Anastasia Anashkina

A hallmark of Alzheimer's disease (AD) is extra-neuronal protein aggregates formed mainly by the amyloid-β peptide (Aβ), that are deposited inside the brain as amyloid plaques. The formation of amyloid plaques requires participation of zinc ions. The 11-Glu-Val-His-His-14 region of Aβ is critical for interaction between Aβ and zinc ions. The engineered peptide Ac-His-Ala-Glu-Glu-NH2 (HAEE) acts as competitive inhibitor of such interactions and suppresses formation of Aβ aggregates in animal models of AD. We sought to develop a reliable method for studying the behavior of the synthetic HAEE peptide in the human blood in preparation for clinical trials of this peptide as a potential anti-amyloid drug for AD. The analytical method to monitor HAEE concentration in blood plasma combines separation by high-performance liquid chromatography and registration on a mass detector of the parent quasi-molecular ion and fragment ions. We discover that HAEE peptide represents a normal endogenous component of human blood plasma. Moreover, the HAEE level has been significantly reduced in patients with a clinical diagnosis of AD (n = 200) as compared with the control participants with no clinical diagnosis of cognitive impairment (n = 150). Deficiency of endogenous HAEE may be considered as a potential blood-based biomarker in the diagnosis of AD, while exogenous synthetic HAEE may serve as a drug in AD-modifying therapy.

This article overviews current trends in the molecular mechanisms of gene expression regulation studies published in the “Bioinformatics of Gene Regulations and Structure—2025” Special Issue (https://www

Nucleotide motifs in the core promoters of eukaryotic protein-coding genes transcribed by RNA polymerase II (Pol II) play an important role in the transcription process. We analyzed the role of an octanucleotide located in the TATA box position. Depending on whether this octanucleotide can form a complex with the TATA-binding protein (TBP), the promoter is classified as either TATA-containing or TATA-less. We analyzed the differences in the primary and spatial structures, as well as their dynamics, in TATA-containing and TATA-less promoters of mammals and plants. We divided the complete promoter sets of six organisms (H. sapiens, M. musculus, C. familiaris, A. thaliana, Z. mays, and H. vulgare) from the EPDnew database into TATA-containing and TATA-less fractions. The sizes of the TATA-containing promoter fractions are significantly smaller than those of the TATA-less fractions in all studied organisms, except in A. thaliana, where the sizes of both fractions are approximately equal. We characterized promoter architecture using variation profiles of various base-pair step parameters, minor-groove width, and the conformational dynamics of native DNA. The architectures of TATA-containing and TATA-less promoters differ significantly. The possible mechanistic influence of DNA structural features on the formation of the pre-initiation complex (PIC) in both types of promoters is discussed.

Antimicrobial resistance in Neisseria gonorrhoeae is a global concern. Spectinomycin is unusual in that resistance can emerge rapidly during localized outbreaks yet often disappears from clinical populations after drug withdrawal, suggesting an associated growth cost. To investigate evolutionary routes to spectinomycin resistance, we performed in vitro selection on two N. gonorrhoeae strains and two commensal Neisseria species. Derived cell lines were characterized by minimum inhibitory concentration (MIC) determination, whole-genome sequencing, growth-kinetics analysis, and molecular modelling of the RpsE (ribosomal protein S5) interface with the ribosome. All high-level resistant isolates (MIC > 2048 mg/L) acquired substitutions or deletions in loop 2 of RpsE. Modelling showed that these mutations perturb the conserved network of stabilizing contacts between RpsE residues Lys25 (Lys23 in E. coli numbering) and Lys28 (Lys26), as well as helix 34 nucleotides G922, A923, and C1069 of 16S rRNA, potentially altering the architecture of the spectinomycin-binding site. These mutations were associated with high-level resistance but reduced growth rates, with the resulting growth costs depending on the specific pattern of contact rearrangements. Convergent evolution towards loop 2 mutations supports the existence of a constrained mutational pathway to high-level spectinomycin resistance in the strains and species examined here. This constraint may help explain the rapid decline of resistant variants in the absence of drug pressure and underscores the importance of genomic surveillance.

Introduction: Beta-amyloid (Aβ) is involved in numerous physiological and pathophysiological processes and is one of the key players in the pathogenesis of Alzheimer’s disease. Aβ interacts with the 35-HAEE-38 site of the α4 subunit of the α4β2 nicotinic acetylcholine receptor. The synthetic tetrapeptide HAEE effectively inhibits the aggregation of endogenous Aβ. HAEE specifically binds to the 11-EVHH-14 site of Aβ both in the absence and presence of zinc ions, leading to the formation of stable complexes. We hypothesized that the HAEE motif could represent a universal binding site for Aβ within the human proteome. Materials and Methods: To test this hypothesis, a large-scale search for all amino acid sequences containing the HAEE motif in the human (Homo sapiens) proteome was performed using our in-house PepString server (http://pepstring.eimb.ru/). The conservation of the identified sites was analyzed across jawed vertebrates using BLAST. Protein localization and structural features were determined based on data from UniProt, PDB, and AlphaFold. Results: We identified 85 proteins (including 200 isoforms) containing the HAEE motif. Of these, 26 proteins are membrane proteins, including receptors, ion channels, and transporters (e.g., CACNA1B, MRS2, SLC15A2), and 59 are intracellular proteins, mostly nuclear transcription factors (including 13 zinc finger proteins). Structural analysis revealed that the HAEE motif is often located within functionally important domains, such as cytoplasmic loops of transmembrane proteins or DNA-binding domains. Conclusion: Given that Aβ acts as an extracellular ligand and can also penetrate various intracellular compartments, all identified proteins with the HAEE motif are considered potential physiological and pathophysiological targets for Aβ. The most promising candidates are proteins whose HAEE sites are structurally similar to that in α4β2-nAChR and/or coordinate zinc ions. These findings enhance our understanding of the molecular mechanisms of Aβ function and open new avenues for the search of therapeutic targets in AD.

This paper presents a new bioinformatics tool to meet the needs of researchers in the search for short (≥ 3) amino acid subsequences in protein sequences annotated in public databases (UniprotKB, SwissProt) and illustrates its efficacy with the example of a search for the EVHH tetrapeptide in the human proteome, which is a molecular determinant of amyloid beta and is involved in interactions that are crucial in Alzheimer’s disease pathogenesis. The topicality of developing such a tool is, on the one hand, supported by experimental data on the role of short tetrapeptide motifs in the architecture of intermolecular interfaces. On the other hand, there are currently no software products for efficient search for short (≥ 3) amino acid sequences in public databases, which drastically limits researchers’ ability to identify proteins with exact matches of short subsequences. This tool (PepString server, http://pepstring.eimb.ru/) allows one to use intuitive queries to retrieve information about all the proteins that contain sequences of interest, as well as their combinations.

Summary Overall, the school collected presentations on molecular biophysics and experimental techniques, addressed major unresolved challenges in the field, and shared an overall perspective on future directions that might help to clarify the important questions that emerged during the last decade of intensive research. To conclude, we note growing interest in AI applications for biophysical modeling, new physical experimental techniques such as cryo-microscopy, applications of modeling in pharmaceutical research, and drug design. We believe this special journal issue will be of interest to readers.

SUMMARY: A hallmark of Alzheimer’s disease (AD) is extra-neuronal protein aggregates formed mainly by the amyloid-β peptide (Aβ), that are deposited inside the brain as amyloid plaques. The engineered peptide Ac-His-Ala-Glu-Glu-NH ₂ (HAEE) suppresses the formation of amyloid plaques in vivo and is being tested as an anti-amyloid drug candidate. Here, by using a quantitative mass-spectrometry method we discover that HAEE peptide represents a normal endogenous component of human blood plasma. Moreover, the HAEE level has been significantly reduced in patients with a clinical diagnosis of AD (n=200) as compared with the control participants with no clinical diagnosis of cognitive impairment (n=150). Thus, endogenous HAEE may be considered as a potential blood-based biomarker in the diagnosis of Alzheimer’s disease, while exogenous HAEE may serve as a drug in AD-modifying therapy.

This article overviews recent findings on molecular mechanisms of gene expression regulation published in the “New Sights into Bioinformatics of Gene Regulations and Structure” (https://www

NADPH oxidase enzymes (NOXs) are a family of enzymes generating superoxide, which form reactive oxygen species. NOX2 activity is a causative agent for the progression of many diseases: neurodegenerative, cardiovascular, immune dysregulations, and even hereditary diseases and cancer. Administering antioxidants helps in inhibiting NOX2 activity; however, the development of selective inhibitors may provide greater improvement in the therapy of diseases. Here, an optimized synthesis of two most promising NOX2 inhibitors based on the 3-(indolin-6-yl)-4-(N-pyrazole-sulfonamide)-1H-pyrrolo [2,3-b]pyridine structure, namely, GSK2795039 and NCATS-SM7270, and an isomeric derivative of the same class, IMBIOC-1, is reported. The new modified procedures simplify the isolation, reduce byproduct formation, and improve the yields in 0.1–1 g scale preparations. Molecular modeling of the structures of NOX2 complexes with inhibitors validated their binding at the same site as NADPH, with IMBIOC-1 forming the largest number of intermolecular interactions with the NOX2 active site. Testing the effects of the compounds on amyloid beta-induced oxidative stress and toxicity in HMC3 microglial cells showed that all three inhibitors completely prevented the pathological amyloid-beta effect. At the same time, NCATS-SM7270 and IMBIOC-1 provided a stronger protective effect on microglial cell survival than GSK2795039, which allowed us to assert the potential of those compounds as neuroprotective agents.