AI Tools for Cell and Gene Therapy (2nd part)

Cell and Gene Therapies (CGT) and Artificial Intelligence

@WhimsyNico

For the first part of this newsletter: AI Tools for Cell and Gene Therapy.

Gene therapy is a medical technology that aims to produce a therapeutic effect through the manipulation of gene expression or through altering the biological properties of living cells. Often, gene therapy works by adding new copies of a gene that is broken, or by replacing a defective or missing gene in a patient's cells with a healthy version of that gene. When it comes to the gene therapy modality (with both viral and non viral vectors) we have

• DNA based therapies such as:

  • CRISPR gene editing—which stands for “Clustered Regularly Interspaced Short Palindromic Repeats”—that enables a correction of a particular genetic defect,

    • DL in CRISPR-Cas systems: a review of recent studies,

  • Prosthetic gene therapy,

    • DNA Chisel, a versatile sequence optimizer,

    • OPTIMIZER: a web server for optimizing the codon usage of DNA sequences (Monte Carlo algorithm),

    • The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. And

• RNA based based therapies: mRNA, antisense oligonucleotides, shRNA, siRNA, miRNA

  • TREAT: Therapeutic RNAs exploration inspired by AI technology.

Very briefly, the “Gene Delivery Systems” are categorized as:

1. viral-mediated gene delivery systems that consist of viruses—adenoviruses, retroviruses and lentiviruses—that are modified to be replication-deficient, but which can deliver DNA for expression into human cells.

   1. BioMap—building xTrimo, the first and largest protein-centric large language model platform—has a strategic partnership with Proton Advanced—that offers a cGMP-compliant manufacturing platform for plasmids, cell therapy, gene therapy, oncolytic virus, mRNA therapy and bacterial therapy—in order to leverage Porton Advanced's unique Adeno-Associated Virus (AAV) vector technology platform and research data to develop AAV assembly efficiency models and an assembly distribution model. The goal is to harness the power of large-scale life science models, accelerating the design of AAV vectors, and expanding the application of AI models in the field of gene therapy,

   2. For cell media optimization Cytiva, has access to XURI Media AI Guide, an AI platform for optimizing cell culture formulations, and XURI Media Designer System, a cell media configurator that enables customization of cell culture media by Nucleus Biologics, and

   3. To increase viral vector productivity with AI/ML tools we have 4x Bio.

2. non-viral gene delivery systems for improved gene transfection, that can be

   • physical types: microinjection, electroporation, ultrasound, gene gun, microscale robots and hydrodynamic applications. Or

   • chemical types: utilize natural or synthetic carriers to deliver genes into the target cells (polymers, liposomes, dendrimers and cationic lipid systems are used as gene delivery systems).

     • Nanite Bio headquartered in Boston, is a next-generation non-viral gene delivery company that is developing an AI-driven platform, SAYER™, that combines cutting-edge high-throughput experimental and computational methods to design fit-for-purpose delivery vehicles (a new class of programmable polymer nanoparticles) delivering a broad range of genetic cargoes with tissue specificity. And

3. combined hybrid systems.

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AI and mRNA-based therapeutics

🟢 Anima Biotech, founded in 2005, is advancing mRNA Lightning AI Imaging, that is a novel platform for the discovery of selective small molecule mRNA drugs and their mechanisms of action (MoA), combining high scale phenotypic screening and AI.

Their platform mRNA Lightning™—at the intersection of mRNA biology imaging and AI—is used to visualize the biology of mRNA and builds on this unique capability of image neural networks that recognize disease signatures. Their large language model and AI co-pilot rapidly decode the mRNA biology signature underlying the disease, identifying active compounds against it and uncovering their mechanisms of action and molecular targets. They have amassed a tremendous amount of mRNA biology expertise and knowledge that is continuously updated in their mRNA biology LLM, an augmented large language model that is used by the Lightning AI co-pilot, an mRNA AI biologist that works hand in hand with scientists along the drug discovery process, suggesting hypotheses for MOAs and molecular targets along with validation experiments.

Anima Biotech has strategic collaborations with Lilly, Takeda and Abbvie and just this week announced positive preclinical data of its lung fibrosis candidate, that operates through a novel mRNA biology mechanism of action, opening new avenues for treating Idiopathic Pulmonary Fibrosis patients.

Anima Biotech was founded by Yochi Slonim ​M.Sc. and Iris Alroy PhD, and raised a total funding of $11.5M over 3 rounds.

Anima Biotech, which is considered a leader in the discovery of small molecule mRNA drugs, launched a groundbreaking webinar series in partnership with leading life science media outlets, to provide up-to-date, high-quality information on mRNA biology: Exposing hidden targets within the mRNA regulation space.

🟢 Nuntius Therapeutics founded in 2021 by Albert Kwok and Benita Nagel in UK, is developing a field-leading proprietary technology for systemic nucleic acid delivery, based on scalable non-immunogenic materials. Their patented data-driven high-throughput screening platform allows them to screen novel cell-specific nanocarrier formulations in order to develop mRNA and gene editing therapies for currently incurable diseases. Their pipeline also includes immunotherapies.