Each analysis identifies volatile organic compounds (VOCs) in exhaled breath (something like 500 molecules in each exhalation) and provides insights into an individual’s metabolic state. This is important because metabolization of epilepsy medication is highly specific to individuals, especially for medications with a narrow therapeutic range like VPA that is the treatment of choice for generalized or difficult to classify epilepsy.
Other applications include breath analysis tests for : Chronic obstructive pulmonary disease (COPD), Obstructive sleep apnea (OSA), Asthma, Pulmonary fibrosis, Pulmonary hypertension, Cystic fibrosis, Pneumonia, Lung Cancer, Long Covid, and Metabolism.
In 2023, the company announced that Emergo will become its authorized DBI-EPIbreath representative in the European Community, helping Deep Breath Intelligence to speed up their time to market and move boundaries in therapeutic drug monitoring for people living with epilepsy.
Deep Breath Intelligence has raised $2.8M and was founded by Prof. Dr. Malcolm Kohler, Prof. Dr. Pablo Sinues, Paul Schenker and Sigi Föhn.
Atavistik Bio
Atavistik Bio is discovering the next generation of precision allosteric therapeutics, by integrating their propriety screening technology using the body’s natural regulators with their powerful AI-enabled drug discovery platform, to efficiently identify novel, biologically relevant allosteric sites for protein or RNA targets, and rapidly advance structural insights into small molecule therapeutics design. The site to which a molecule binds is termed the allosteric site or regulatory site. Allosteric sites allow molecules to bind to a protein, often resulting in a conformational change and/or a change in protein dynamics. Molecules that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
Unlike conventional, small molecule approaches to drug discovery, which focus on targeting active sites or serendipitously drugging allosteric sites, Atavistik’s approach enables to efficiently and systematically uncover functional allosteric pockets not detectable 🕵️ with other techniques. Built upon the technology platform of co-founder Jared Rutter, PhD, Professor of Biochemistry at the University of Utah and the discoveries of Ralph DeBerardinis, MD, PhD at the University of Texas Southwestern Medical Center, the proprietary Atavistik Metabolite-Protein Screening (AMPS) technology is integrated with the proprietary AI-enabled discovery engine allowing to evaluate metabolite-protein interactions by screening proteins with their proprietary metabolite library. In this way, they determine where binding sites with biological relevance might exist and they build an extensive protein-metabolite database map (the “Interactome”) to reveal unique insights into the crosstalk between metabolite-protein pathways that were previously thought to be unrelated.
Utilizing advanced informatics tools, deep expertise in chemistry and computationally rich structure-based drug design (namely mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically), they are able to identify and understand the role of these interactions across important biological and disease-relevant pathways to drive the discovery of novel therapeutics.
In 2023, Atavistik Bio announced that it has raised an additional $40M to advance its lead precision allosteric small molecule therapeutic in oncology into the clinic for a $100M in aggregate since its launch in August 2021.
Pixelgen Technologies
Pixelgen Technologies in Sweden specializes in molecular pixelation (MPX) technology that enables highly resolved cell surface protein maps for deep phenotyping of immune cells. In particular, DNA tagged monoclonal antibodies ensure high multiplex analysis of cell surface proteins with validated target specificity. The barcoding approach enables a smooth transition from analog to digital data readout. And by using a single tube 🧪, partition-free sample preparation, they are providing spatially resolved abundance data similar to Confocal and Flow Cytometry, always in focus and from every angle.
In particular, the Pixelgen Single Cell Spatial Proteomics Kit, Immunology Panel I, Human (Pixelgen SCSP Kit) is the first high-multiplex and high-throughput product to convey spatial polarization and co-localization of proteins on the cell surface in 3D, offering new insights into the biology in health and disease.
Co-founded by Simon Fredriksson, Alvaro Martinez Barrio and Filip Karlsson in 2020 in Stockholm, Sweden the company successfully closed in 2023 a $7.3M Series A financing round led by Industrifonden and Navigare Ventures (for a total funding amount of $13.3M).
In February 2024, Pixelgen announced a non-exclusive agreement with leading distributor Australian Biosearch that will bring Pixelgen's MPX kits for high-multiplex spatial analysis of membrane proteins to the Australian 🐨 and New Zealand markets.
Jeff Spitzner is a founder and executive of nine Life Sciences, Software, Investment, Bio-Technology and Healthcare companies that contributed over $35M to the Columbus, OH community. For example, he is the
CEO & Founder at DNA Nanobot: DNA Nanobot is a platform biotechnology company with IP-based products and services for improved design and delivery of therapeutics (drugs, antigens, siRNAs, mRNAs, genes, peptides, antibodies, biologics, small molecules, etc) including better targeting and larger payloads.
AMPLY Discovery
Belfast based AMPLY Discovery, founded as a spinout from the Queen’s University Belfast in 2021, digitizes 🧑💻 life’s diversity, using next-generation sequencing for drug discovery.
The AMPLY platform connects the digital biological biome to high volume peptide, protein and RNAi extraction technology to unlock a new frontier in drug discovery. In particular, AMPLYfolio AI can process genomic, transcriptomic, meta-transcriptomic, metagenomic or synthetic data, and uses custom data-scanning techniques to locate regions of interest in digital biological data that other tools miss. Then utilizes black-box unpublished ML and bioinformatic methodologies to highlight novel compounds using a complex web of thousands of metadata tags.
Moreover, AMPLY uses approaches leveraged from predictive marketing and the financial services industry and creates a "stock picking" dashboard view of the data it processes. This allows a user-driven selection of novel compounds. Additionally, AMPLY uniquely connects the digital discovery technology to high throughput peptide and RNAi synthesis and protein extraction techniques. Once a compound is identified the AMPLY pipeline includes a full lab validation of the kill-efficiency of the compound against target diseases. Testing such as toxicity, anti-biofilm, biochemical handling criteria and resistance studies can be performed as desired.
In February 2024, AMPLY raised over €1.6M in grant funding from Innovate UK. AMPLY Discovery was co-founded by Dr Ben Thomas and Dermot Tierney.
Genesis Therapeutics
Genesis Therapeutics (South San Francisco, California, US 2019 out of Stanford's Pande Lab) is a privately-held company inventing and deploying state-of-the-art 👩🎨 AI techniques to augment drug discovery and development. Its platform GEMS: Genesis Exploration of Molecular Space, integrates DL and molecular simulations for property prediction, and language models for molecular generation.
Dynamic PotentialNet of GEMS predicts potency, selectivity and ADMET even for data-poor and previously undruggable targets. Dynamic PotentialNet represents the 3D structure and interactions of protein-ligand complexes as spatial graphs. By training on a combination of molecular simulations and experimental data, it learns representations of the physical interactions underlying binding affinity. This enables the model to generalize to novel protein targets and make accurate predictions based on 3D structures alone, without requiring on-target binding affinity data.
In addition to these predictive models, GEMS uses chemically aware ML models that can be directed to create novel molecules and explore specific regions of chemical space for each drug program. During Hit ID, GEMS generates billions of drug-like and synthetically accessible molecules, enabling a diverse exploration of chemical space. During Hit-to-Lead and Lead Optimization, their chemists direct GEMS to generate novel molecules from a specific starting point, to explore scaffold hops and optimize promising series.
In 2023, Genesis announced that it had closed an oversubscribed $200M round of Series B financing. This funding brings the total capital raised by Genesis Therapeutics to over $280M 🤑, from top technology and biotech investors, including Andreessen Horowitz, Rock Springs Capital, T. Rowe Price, Fidelity, Radical Ventures, NVentures (NVIDIA's VC arm), BlackRock, and Menlo Ventures. Co-founders of Genesis are Evan Feinberg and Ben Sklaroff.
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