REVIEW: Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents

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Shamsudin Sh. Nasaev¹, Artem R. Mukanov¹, Ivan V. Mishkorez^1,2, Ivan I. Kuznetsov¹, Iosif V. Leibin³, Vladislava A. Dolgusheva¹, Gleb A. Pavlyuk¹, Artem L. Manasyan¹, Alexander V. Veselovsky^2,a*

¹Research & Development Department, Xelari Ltd., 121601 Moscow, Russia

²Institute of Biomedical Chemistry, 119121 Moscow, Russia

³Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, 121205 Moscow, Russia

^* To whom correspondence should be addressed.

Received: April 12, 2024; Revised: June 12, 2024; Accepted: July 11, 2024

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High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

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KEY WORDS: antibody, antibody mimetics, aptamers, molecularly imprinted polymers, molecular modeling

DOI: 10.1134/S0006297924080066

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