Research publications

A Paradigm Shift in Experimental Biochemistry: A Priori Estimation of Physical Parameters of Biomolecules.
This paper proposes a new paradigm for the biophysical concept of measuring the affinity of molecular complexes, based on a matrix representation of biological interactions and subsequent numerical analysis of the stability of this matrix. Our numerical criterion of stability correlates well with experimental values such as Kd and IC50 as well as with experimental data of aggregation kinetics in studies of amyloid peptides. The main goal of this work is to reduce the cost of biochemical experiments by obtaining preliminary information on the interaction of chemical compounds. The paper also presents our numerical calculations in comparison with a large amount of experimental data on the examples of binding of small chemical molecules gefitinib, erlotinib, imatinib, naquatinib, and CO-1686 with proteins, protein–peptide interactions of the Bcl-2 protein family, antibody–antigen CD20–rituximab, and aggregation of amyloid peptides. The description of the software package that implements the presented algorithm is given on the website: https://binomlabs.com/.

Analysis to determine the effect of mutations on binding to small chemical molecules.
In this paper, the authors present and describe, in detail, an original software-implemented numerical methodology used to determine the effect of mutations on binding to small chemical molecules, on the example of gefitinib, AMPPNP, CO-1686, ASP8273, erlotinib binding with EGFR protein, and imatinib binding with PPARgamma. Furthermore, the developed numerical approach makes it possible to determine the stability of a molecular complex, which consists of a protein and a small chemical molecule. The description of the software package that implements the presented algorithm is given in the website: https://binomlabs.com/. © 2022 World Scientific Publishing Europe Ltd.

An innovative method for the selection of inhibitors of the viral spike-glycoprotein of the SARS-CoV
This paper has developed and described a detailed method for selecting inhibitors based on modified natural peptides for the SARS-CoV BJ01 spike-glycoprotein. The selection of inhibitors is carried out by increasing the affinity of the peptide to the active center of the protein. This paper also provides a step-by-step algorithm for analyzing the affinity of protein interactions and presents an analysis of energy interactions between the active center of a protein and the wild-type peptide interacting with it, taking into account modifications of the latter. A description of the software package that implements the presented algorithm is given on the website https://binomlabs.com/covid19. (2021)

Analysis of Electrostatic Interaction between Dimer Complexes. Part II: Criteria and Conditions on Inhibitors of APP Protein Derivatives
We communicate the results of calculations and selection methods, and identify the properties, of inhibitors that block the formation of high-molecular-weight structures from amyloid peptides, with their block...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2020)

Analysis of Electrostatic Interaction between Dimer Complexes. Part I: A Method for Selecting Inhibitors of APP Protein Derivatives
We present an unconventional method that provides qualitative evaluation of the ability of amyloid peptides to form high-molecular-weight structures and enables us to resolve the stability issue of amyloid dim...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2020)

Simulation of the Effect of Point Mutations on the Stability of Protein Dimers Using the Bcl-2 Protein Family as an Example
A new method has been developed that enables synthesizing peptides with desired physicochemical properties, for example, with high affinity to one target protein and low affinity to other proteins, and determi...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2020)

Analysis of Electrostatic Interactions of Amino Acid Residues by the Example of Formation of a Nap1–Nap1 Dimer
A new method, which analyzes the potential energy of electrostatic interaction of protein complexes at point replacements of amino acid residues assuming a three-dimensional structure of the complex on the exa...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2020)

Mathematical Modeling of Linear Docking. II. Estimating the Effect of Point Mutations on the Affinity between Protein Molecules
A new method enabling the qualitative determination of the dissociation constant of peptides to full-length proteins and the estimation of the effect of point mutations in peptides on the stability of a formed...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2018)

Mathematical Modeling of Linear Docking. I. Determination of Regions of Binding of Protein Molecules
We report on the results of mathematical simulation of the interaction of various sequences of proteins Mdm2, P53, and Nap1 in accordance with the developed algorithms that were used for identifying the region...
K. G. Kulikov, T. V. Koshlan in Technical Physics (2018)

Mathematical modeling of the temperature effect on the character of linking between monomeric proteins in aqueous solutions
This work is devoted to the mathematical modeling of the temperature effect on the stability of H2A–H2B and Н3–H4 histone dimers by studying their behavior in different temperature regimes of 20–50°C. The stud...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2017)

Mathematical modeling the formation of a histone octamer
A physical model of the interaction of protein molecules and their ability to form complex biological systems for the in vitro case in a solution of monovalent salt has been developed. Their reactive abilities...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2017)

Mathematical simulation of complex formation of protein molecules allowing for their domain structure
A physical model of the interactions between protein molecules has been presented and an analysis of their propensity to form complex biological complexes has been performed. The reactivities of proteins have ...
T. V. Koshlan, K. G. Kulikov in Technical Physics (2017)

Mathematical simulation of interactions of protein molecules and prediction of their reactivity
A physical model of interactions of protein molecules has been developed. The regularities of their reactivity have been studied using electrostatics methods for two histone dimers H2A–H2B and H3–H4 assembled ...
K. G. Kulikov, T. V. Koshlan in Technical Physics (2016)

Measurement of sizes of colloid particles using dynamic light scattering
Size distribution functions of colloid particles are obtained with the aid of dynamic light scattering for both polarized and depolarized components. Electron microscopy of the colloid particles is used to con...
K. G. Kulikov, T. V. Koshlan in Technical Physics (2015)

Simulation of the type of coralin alkaloid-DNA binding
Interaction between a synthesized coralin protoberberine alkaloid and the DNA double helix of the calf's thymus in a salt solution is studied by optical absorption spectroscopy and spectropolarimetry. The depe...
K. G. Kulikov, T. V. Koshlan in Technical Physics (2015)