Flavonoids are one of the largest classes of secondary metabolites that have been shown to be potent antimicrobials against a wide range of pathogenic organisms in vitro. The interest in the antimicrobial properties of flavonoids and their use to treat human diseases has increased with respect to plants that synthesize these compounds as a response to microbial infection. The objective of this study was to evaluate the antimicrobial potential of certain flavonoids from an Algerian medicinal plant. A molecular docking study against DNA Gyrase Topoisomerase II (E. coli, PDB ID: 1Kzn), Penicillin Binding Protein 3(PDB ID: 3Vsl), Cytochrome P450 14 alpha-sterol Demethylase (PDB ID: 1EA1) and N-Myristoyl Transferase (PDB ID: 1Iyl) was performed to assess the antimicrobial effects of the selected compounds. In addition, the parameters of bioavailability, pharmacokinetics and toxicity were estimated. According to computational studies, the highest scores were presented by quercetin-3,7-di-O-glucoside, vicenin-2 and vitexin, indicating a good binding affinity towards the tested targets. The docking score values of quercetin-3,7-di-O-glucoside against 1Kzn, 3Vsl, 1EA1 and 1Iyl were in theorder of -8.110, -10.285, -13.101 and -15.043 Kcal.mol^-1, respectively. Vicenin-2 showed binding affinity toward 1Kzn, 3Vsl, 1EA1 and 1Iyl with scores equal to -7.507, -11.125, -13.465 and -14.094 Kcal.mol^-1, respectively. Finally, the docking scores of vitexin against 1Kzn, 3Vsl, 1EA1 and 1Iyl were -6.950, -7.944, -12.592 and -12.728 Kcal.mol^-1, respectively. The in silico investigation shows that by targeting specific proteins, the best hits have significant anti-antimicrobial activity; however, more studies are required.

Fungal infections have retained their status as a significant human health threat, resulting in the publication of the first fungal priority pathogens list by the World Health Organization. Thus, the development of new antifungals is essential in the mainstream of drug design to combat fungal infections. Computer-aided calculations have become a necessary part of works devoted to new drug design. Virtual libraries of structural files for both low-molecular electrophilic phytochemicals and proteins from Saccharomyces cerevisiae and Candida albicans have been created based on experimental databases as well as using the AlphaFold resource for some proteins with unsolved 3D structures. During the virtual screening process, many affine interactions were identified as having binding energies calculated using the Autodock Vina program of no more than -9 kcal/mol. In particular, ixerin D (Pubchem code CID101553163) from dandelion was predicted to bind to proteins with PDB structures codes 3of7, 5t94, 4uuy, 2cnq, 2zeu, and 3bnu, demonstrating the possibility of covalent modifications of CYS453. Inuloxin (CID102194603) was bound in silico to the protein with PDB code 5TZ1 and lactucin (CID442266) to the protein with PDB code 1IYL. Similar affine interactions of an unsaturated ketone (CID5318099) from Helichrysum and Orthosiphon aristatus were predicted using modeled protein structures with Uniprot database codes A0A1D8PEV1, A0A1D8PSE5, P29717, Q59U61, Q59YG2, Q5A5N0, A0A1D8PN96, and Q59Q43. These results have provided valuable insights into the possible repurposing of well-known phytochemicals with the aim of developing new tools for yeast infection management. The work was supported by the BRFFR (Belarus) grant X23MH-005.

Introduction. Antibodies to nucleic acids (NAs) represent a significant subject of investigation in medicine, yet they have not gained wide dissemination due to the low immunogenicity of NAs and the high cross-reactivity of antibodies, which can lead to autoimmune diseases when using modern mRNA vaccines. Diagnostic antibodies for detecting RNA antigens hold considerable importance in various domains of knowledge.

Methods. A promising predictive model, "polyclonal antibody - potato pathogen," can aid in enhancing the specificity of polyclonal antibodies to NAs. In this study, the selected pathogens include PSTVd, PVX, and PVY. Using Python, the program can identify unique sequences within the genome of the specified pathogen—sequences of user-defined length (ribotopes) absent in the host genome, which can subsequently serve as targets for antibody generation. Additionally, the program identifies the most unique sequence among those found by breaking them into all possible sub-sequences of, for example, length 4 (the minimum length of an NA where antibodies can bind to it) and more nucleotides. The program analyzes these subsequences for their occurrence in the host genome. The sequences with the least number of occurrences of their subsequences in the host genome are assigned the status of the most unique and are displayed on the screen.

Results. Calculations showed that the minimum length of a sequence ensuring the uniqueness of a ribotope is 11. Several unique sequences of this length were found in the genomes of each pathogen. Based on these findings, in vivo experiments are planned on laboratory mice to generate antibodies and test their specificity using the IFA method. Thus, obtaining highly specific antibodies is achieved through the proper selection of the "target".

Conclusions. The obtained model can potentially be extrapolated to human viral pathogens and can subsequently find application in molecular diagnostics as well as in medicine for creating higher quality analogs of modern mRNA vaccines.

Non-steroidal anti-inflammatory drugs (NSAIDs) are a class of drugs commonly used worldwide for their analgesic and antipyretic effects. However, an overdose of NSAIDs can have negative effects on various systems, including the cardiovascular, gastrointestinal, hepatic, renal and neural systems. The search for new, safer and more effective anti-inflammatory agents has now become a necessity. The aim of the present study is to identify new natural compounds that act against cyclooxygenase-2 (COX-2), one of the main anti-inflammatory targets, by means of computational approaches. For this purpose, molecular docking and MM/GBSA binding free energy calculations were utilized to discover new natural inhibitors for COX-2. In addition, several prediction tools, such as SwissADME server, QikProp and Pro-Tox II were used in this study to elucidate the pharmacokinetic properties, drug-likeness ability, safety and the lethal dose (LD50) of the studied compounds.

The results of molecular docking have indicated that among all phytochemicals under examination, Canniprene, Oroxylin A and Luteolin have shown high docking score and binding affinity toward COX-2 (-10.587, -10.254 and -9.494 Kcal.mol^-1, respectively) when compared with the reference inhibitor. Moreover, the top hits demonstrated stability during molecular dynamics simulation and were found to conform to drug-like rules with good bioavailability. Toxicity parameters of the best hits indicate that these compounds could be safe COX-2 inhibitors, but further in vitro and in vivo studies are needed to confirm these findings.

Introduction. Testicular germ cell tumors (TGCTs) represent the most common solid malignancy in young men. MicroRNA-371a-3p (miR371) has been suggested as a sensitive biomarker in TGCTs since it increases in the plasma in the early stages. There are five other miRNAs that have a high similarity to the miR371 sequence, which makes it difficult to detect using PCR. The binary deoxyribozyme Dz contributes to the DNA nanomachine's function by serving as a molecular tool for selectively cleaving fluorophore-labeled substrates (F-sub) and can be developed to cleave F-sub in response, selectively, to miR371 recognition for TGCT detection.

Methods. A DNA nanomachine able to recognize miR371 selectively was designed, equipped with a reporter substrate delivery system for high sensitivity. Native polyacrylamide gel electrophoresis was performed to study the assembly and interactions among the designed DNA nanomachine. A fluorescence assay using a spectrophotometer was applied to investigate the selectivity and sensitivity of the designed DNA nanomachine using synthetic miRNA analytes, followed by the examination of its capability to detect miR371 in patient samples.

Results. The designed DNA nanomachine was successfully assembled. The suggested design is selective for miR371 in the presence of the other five similar miRNAs and can induce increasing fluorescence in response to increasing concentrations of miR371, with a limit of detection (LOD) of ~28.9 pM.

Conclusion. Due to the suggested design, we developed a DNA nanomachine based on binary Dz that is highly selective and sensitive for miR371. DNA nanomachines based on binary Dz can be considered as a simple, inexpensive, sequence-specific, and sensitive tool for early TGCT diagnoses.

Self-reproducing protein aggregates of a fibrillar nature (amyloids) are associated with a number of animal and human diseases. Some amyloids (prions) possess infectious properties as they can be transmitted between tissues, organs, and even organisms. However, there are examples of prions and amyloids that have normal biological functions [1]. The number of proteins capable of forming functional and pathological amyloids is constantly expanding. For example, some bioinformatics algorithms predict that over a hundred human proteins may have the ability to form amyloids.

In our study, we applied the ArchCandy algorithm to identify human proteins with amyloidogenic properties. This algorithm is capable of identifying the potential formation of β-arches (structures specific to amyloid proteins). By applying an in silico approach, we selected nine proteins that demonstrated amyloidogenic potential and experimentally validated these predictions. To evaluate the amyloidogenic potential of proteins, we employed an original yeast test system that we developed [2]. This system enables us to assess amyloidogenicity of individual proteins as well as to conduct large-scale screenings of amyloidogenic proteins using a genetic analysis. Using this test system, we demonstrated that six out of the nine predicted amyloidogenic proteins were prone to amyloid formation. Among the proteins that demonstrated amyloidogenic properties, there were proteins involved in chromatin remodeling, transcription regulation, and oncogenesis. For several potentially amyloidogenic proteins identified in the yeast model, their amyloid properties were confirmed both in vitro and in a human cell culture.

This research was supported by St. Petersburg State University (project No. 95444727).

1. Rubel MS, Fedotov SA, Grizel AV, Sopova JV, Malikova OA, Chernoff YO, Rubel AA. Functional Mammalian Amyloids and Amyloid-Like Proteins. Life (Basel). 2020 Aug 21;10(9):156. doi: 10.3390/life10090156.
2. Chandramowlishwaran P, Sun M, Casey KL, Romanyuk AV, Grizel AV, Sopova JV, Rubel AA, Nussbaum-Krammer C, Vorberg IM, Chernoff YO. Mammalian amyloidogenic proteins promote prion nucleation in yeast. J Biol Chem. 2018 Mar 2;293(9):3436-3450. doi: 10.1074/jbc.M117.809004.

Insects represent a large variable class of animals on Earth, playing important roles as pests and as model organisms for scientific research devoted to, for instance, pesticide development, brain functions, and pathologies like Alzheimer's and Parkinson's disease. Insects have cytochrome P450, a unique class of monooxygenases, which are responsible for reactions of fatty acid conversion into hormone-like substances or cuticular hydrocarbons, as well as for destroying pesticides.

Previously, we reported the synthesis of two fluorescent hexanoic acid piperazineamides, namely, N-hexanoyl-N’-(7-nitrobenzofurazan-4-yl)-piperazine (NpipHex) and N-hexanoyl-ciprofloxacin (CPFHex), with the ability to fluoresce. Because there are no available experimentally solved structures of insect P450s, we have created a small library (120 structures) of the enzymes from Lucilia cuprina and L. sericata (a polinator and a cause of cattle myiasis) and Locusta migratoria (a pest) using the AI-based platforms AlphaFold and AlphaFold2/GoogleColab. Autodock Vina (AV) together with the authored helper software for high-throughput virtual screening (HTVS) FYTdock was used for both hem residue positioning and the docking of the derivatives. It was found that affine binding with AV scores of -9 and lower was found, for instance, for NpipHex and CYP6a8 of L. cuprina (Uniprot id A0A0L0CMB2, score -9.9), of which the Drosophila homologue has been recently described as a fatty acid hydroxylase; CYP12A7 of L. cuprina (Uniprot id A9X930, score -9.8); and CYP307A2 of D.melanogaster (A8Y592, score -9.9).

Taking these results together, we have created a virtual library of some insect P450s models suitable for HTVS and found potential new affine interactions with our fluorescent hexanoic acid derivatives, providing a method for the in silico estimation of their new biological properties with respect to the development of new pest control tools.

This study was supported by GSPSR (Belarus) № 20210560.

Introduction: The interaction of nanoparticles with the cell membranes is an important determinant of their physiological effect. Such interactions were proven, mostly by experimental work, to depend on the size, charge and surface properties of nanoparticles. Simulations can bring atomic-level details on the mechanism of these interactions. Therefore, we used simulations to understand the interaction between a fluorescein isothiocyanate (FITC) functionalized gold nanoparticle (FITC-Au-NP) and a lipid bilayer.

Methods: A gold nanoparticle (10 nm) functionalized with glycine-cysteamine spacers was built using CHARMM-GUI Nanomaterial Modeler. On the spacers we additionally linked 71 FITC residues that were parameterized with CHARMM-GUI Ligand Reader & Modeler. The nanoparticle was included in a simulation system comprising a 20 x 20 nm² POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid bilayer. The distance between the nanoparticle and the bilayer was 1 nm. Steered molecular dynamics (SMD) with constant velocity was used to pull the nanoparticle through the lipid bilayer. The resulting trajectories were analyzed.

Results: The interaction energy between the FITC-Au-NP and the lipid bilayers was evaluated, showing a favorable total interaction energy that increased as the nanoparticle entered into the bilayer. The van der Waals interactions had a substantial contribution to the total interaction energy. Although smaller in value, electrostatic interactions were also attractive.

Conclusions: We modeled a FITC-Au-NP and simulated its interaction with a POPC lipid bilayer, highlighting the importance of van der Waals forces for the favorable contacts. Additional experimental and simulation work will bring more details on this interaction.

Acknowledgment: The authors acknowledge the support of UEFISCDI through project no. 81TE/2022 (PN-III-P1-1_1-TE-2021-1375-TRANS-NANO-BIO).

Amyloids are proteins which exist in the form of insoluble aggregates and possess a characteristic cross-beta structure. The formation of amyloid aggregates can be seen during several pathological processes in humans, including neurodegenerative diseases, diabetes, and systemic amyloidoses. Despite their infamous association with the previously mentioned conditions, amyloids can also serve a functional role in biological systems. For example, Pmel17, which is involved in melanin polymerization in mammalian cells, resembles an amyloid structure, and some peptide hormones are also known to be stored in amyloid form in secretory granules of the endocrine system. Thus, studying amyloids as functional proteins may aid in both determining targets for the treatment of pathological conditions and in understanding their unique role in the organism. The analysis of amyloid-like properties requires a comprehensive approach using bioinformatic prediction, which can later be verified using bacterial and yeast systems as well as various biochemical tests. The object of this study is the protein COL2A1 , better known as type II collagen. This type of collagen forms the basis of cartilage tissue and its mutant form can cause diseases known as collagenopathies. This protein possesses some distinctive features characteristic of amyloids. These features include Congo red staining and a tendency to form fibrillar structures. In addition, the possibility of it forming amyloid structures was predicted for the third isoform of type II collagen via the ArchCandy program. In this work, we present data on the investigation of COL2A1's amyloid properties in a C-DAG system and a yeast model. Currently, additional studies are being conducted to obtain the protein in a bacterial system to assess its biochemical properties.

Introduction
Various factors such as aging, inactivity, and accidents can cause musculoskeletal disorders, often requiring surgical intervention for severe damage. The increasing number of implant surgeries has sparked interest in bone tissue engineering. Commercially pure titanium (CP-Ti) is highly favored in medicine for its biocompatibility, stability in body fluids, and tensile strength. However, a drawback is its lack of bioactivity. Bioactive coatings can address this issue by improving bone cell interaction with the material.

Materials and Methods
CP-Ti surfaces were modified using micro-arc oxidation (MAO) and ultrasound micro-arc oxidation (UMAO) in an electrolyte with calcium and phosphorus ions. This study assessed various process parameters, including voltage (400 V), duration (450 or 600 s), current density (120 or 60 mA/cm²), and two ultrasound operating modes (sinusoidal and unipolar rectangular). The coatings were analyzed through the assessment of morphology, chemical composition, topography, wettability, nanomechanical properties, corrosion behavior, coating thickness and adhesion, cytocompatibility, as well as cell adhesion and proliferation of the hFOB 1.19 cell line.

Results
Porous calcium phosphate coatings produced on CP-Ti samples exhibited hydrophilicity, an isotropic structure, and strong adhesion to the substrate. They also had a corrosion rate suitable for biomaterial applications. Further, this study showed that various MAO process parameters and ultrasound types significantly influenced the chemical composition as well as the physicochemical and mechanical properties of the coatings. Incorporating ultrasound during the MAO process enhanced coating thickness, porosity, roughness, isotropy, skewness, and calcium integration. Overall, they were characterized by favorable cytocompatibility.

Conclusions
The findings highlight the importance of surface treatment for the biomedical use of titanium. Optimal coating characteristics were achieved at a current of 136 mA, a duration of 450 s, and using unipolar rectangular ultrasound. Combining micro-arc oxidation with ultrasound improves CP-Ti properties concerning biomedical applications, such as customizing implants for knee joint resurfacing or craniofacial reconstruction.