Selection of Aptamers for Use as Molecular Probes in AFM Detection of Proteins.

Currently, there is great interest in the development of highly sensitive bioanalytical systems for diagnosing diseases at an early stage, when pathological biomarkers are present in biological fluids at low concentrations and there are no clinical manifestations. A promising direction is the use of molecular detectors-highly sensitive devices that detect signals from single biomacromolecules. A typical detector in this class is the atomic force microscope (AFM). The high sensitivity of an AFM-based bioanalysis system is determined by the size of the sensing element of an atomic force microscope-the cantilever-the radius of the curvature of which is comparable to that of a biomolecule. Biospecific molecular probe-target interactions are used to ensure detection system specificity. Antibodies, aptamers, synthetic antibodies, and peptides can be used as molecular probes. This study has demonstrated the possibility of using aptamers as molecular probes for AFM-based detection of the ovarian cancer biomarker CA125. Antigen detection in a nanomolar solution was carried out using AFM chips with immobilized aptamers, commercially available or synthesized based on sequences from open sources. Both aptamer types can be used for antigen detection, but the availability of sequence information enables additional modeling of the aptamer structure with allowance for modifications necessary for immobilization of the aptamer on an AFM chip surface. Information on the structure and oligomeric composition of aptamers in the solution was acquired by combining small-angle X-ray scattering and molecular modeling. Modeling enabled pre-selection, before the experimental stage, of aptamers for use as surface-immobilized molecular probes.

Methylene blue in anticancer photodynamic therapy: systematic review of preclinical studies.

Background: Methylene blue has a long history of clinical application. Thanks to phenothiazine chromophore, it has potential in photodynamic anticancer therapy. In spite of the growing body of literature that has evaluated the action of this dye on different types of cancer, the systematic understanding of this problem is still lacking. Therefore, this systematic review was performed to study the efficacy of methylene blue in photodynamic anticancer therapy. Methods: This systematic review was carried out in accordance with the PRISMA guidelines, and the study protocol was registered in PROSPERO (CRD42022368738). Articles for the systematic review were identified through the PubMed database. SYRCLE's risk of bias tool was used to assess the studies. The results of systematic analysis are presented as narrative synthesis. Results: Ten studies met the inclusion criteria and these full texts were reviewed. In the selected articles, the dosage of dye infusion ranged from 0.04 to 24.12 mg/kg. The effectiveness of photodynamic therapy with methylene blue against different types of cancer was confirmed by a decrease in tumor sizes in seven articles. Conclusion: The results of the systematic review support the suggestions that photodynamic therapy with methylene blue helps against different types of cancer, including colorectal tumor, carcinoma, and melanoma. In cases of nanopharmaceutics use, a considerable increase of anticancer therapy effectiveness was observed. The further research into methylene blue in photodynamic anticancer therapy is needed. Systematic Review Registration: (https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=368738), identifier (CRD42022368738).

Insights into the Pharmacological Effects of Flavonoids: The Systematic Review of Computer Modeling.

Computer modeling is a method that is widely used in scientific investigations to predict the biological activity, toxicity, pharmacokinetics, and synthesis strategy of compounds based on the structure of the molecule. This work is a systematic review of articles performed in accordance with the recommendations of PRISMA and contains information on computer modeling of the interaction of classical flavonoids with different biological targets. The review of used computational approaches is presented. Furthermore, the affinities of flavonoids to different targets that are associated with the infection, cardiovascular, and oncological diseases are discussed. Additionally, the methodology of bias risks in molecular docking research based on principles of evidentiary medicine was suggested and discussed. Based on this data, the most active groups of flavonoids and lead compounds for different targets were determined. It was concluded that flavonoids are a promising object for drug development and further research of pharmacology by in vitro, ex vivo, and in vivo models is required.

Changes in Protein Structural Motifs upon Post-Translational Modification in Kidney Cancer.

Post-translational modification (PTM) leads to conformational changes in protein structure, modulates the biological function of proteins, and, consequently, changes the signature of metabolic transformations and the immune response in the body. Common PTMs are reversible and serve as a mechanism for modulating metabolic trans-formations in cells. It is likely that dysregulation of post-translational cellular signaling leads to abnormal proliferation and oncogenesis. We examined protein PTMs in the blood samples from patients with kidney cancer. Conformational changes in proteins after modification were analyzed. The proteins were analyzed using ultra-high resolution HPLC-MS/MS and structural analysis was performed with the AMBER and GROMACS software packages. Fifteen proteins containing PTMs were identified in blood samples from patients with kidney cancer. For proteins with PDB structures, a comparative analysis of the structural changes accompanying the modifications was performed. Results revealed that PTMs are localized in stable and compact space protein globule motifs that are exposed to a solvent. The phenomenon of modification is accompanied, as a rule, by an increase in the area available for the solvent of the modified amino acid residue and its active environment.