_______This article described a method for phasing the affinity of a natural peptide to a target viral protein by modifying the peptide. The selection criteria for the most suitable modifications were given, among which the following can be listed: the stability of the dimer complex by calculating the value of log (cond (W)) and comparing the obtained value with the value of log (Cond (W)) obtained for the wild-type dimer and other modified dimers .
_______The next indicator was the measure of the change in differential entropy ∆Н, which characterizes the ordering of the system. Moreover, the values of lg (cond (W)) and ∆Н are interrelated: the minimum number lg (cond (W)) must correspond to a negative value of ∆Н, otherwise, the dimeric complex does not satisfy the necessary criteria.
________As an example of the selection of suitable modifications of natural peptides, the Spike-glycoprotein viral protein was selected, which is responsible for the attachment of the virus to the cell and the incorporation of the viral genome into the cell. In this work, we analyzed the Central helix region of this protein, performed mutagenesis, and calculated the stability of the formed dimeric complexes upon modification of the natural peptide in the region of the Central helix region. The calculation results showed that the modification of the site from 995 a.a. till 1014 a.a. most likely to affect the affinity of the modified peptide for the Spike-glycoprotein viral protein. In the course of the numerical simulation, wild-type peptide mutagenesis was performed, the calculation of the values of log (cond (W)) and ΔH, the minimum values of log (cond (W)) were compared with negative values of ΔH, since these values are analyzed in pairs. If the log (cond (W)) values take the minimum values, and the ΔH value is in the range of positive values, then this modified peptide does not pass the test according to the criteria.
________To reduce false results, we remove from further analysis all dimeric complexes that are characterized by a ∆H value in the positive range of values. We also believe that an important aspect affecting the results of the modification of a natural peptide is the environment of the modified portion of the polypeptide chain with other amino acid residues, the location of which in turn depends on the solvent (water, impurities, salts, temperature, pH). in three-dimensional space is characterized by the distribution of potential energy of interaction with other amino acid residues in three-dimensional space. Replacing even one amino acid residue in a polypeptide chain can serve as a substantial redistribution of the potential energy of interaction with all amino acid residues of the adjacent polypeptide chain, which in turn will affect the stability of the dimer complex and the entropy of the dimer complex, and more precisely, entail measures to change the differential entropy of the dimer complex ∆H , which we calculate for each replacement.
______By analyzing the Spike-glycoprotein protein peptide in this way, we determined amino acid residues, the replacement of which can affect the affinity, namely, the increase in affinity due to increased stability of the dimeric complex and ordering of the system of two proteins. The aim of this work was to develop and describe in detail a methodology for increasing the affinity of a natural peptide for a target protein by modifying the peptide, namely, replacing amino acid residues. In the course of the work done, several key amino acid residues found were replaced with 997, 998, 1002, 1006, 1008, see fig. on MET (M), GLN (), ASN ().
________The results presented in fig. and in the table it was possible to determine the most suitable modification of the peptide to increase the affinity of interaction with the Spike-glycoprotein viral protein. These modifications are two substitutions ALA997MET and ALA1002 MET, since two simultaneous substitutions significantly reduced the value of log (cond (W)), and the value of ∆Н was characterized by the lowest negative value. A good result was also obtained with the simultaneous replacement of two amino acid residues in the peptide ALA997MET and ALA1002GLN, as well as ALA997MET and ALA1008MET. The worst result was obtained with the simultaneous replacement of ALA998MET and LEU1006GLN, since the value of log (cond (W)) was obtained in a high range of values, and the value of ΔН was in the range of positive values.
To identify a high affinity modified peptide for the wild-type virus virus Spike-glycoprotein, it is necessary to perform large-scale numerical calculations and, based on the results, obtain the most suitable modifications of the peptide for further refinement by increasing the resistance of peptides against protease cleavage and increasing the circulation time in the body to achieve a significant therapeutic effect .