Darwin and Fisher meet at biotech: On the potential of computational molecular evolution in industry

Abstract

Today computational molecular evolution and bioinformatics are vibrant research areas that flourish on large amounts of complex datasets generated by new generation technologies – from full genomes and proteomes to microbiomes, metabolomes and epigenomes. Yet the foundations for successful mining and the analyses of such data were established long before the structure of the DNA was discovered. Darwin’s theory of evolution by means of natural selection not only remains relevant today, but also provides solid ground for computational research with a variety of applications. The data size and its complexity require empirical scientists to work in close collaboration with experts in computational science, modeling and statistics, as Sir R. Fisher has beautifully demonstrated in early 20th century. Particularly, modern computational methods for evaluating selection in molecular sequences are very useful for generating biological hypotheses and candidate gene sets for follow-up experiments. Evolutionary analyses of selective pressures in genomic data have high potential for applications, since natural selection is a leading force in function conservation, in adaptation to emerging pathogens, new environments, and plays key role in immune and resistance systems. At this stage, pharma and biotech industries can successfully use this potential, taking the initiative to enhance their research and development with the state-of the art bioinformatics approaches. This mini-review provides a quick “why-and-how” guide to the current approaches that apply the evolutionary principles of natural selection to real life problems – from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.

Positive selection in multiple salivary gland proteins of Anophelinae reveals potential targets for vector control

“…CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint this version posted February 17, 2021. ; https://doi.org/10.1101/2021.02.16.431392 doi: bioRxiv preprint blood-feeding and also can lead to the development of new strategies for vector control (Anisimova 2015;Hammond et al . 2016) .…”

“…2003) 2017, and they added other evolutionary analysis using site models to detect signatures of positive selection in individual sites. However, they did not report which sites were subjected to positive selection, an important result that can help us to understand the evolution of blood-feeding and also can lead to the development of new strategies for vector control (Anisimova 2015;Hammond et al . 2016) .…”

Bioinformatics and Drug Discovery

“…Genomics sequence analysis and phylogenetics have been frequently used to identify conserved sequence or structure that can guide the development of vaccine [252][253][254] and ligand designed as inhibitors against bacterial or viral pathogens because sequence and structural similarities often imply similarity in ligand binding. However, strongly conserved sites in a gene does not imply that mutations at these sites will necessarily cripple the gene function.…”