ITMO Laboratory Enzyme and Aptamer Generative Design

History

2024: Discovery of the laboratory "Generative design of enzymes and aptamers"

The laboratory "Generative design of enzymes and aptamers" was opened in ITMO. The university announced this on January 29, 2024. In it, scientists are developing tools for creating molecular machines - nanodevices that are able to accelerate chemical reactions, selectively bind molecules and even act as bioprocessors. The tools are based on artificial intelligence (AI) methods. The research results will help in the development of drugs for personalized medicine and POC systems - mobile devices for laboratory diagnosis of diseases.

Molecular machines are biological structures that perform important tasks within cells quickly and with high accuracy: allowing them to respond to environmental signals and communicate with each other. They also help synthesize DNA molecules, produce energy and contract muscles. Molecular machines are invented by nature, but scientists also seek to artificially create similar devices that make it possible, for example, to carry out subtle manipulations with molecules (including RNA, DNA and proteins), regulate cell metabolism (biochemical reactions that ensure cell life) and edit the genome.

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The development of molecular machines is quite complex - a huge amount of point knowledge has been accumulated, but there is still no single theory. This ITMO laboratory is designed to simplify the development of such nanodevices. It was headed by Nikita Serov, a junior researcher at the ITMO chemical and biological cluster. Nikita's team already includes master's students of the Chemistry and Artificial Intelligence program and bachelors from different cities of Russia.

The purpose of the laboratory is to develop a "family" of tools based on AI, data science and calculation methods that will create molecular nanodevices for applied tasks. Also in the future, we want to form a system of "Lego molecular machines." It will include the search and creation of separate independent functional modules, as well as ways to assemble them "turnkey" into molecular machines with pre-programmed behavior, - said Nikita Serov, head of the laboratory.

One of the directions of the laboratory is "Turnkey Enzyme." Scientists will rebuild using generative neural networks and evolutionary algorithms existing natural molecular machines for the specific tasks of medicine and biotechnology. For example, in the case of the generative design of catalytic (short DNA chains that accelerate reactions) and sensory DNA (short DNA chains that detect specific molecules in solution), this will allow directional regulation of cell metabolism and selective detection of disease markers in complex biological fluids. Such tools are extremely important in developing systems for diagnosing diseases at the point of care medical.

Another direction in which scientists will look for elementary details for molecular machines is "Minimal Enzyme." To do this, algorithms are being developed for finding minimal catalytic modules, as well as a modifier algorithm that provides their structural autonomy, allowing modules to be connected in any order without losing functions.

In the future, the laboratory team plans to find out what capabilities hybrid molecular machines from different types of biopolymers provide: proteins, nucleic acids, lipids. The end product that will combine all the developed tools will be a digital platform with an intuitive interface. Some of the algorithms will be available to people without special knowledge - they will be able to make their contribution to science by solving complex problems in an accessible format.

The opening of the laboratory was supported by the Fund for Support of Innovations and Youth Initiatives of St. Petersburg.