Scientists have developed an innovative method for computer simulation of aptamers. This will allow one to quickly obtain an affinity agent for binding to any protein for which one can build a tertiary structure. An aptamer has been created as an example, which binds to the coronavirus spike protein. Using it, researchers plan to fight various variants of COVID-19 and other similar viruses. The results of the study were published in Chemistry-A European Journal.

The COVID-19 pandemic has shown that viruses pose a huge threat to modern society. Antibodies previously developed to detect and block coronavirus proteins do not always show good binding affinity to the virus. Moreover, antibodies are characterized by poor bioavailability, high cost, and time-consuming development. Obviously, a new methodology is needed for the rapid construction of stable molecules capable of selectively binding to a specific target protein.

An international group of scientists from Russia, Finland, Italy, China, Taiwan and Canada, including researchers from the Krasnoyarsk Science Center SB RAS, has developed a new method for creating aptamers to detect or “neutralize” viruses. With its help, scientists have created a new 31-mer DNA aptamer for the coronavirus spike protein.

Aptamers are artificial single-stranded RNA or DNA molecules. They can be designed to bind to target proteins with high specificity and strength. Such molecules are promising for detecting SARSCoV-2 and blocking its viral activity. The mechanism of their interaction with the target is similar to that of antibodies. They are able to attach to a specific biological target, such as the spike protein of the coronavirus, which is important for the virus entry into host cells.

Traditionally, aptamers are selected in the laboratory from DNA libraries. A new approach to the virtual design of aptamers, called SIBDD (Structure and Interaction Based Drug Design), is based on knowledge of the structures of molecules and forces of their interaction. Aptamers are created using this technique in two main stages: digital computer simulation and experimental analysis of theoretical results. First, using computer simulation methods with supercomputer calculations, nucleotide sequences in the aptamer responsible for selective attachment and construction of the aptamer structure are searched for. The scientists then test the selected variants for their ability to bind to the desired protein. As the authors of the technology note, this is a combination of computer modeling, screening and site-directed mutagenesis with experimental verification in each cycle to obtain molecules with high binding affinity and selectivity. The method allows the rapid development of molecules for the diagnosis and treatment of any disease with a known target, including SARS-CoV-2.

“Selecting aptamers is a complex and time-consuming process. It can be simplified by combining calculations and experiments. We have developed a robust aptamer design technology. Its advantage is in using the power of a supercomputer to quickly design molecules that block virus infection. This will help to quickly and timely respond to potential new viruses. Our approach combines several steps: molecular design based on virtual screening of DNA aptamer libraries and site-directed mutagenesis to increase protein tertiary structure conformance; 3D molecular modeling of the target and docking of the aptamer with the protein; molecular dynamics simulation of complexes and quantum mechanical evaluation of the interaction between the aptamer and the target with further experimental analysis. This technique can be used to improve the structure of the aptamer,” says Anna Kichkailo, Doctor of Biology, Head of the Laboratory of Digital Controlled Drugs and Theranostics of FRC KSC SB RAS, Head of the Laboratory of Biomolecular and Medical Technologies at the V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University.

Using the developed technology, the researchers have created a modified Apt31 which is highly specific to the coronavirus spike protein. As compared to previously used molecules, it has the strongest protein binding.

“The efficiency of Apt31 coupling with the coronavirus spike protein has been proved using three different experimental methods. Experiments are currently underway to evaluate the antiviral properties of Apt31. Two ways of using the new aptamer can be envisaged. The first is therapeutic use to prevent entry of the virus into human cells, and the second is diagnostic use to detect the presence of the virus in body fluids. The preliminary results show that the resulting aptamers are promising candidates for detecting and blocking the SARS-CoV-2 virus. In addition, our approach to creating aptamers can contribute to the development of diagnostic and therapeutic tools for other viruses of the coronavirus family or their mutated variants. Given the high versatility of aptamers, the computer-aided design of molecules offers promising opportunities for the development of diagnostic and therapeutic tools for other diseases,” concludes Anna Kichkailo.
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The study was carried out within the framework of project No. 21-73-20240 of the Russian Science Foundation.