Introduction to Sodatana services offers & work approach by Johannes Söllner
Protein and mRNA engineering
A common prerequisite for efficient protein engineering has long been the availability of reliable protein structures, which has recently seen a tremendous boost from artificial intelligence. We apply diverse methods combined with biological rationale to modify or optimize proteins towards our clients' needs, such as solubility, focus on critical antigenic regions, chimerization, abolishing binding of prosthetic groups or in some cases even affecting enzymatic activity. Together with in-house developed methods for tissue adapted bicodon optimization and selection of tissue optimized UTRs from our RNAtech database we offer a comprehensive portfolio of services for designing and optimizing protein and mRNA based drugs.
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Vaccines & immunoinformatics
We have so far supported numerous companies, frequently during the startup phase. Typically with antigen designs, choosing peptides or domains, supporting/complementary information, data backends of vaccine pipelines, methods to make sense of their data or for further limiting antigens resulting from experimental screening or biopanning. Depending on preferred technology requests can be to select suitable and broadly covering B-cell epitopes from functional sites, achieving patient HLA coverage through T-cell epitope assemblies, pathogen coverage through sequence consensus or centroid sequence selection, engineering proteins to focus only on most relevant sub-domains, or point mutations for abolishing hydrophobic regions or preventing glycosylation especially in mRNA vaccines. And many more. The goal remains the same for us, assisting our clients to create vaccines or monoclonal antibodies using the technologies they prefer and are available, suitable for the challenges they currently face. Often with IP generation in mind.
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From genome to candidate
Identification of potential (vaccine) targets from genomic sequences is a common process now. From eukaryotes, but to an even higher degree from bacteria. Either based on whole genomes or metagenomes. Very often projects start with a growing bulk of public and/or in-house genome sets. Those will be annotated, screened for targets of interest according to biologically meaningful criteria. Optimally homologues within and between organisms are included for selection of most robust candidates.
Gene/Protein/Drug/Disease association networks
Networks can be an interesting basis for ranking gene/protein targets, inferring new applications for existing targets (including drugs) or finding associated molecules not protected by current intellectual property. Public databases such as STRING, STITCH and many more as well as client's in-house sources, optionally with differential gene regulation data, allow to infer relationship networks of genes, proteins, drugs and diseases.
Those networks can be made use of in various ways, such as selecting closely associated factors not protected by IP or those closely associated with a disease and having known drugs associated.
Those networks can be made use of in various ways, such as selecting closely associated factors not protected by IP or those closely associated with a disease and having known drugs associated.
Mining patent and literature databases
Unstructured text sources such as NCBI Medline have grown to extents impossible to survey manually. Automated keyword searching and interlinking is a useful approach to find associations of genes/proteins, drugs and diseases from public databases, including IP databases or protein annotation resources. Those associations can be made use of for ranking targets or also to identify potential problems such as possible side-effects, early on in the development process.
Competence & Consulting
Being only human we tend to lose perspective when spending too much time in a single focused project or a related set of projects within our peer group. Frequently no extensive analysis is required, but primarily ideas how to proceed strategically. In those cases sodatana can assist by providing competence in computational biology, where automation may be a good choice or simply by providing biological or immunological competence. No-one is a specialist in all aspects of a field or even a project, and here a fresh mind coming from outside can make a critical difference. First by providing summaries of state-of-the art (which is also important for IP matters) but also by providing an outside perspective, connecting to novel applications, pointing out potential flaws and risks and suggesting experimental methods or cooperation with third parties.
Your project
Every project is new and unique. Although often existing technologies can be re-used, every project needs its own set of perspectives and utilities, sometimes to be newly developed. More on the technical side compared to consulting, sodatana can help you to find or develop the solution you actually need.
