Biomedical Chemistry: Research and Methods

Protocols for Proteomic Analysis: Isolation, Solubilization and Hydrolysis by Proteases

2025-05-05T11:12:48+00:00

High-throughput studies of protein composition of biological samples have become routine and are used practically in all areas of life sciences. Modern proteomics methods allow reliable identification and quantification of thousands of proteins in a single experiment. The standard procedure for proteomic analysis includes the following steps: 1. isolation and solubilization of proteins, their hydrolysis by proteases; 2. analysis of the resulting peptides by high-performance liquid chromatography with mass spectrometric detection; 3. bioinformatics and statistical processing of the results. This paper presents protocols of the first stage of proteomic analysis, i.e. sample preparation, which are routinely used in the Laboratory of Systems Biology of the Institute of Biomedical Chemistry.

MetaPASS 2024: Visualization of Biological Activity Spectra of Organic Compounds Taking into Account Their Biotransformation

2024-07-23T14:21:35+00:00

In the human body, pharmacological substances undergo biotransformation, therefore, during drugs development, it is necessary to take into account the biological activity spectra of their metabolites. Previously, we created the MetaPASS web application to analyze the probable spectra of biological activity of drug-like organic compounds taking into account their metabolism. Here we describe a new version of MetaPASS 2024 (https://www.way2drug.com/metapass), containing increased number of known metabolic pathways, and added procedures for searching structural similarity based on MNA and QNA descriptors and searching for compounds with the highest probability estimate for target biological activity; we have also implemented representation of the spectrum of biological activity in the form of treemaps.

On the Question of the Molecular and Genetic Mechanisms by which Bone Tissue Osteoblasts Interact with Biological Materials During Osteoplasty

2024-12-25T07:34:11+00:00

The article herein sets out to show the molecular and genetic mechanisms underpinning regenerative processes in bone tissue during the implantation of biological materials. The adhesion of osteoblasts to biological materials is a pivotal step in the transfer of physicochemical signals from biomaterials to osteoblasts. Initially, bone tissue cells interact with the biological material indirectly, through specific extracellular matrix proteins, especially vitronectin, fibronectin, and type I collagen. During the period preceding direct contact of osteoblasts with the implant, it is possible for blood proteins to be absorbed on the surface of the biological material in few seconds. Exactly the formation of a "protein layer" on the implants has been demonstrated to favour the adhesion of osteoblasts. The process of adhesion of osteoblasts to blood proteins is facilitated by a specific sequence, RGD, a tripeptide consisting of the amino acids Arg, Gly and Asp. This sequence is characteristic of vitronectin, fibronectin, type I collagen, osteopontin, bone sialoprotein and thrombospondin. Integrin-related signalling pathways can be categorised into two distinct types: those that are contingent on the Src-FAK complex and those that are not. It has been established that the phosphorylation of FAK at various sites can trigger multiple signalling pathways, including the PI3K/Akt/mTOR pathway, the Ras/MAPK/ERK1/2 pathway, and the p130Cas-RhoA GTPase pathway. For signalling pathways whose action is not contingent on the Src-FAK complex, integrin-linked kinase (ILK) is a pivotal regulatory factor. Among other significant cell membrane proteins, cadherins have been demonstrated to function as signal transduction molecules, contributing to the regulation of critical cellular activities. Consequently, in addition to the physical attachment of osteoblasts to biomaterials, cell adhesion leads to the activation of several signalling pathways, among which integrin- and cadherin-related signalling pathways are the most significant.

Superoxidizing and Antioxidant Activity of Nicotinamide Coenzymes in Vitro

2025-05-19T15:33:44+00:00

New properties of nicotinamide coenzymes (NAD, NADP, NADH, NADPH) have been discovered: superoxide-generating and antioxidant activities. Coenzymes are capable of generating superoxide anions (O₂^─●), entering an alkaline environment; and can be O₂^─● traps, inhibiting the generation process in superoxide-generating model systems, thus exhibiting antioxidant properties. Actually, nicotinamide itself, which is a functional part in the coenzyme molecule in oxidation-reduction processes, showed only antioxidant activity in vitro. Antioxidant properties have also been found in adenosine, which is part of the coenzyme molecule. Thus, it has been established for the first time that coenzymes, according to their chemical properties, are bifunctional molecules. It is assumed that they participate in cellular signaling through the generation of superoxide and, in the case of excess superoxide in the environment, they can be antioxidants. All these properties of coenzymes and their components must be taken into account when used in scientific research and medicine.