Biophysical Bulletin

In silico analysis of binding sites for potential inhibitors targeting the complex of furin protease

N. V. Khmil — 2025-12-18

Background. COVID-19 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Efforts to fight the virus include the development and investigation of vaccines, monoclonal antibodies, and specific antiviral drugs targeting key stages in the viral life cycle.

Objectives. The aim of the study is to investigate the binding sites of furin protease with the SARS-CoV-2 spike protein (S protein) in different conformations and to evaluate the binding affinities of non-specific antiviral drugs and the macrocyclic peptidomimetic inhibitor 8 (PI8) to the S protein–furin protease complexes using a molecular docking approach.

Material and Methods. The three-dimensional structures of the S protein (PDB IDs: 6VYB, 6VXX, 7VHJ) from the Protein Data Bank (www.rcsb.org ) were docked with furin protease (PDB ID: 5JXG) using the ClusPro 2.0 server. Non-specific antiviral drugs, such as remdesivir, chloroquine, favipiravir, nelfinavir, and PI8, were docked onto 6VYB-5JXG, 6VXX-5JXG, and 7VHJ-5JXG complexes using the AutoDock Vina program. The ligands were energy-minimized using the Universal Force Field (UFF) and converted to PDBQT format with OpenBabel. Protein optimization was performed using AutoDock Tools. Docking results were visualized using the Discovery Studio 2024 Visualizer.

Results. The binding affinity of the studied ligands with the S protein-furin protease complexes was verified by molecular docking studies. PI8, nelfinavir, and remdesivir showed high binding affinity with the 7VHJ-5JXG structure due to the presence of amino acid residues at the furin cleavage site. The best docking scores of PI8 with 6VYB-5JXG, 6VXX-5JXG, and 7VHJ-5JXG complexes were -9.7 kcal/mol, -9.5 kcal/mol, and -9.9 kcal/mol, respectively. The interaction between the S protein-furin complexes and PI8 involves specific amino acid residues, primarily within the catalytic site of furin and the reactive site loop of PI8. Docking studies showed that remdesivir acts directly on the furin cleavage site of the S protein (in the 7VHJ-5JXG complex), forming energetically favorable interactions through hydrogen bonds and hydrophobic contacts, with a high binding affinity (binding energy score is -9.1 kcal/mol). The energetically favorable interactions of the 6VYB-5JXG, 6VXX-5JXG, and 7VHJ-5JXG complexes with nelfinavir are also confirmed by their low binding energy scores of -8.2 kcal/mol, -8.9 kcal/mol, and -9.3 kcal/mol, respectively.

Conclusion. According to the results of molecular docking, PI8, nelfinavir, and remdesivir demonstrate energetically favorable interactions with the studied complexes and can be considered promising inhibitors targeting the SARS-CoV-2 S protein–furin protease complexes.

Modeling the interaction of C60 fullerene with SARS-CoV-2 protein targets

V. V. Hurmach — 2025-12-26

Background: The discovery of effective therapeutics against the dangerous disease caused by SARS-CoV-2 is an important direction of biomedical research. Molecular docking and molecular dynamics methods are key tools of modern pharmaceutical science, providing rapid search and optimization of antiviral compounds, allowing to predict their effectiveness and adapt therapy to new strains of SARS-CoV-2. Fullerene C₆₀ attracts considerable attention as a promising nanomaterial in the fight against SARS-CoV-2 due to its ability to form stable complexes with key viral proteins, such as the main protease (3CLpro) and RNA-dependent RNA polymerase (RdRp). Molecular modeling and biophysical studies have shown that C₆₀ can penetrate the lipid envelope of the virus and block the functional activity of its proteins, which opens up opportunities for the creation of new antiviral drugs. Given the constant mutations of SARS-CoV-2 and the limitations of existing therapeutics, the study of C₆₀ fullerene as a potential inhibitor is a relevant direction of nanotechnology for the development of innovative strategies for the treatment of COVID-19.

Aim of the work was to assess in silico the ability of C₆₀ fullerene to interact with the protein targets 3CLpro (3-Chymotrypsin-Like protease) and RdRp (RNA-dependent RNA polymerase) of the SARS-CoV-2 coronavirus and, thus, to specifically block them, inhibiting the functional activity of SARS-CoV-2.

Methods: Structural data of the 3CLpro and RdRp proteins of the SARS-CoV-2 coronavirus were obtained from the Protein Data Bank, and the geometry of C₆₀ fullerene was generated using the online server SwissParam. Interactions between С₆₀ fullerene and the studied proteins were modeled using the system molecular docking algorithm (sdock+). Potential binding sites were determined using the Caver software package. Molecular dynamics calculations were performed in the Gromacs 2020 software environment. Energy minimization of potential C₆₀ fullerene — protein complexes was performed using the g_mmpbsa software.

Results: Putative mechanism of binding of C₆₀ fullerene to the protein targets 3CLpro and RdRp of the SARS-CoV-2 coronavirus was established. Molecular docking and molecular dynamics data demonstrate that C₆₀ fullerene forms stable complexes with these proteins, which can lead to inhibition of their functional activity.

Conclusions: It is shown that C₆₀ fullerene is able to form stable complexes with the 3CLpro and RdRp proteins of SARS-CoV-2, which potentially reduces their activity and, accordingly, can affect the overall activity of the coronavirus.

AgNPs Incorporated in PMMA-PVP blended nanofibers: spectroscopy monitoring of AgNP dissolution in PMMA nanopores

Alexander Plokhotnichenko — 2025-12-18

Background: Electrospun polymeric nanofibers incorporated with some biologically active nanoparticles have a huge range of various applications in biomedical fields. Blending several polymers with different properties allows one to obtain a new material with improved characteristics, as well as to control the incorporation and release of medical agents.

Objectives: To elaborate an approach for the preparation of biocompatible nanofibers using a blend of two polymers (polyvinylpyrrolidone (PVP) and polymethyl methacrylate (PMMA)) with incorporated silver nanoparticles (AgNPs) and to apply the absorption spectroscopy for determining of the average nanoparticle diameter and monitoring of AgNP dissolution from PMMA nanopores.

Materials and methods: A blend of hydrophilic (PVP) and water-insoluble (PMMA) polymers is proposed for nanofiber preparation with incorporated AgNPs. The absorption peak position of the band due to localized surface plasmon resonance (LSPR) and its intensity in the UV-vis spectrum were used to characterize AgNPs and to estimate the influence of the environment.

Results: A new method for fabricating nanofibers from a mixture of two polymers, one water-soluble (PVP) and the other soluble only in organic solvents (PMMA), with AgNPs, has been developed. The diameter of the nanofibers is determined to be in the range of 2-4 μm. The average nanoparticle diameter determined by the position of the absorption peak due to LSPR in the UV-vis spectrum is 35-40 nm. The peak shift of this band in different environments was determined in comparison with the spectrum obtained in an aqueous solution. A decrease in the intensity of the band was observed with an increase in the mat incubation time in the oxidizing solution, and a blue shift of the band maximum was detected, which indicates a decrease in the average size of AgNPs during their dissolution.

Conclusions: In the blended nanofibers, PVP environment of AgNPs facilitates their incorporation into PMMA and provides access of water molecules to nanoparticles, while PMMA provides the mechanical strength of the nanofibers. The appearance of AgNPs from the polymeric nanofibers soaked in water was not detected, since they are fixed in the structure of the water-insoluble polymer. Nevertheless, the experiments with the mat soaking in the oxidative solution showed that the nanopores in PMMA incorporated with AgNPs are open. This observation indicates the possibility of a gradual release of Ag⁺ ions from such nanofibers.

Express method for investigating natural water quality using a sensor device based on surface plasmon resonance and a conductometer

N. V. Kachur — 2025-12-19

Background: One of the urgent contemporary issues is natural water pollution, which directly affects humanity's life support. This problem is associated with industrial and agricultural intensification and climate change. Water quality standards in Ukraine are defined by state standards, which regulate both organoleptic properties, such as turbidity and odor, and permissible concentrations of harmful substances.

Objective: The objective of this study was to develop a methodology for rapid natural water quality assessment using the SPR method and a conductometer and to simultaneously determine the durability of sensors with protective coatings.

Materials and methods: This study explores the feasibility of combining surface plasmon resonance (SPR) and conductometric methods to monitor the quality of natural water. The first stage involved modeling the concentration dependencies of SPR parameters and conductivity when adding controlled amounts of organic (sugar) and inorganic (table salt and soda) impurities to distilled water. Biological contamination was simulated using live yeast suspensions. Subsequently, samples of coastal water from the Dnipro River in Kyiv, the Stugna River near Vasylkiv, and a pond connected to the Stugna River near Borova village in Fastiv district were analyzed. All SPR studies were conducted using an improved sensor element with an additional protective zinc oxide layer, which reduced measurement errors typically associated with sensor replacement. To validate the reliability of the rapid assessment methods, water samples were additionally analyzed using standard laboratory methods at "Ukrkhimanaliz".

Results: The SPR results indicated that the Stugna River was the most polluted, followed by the pond, with the Dnipro River exhibiting the least pollution.

Conclusions: Summarizing the measurement results, it can be concluded that combining SPR and conductivity measurements enables rapid and objective assessment of natural water pollution levels. This corresponds to the total harmful impurities. Given the small dimensions and autonomy of the devices used in the developed methodology, river water monitoring can be carried out in field conditions by one person.

Methods and means of polarization-interference layer reconstruction and discrete phase scanning of jones matrix images of polycrystalline films of dehydrated bile

Yuriy Ushenko — 2025-12-25

Background: Modern methods of Mueller matrix polarimetry are aimed at determining the criteria and practical application of such markers in the differential diagnosis of pathological and necrotic changes in biological tissues of human organs. At the same time, little-studied and relevant are the issues related to matrix studies of another class of objects – dehydrated (dried) films of biological fluids (BF), the polycrystalline structure of which is associated with the composition and ratio of dissolved substances. Polarimetric analysis of the BF dehydrated film at the macroscopic level enables the retrieval of information about its molecular microstructure. In addition, BF are more easily accessible and do not require traumatic, sometimes dangerous, biopsy.

Objectives: Development and experimental testing of the diagnostic efficiency of a new technique of polarization-interference reconstruction and layer-by-layer phase scanning of object fields of complex amplitudes with algorithmic reproduction of the real and imaginary components of Jones matrix images of polycrystalline films of dehydrated bile from healthy donors and patients with cholelithiasis.

Materials and methods: Polarization interferometry, digital phase scanning and statistical analysis of algorithmically reproduced real and imaginary components of Jones matrix images of dehydrated bile films were used.

Results: The results of the statistical analysis of the polarization-interference mapping method with digital Fourier reconstruction and phase scanning of complex amplitude distributions and algorithmic calculation of the real and imaginary components of Jones matrix images of bile film samples are presented and physically analyzed. Statistical markers that are most sensitive to changes in the polycrystalline structure of dehydrated bile films are established and high accuracy (97.6%) of differential diagnosis of cholelithiasis is demonstrated.

Conclusions: General scenarios for the transformation of the statistical structure of the set of Jones matrix images, which are reproduced in different phase planes of the object field of dehydrated bile films, are established. A set of structures of self-assembled molecular networks (hereinafter referred to as supramolecular networks) formed during the dehydration of bile films, which are diagnostic markers most sensitive to pathological changes, has been identified. They turned out to be asymmetry and kurtosis, which characterize the coordinate distributions of the values of the real and imaginary components of the Jones matrix.

The impact of different lyophilization regimes on the protein composition of human cord blood serum

V. S. Hoidina — 2025-12-26

Background: Modern medicine is confronted with the challenge of minimizing the side effects of drug treatment of serious diseases, including oncological pathologies. One of the most perspective concepts is the use of cord blood serum as a source of regenerative components to support the patient's health. The serum contains a variety of growth factors, cytokines and immunosuppressive cells that promote tissue repair and regulation of the immune response. An important goal is to preserve the biological activity of cord blood serum protein fractions during long-term preservation. Lyophilization is considered one of the most effective methods of stabilizing biological substances. However, the optimal temperature regime for the preservation of cord blood proteins during lyophilization requires further investigation.

Objectives: To evaluate the effect of different lyophilization regimes on the composition and stability of cord blood serum proteins.

Materials and methods: Cord blood serum was examined after freezing to -20°C and lyophilization with previous cooling to -20°C and -80°C. The total protein content was calculated using a standardized determination kit, and the remaining dry mass was weighed on an analytical balance. The protein composition was examined by spectrofluorimetry and polyacrylamide gel electrophoresis. The residues of aromatic amino acids (tyrosine-tryptophan, tryptophan) were analyzed by spectrofluorimetry. The peaks in the protein profiles of the analytical samples were electrophoretically examined and the preservation of the biomaterial was compared.

Results: It has been shown that freezing and lyophilization at -80°C provide high stability of protein fractions without significant loss of total protein or its structural changes. On the contrary, lyophilization at -20°C was accompanied by a significant decrease in the total amount of protein and protein fractions, changes in protein structure, indicating aggregation, denaturation, and degradation of protein molecules. The densitogram of lyophilized cord blood serum when cooled to -80°C was significantly close to the result of the frozen sample, while the analysis of the peaks of lyophilized serum cooled to -20°C showed a significant decrease in parameters.

Conclusions: Lyophilization of human cord blood serum with preliminary cooling at -80°C allows preserving the protein concentration, the number of fractions and the structure of proteins according to electrophoresis and spectrofluorimetry. Lyophilization of cord blood serum with preliminary cooling at ‑20°C significantly reduces the protein concentration, the number of fractions and changes the structure of proteins compared to frozen serum.

Analysis of phenotypic diversity of true leaves in lettuce lines (Lactuca sativa var. secalina L.) created by physical and chemical mutagenesis

S. I. Kondratenko — 2025-12-26

Background: To expand the genotypic diversity of lettuce (Lactuca sativa var. secalina L.), it is advisable to use physical and chemical mutagenesis methods that allow changing beneficial traits of the original form, which can then be stabilized rapidly as a result of inbreeding. Biophysical methods of analysis based on multispectral imaging technologies for phenotypic identification and classification of the studied are not yet sufficiently improved. Therefore, it is advisable to conduct biometric measurements and morphological and identification analyses of the phenotype of mutant genotypes by scoring the levels of manifestation of quality traits.

Objectives: To determine the characteristics of the mutagenic effect of γ-radiation and biologically -active substances of mutagenic action on the genotypic variability of qualitative traits of leaf blade of lettuce plants in the vegetative phase of development and to investigate the correlation between the association of qualitative traits that determine the phenotype of the true leaf and quantitative traits of lettuce lines of mutant origin.

Materials and methods: Non-parametric statistics and criteria for comparing plant objects, methods of botanical classification of leaf lettuce, correlation analysis.

Results: The mutagenic effect of three biologically active substances (DMS (reference), DMU-1, DMU-5) and γ-rays at doses of 11 and 15 kR on the genotypic variability of leaf lettuce based on a set of qualitative characteristics was studied. A comparative analysis of the differences between the qualitative characteristics of the original form (Shar malynovyi variety) and 17 mutant lines created on its basis was carried out. As a result of testing the different mutagens, their high efficiency in inducing mutational changes in the lettuce genome associated with the leaf blade morphology was confirmed. DMU-1 showed the highest efficiency, and 6 mutant lines were obtained under its action. Under the action of γ-irradiation with a dose of 15 kR, 4 lines were obtained. Under the action of γ-irradiation with a dose of 11 kR and DMS, 3 lines were created, respectively.

Conclusions: The established correlations between the levels of qualitative and quantitative traits allow for the selection of potentially high-yielding mutant lines of leaf lettuce depending on the inherited mutational changes that determine the morphology of the real leaf. In particular, it becomes possible to select mutant genotypes based on predicting the level of manifestation of the quantitative trait “Leaf width” (r_s = 0,483), which is essential in predicting potential productivity.

Biophysics week in Ukraine: online meeting of the Kharkiv branch of the Ukrainian biophysical society

V. P. Berest — 2025-12-26

As part of Biophysics Week 2025, V. N. Karazin Kharkiv National University on March 24 hosted the event “Biophysics Week in Ukraine: Experience Across the Borders”, bringing together researchers, students, and professionals to highlight the latest advancements in biophysics. This event served as a platform for sharing experiences, expertise and forecasts between Ukrainian biophysicists working at home and abroad, discussing cutting-edge research, fostering collaboration, and promoting the role of biophysics in addressing global scientific and educational challenges.