PDSTP Is the First Drug in Class to Treat Coronavirus Infection

The results of a comprehensive study are presented on the development and creation of an original small PDSTP molecule, able to prevent the SARS-CoV-2 coronavirus infection from binding to the host cell. The PDSTP molecule was designed to electrostatically interact with heparan sulfate proteoglycans on the cell surface, and coronaviruses, particularly SARS-CoV-2, use this mechanism as the first stage of interaction with the cell. By blocking this process, it is possible to stop the life cycle of the virus, thus leading to its death. The drug candidate PDSTP, with its unique mechanism of action, is characterized by a very low toxicity and a high safety profile and demonstrates good efficacy in animal experiments.

Highly-Active Recombinant Formate Dehydrogenase from Pathogenic Bacterium Staphylococcus aureus: Preparation and Crystallization

# These authors contributed equally to the work. NAD+-dependent formate dehydrogenase from Staphylococcus aureus (SauFDH) is one of the key enzymes responsible for the survival of this pathogen in the form of biofilms. 3D structure of the enzyme might be helpful in the search for highly specific SauFDH inhibitors that can be used as antibacterial agents exactly against S. aureus biofilms. Here, we prepared a recombinant SauFDH in Escherichia coli cells with a yield of 1 g target protein per liter medium. The developed procedure for the enzyme purification allowed to obtain 400 mg of homogenous enzyme with 61% yield. The specific activity of the purified recombinant SauFDH was 20 U per mg protein, which was 2 times higher than the previously reported activities of formate dehydrogenases. We also found crystallization conditions in the course of two rounds of optimization and obtained 200- and 40-µm crystals for the SauFDH apo- and holoenzymes, respectively. X-ray analysis using synchrotron X-ray sources produced diffraction data sufficient for solving the three-dimensional structures of the apo- and holoenzymes with the resolution of 2.2 and 2.7 Å, respectively. Crystals of the apo- and holoforms of SauFDH had different crystal space groups, which suggest coenzyme binding in the SauFDH holoenzyme.

Effect of Ketosubstrate on the Product Yield in the Transamination Reaction Catalyzed by Transaminase from Thermoproteus uzoniensis

The study of the equilibrium of reactions catalyzed by thermostable enzymes is in demand for the development of biotechnological enzyme processes. The results of the analysis of equilibrium of transamination reaction catalyzed by thermostable transaminase from the archaeon Thermoproteus uzoniensis are presented below. A comparison of the conversion of substrates was performed for reactions with L-leucine and pyruvate and L-leucine and 2-oxobutyrate at 65°C. The establishment of the equilibrium was controlled by a decrease in the concentration of 2-oxobutyrate or pyruvate and by the accumulation of the keto analog of L-leucine. It was shown that the degree of conversion of L-leucine in the reaction with specific 2-oxobutyrate is higher than in the reaction with nonspecific pyruvate.

Expression, purification and biophysical characterization of recombinant Streptomyces violaceoruber phospholipase PLA2 overproduced in Pichia pastoris

Aim: The main purpose of this work was to develop new protocols for high yield purification of secretory phospholipase A2 (PLA2) and to investigate its biophysical properties.Materials and methods: We have used a Pichia pastoris expression system for PLA2 expression and two-stage chromatography for its purification. The biophysical properties of PLA2 were investigated by circular dichroism.Results: A scalable method for high yield purification of recombinant Streptomyces violaceruber PLA2 was developed. The PLA2 from S. violaceruber was expressed in the methylotrophic yeast P. pastoris. Functional active phospholipase A2 with specific activity 73 U/mg was purified with a concentration of at least 3 mg/mL. The role of different divalent ions in PLA2 thermostability were evaluated. Ca²⁺ and Ba²⁺ ions significantly increased thermostability of the enzyme.

Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding

The structure of the anti-C60 fullerene antibody Fab fragment (FabC60) was solved by X-ray crystallography. The computer-aided docking of C60 into the antigen-binding pocket of FabC60 showed that binding of C60 to FabC60 is governed by the enthalpy and entropy; namely, by - stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C60. A fragment of the mobile CDR H3 loop located on the surface of FabC60 interferes with C60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C60. The structure of apo-FabC60 has been deposited with pdbid 6H3H.

Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding

The structure of the anti-C₆₀ fullerene antibody Fab fragment (FabC₆₀) was solved by X-ray crystallography. The computer-aided docking of C₆₀ into the antigen-binding pocket of FabC₆₀ showed that binding of C₆₀ to FabC₆₀ is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C₆₀. A fragment of the mobile CDR H3 loop located on the surface of FabC₆₀ interferes with C₆₀ binding in the antigen-binding site, thereby resulting in low antibody affinity for C₆₀. The structure of apo-FabC₆₀ has been deposited with pdbid 6H3H.

Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy

The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.

Three-Dimensional Structure of Cytochrome c Nitrite Reductase As Determined by Cryo-Electron Microscopy

The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the high-resolution X-ray diffraction structure of this enzyme.

The Influence of Myofibrils on the Proliferation and Differentiation of Myoblasts Cocultured with Macrophages

We studied the effect of myofibrils on proliferation and differentiation of myoblasts cocultured with macrophages as well as the effect of incubation of macrophages with myofibrils on the expression by macrophages of the compounds that are cytokines for muscle cells. In the cocultures, macrophages stimulated the proliferation of myoblasts. Myofibrils greatly enhanced the stimulating effect of macrophages, whereas lipopolysaccharide (LPS) completely abolished it. The culture medium conditioned by macrophages activated the proliferation of myoblasts that were incubated with myofibrils but inhibited it when myoblasts were incubated with LPS. Possibly, myofibrils and their constituent proteins activate macrophages in an alternative pathway, enriching the population with M2-type macrophages.Z.

Properties of Bacterial and Archaeal Branched-Chain Amino Acid Aminotransferases

Branched-chain amino acid aminotransferases (BCATs) catalyze reversible stereoselective transamination of branched-chain amino acids (BCAAs) L-leucine, L-isoleucine, and L-valine. BCATs are the key enzymes of BCAA metabolism in all organisms. The catalysis proceeds through the ping-pong mechanism with the assistance of the cofactor pyridoxal 5'-phosphate (PLP). BCATs differ from other (S)-selective transaminases (TAs) in 3D-structure and organization of the PLP-binding domain. Unlike other (S)-selective TAs, BCATs belong to the PLP fold type IV and are characterized by the proton transfer on the re-face of PLP, in contrast to the si-specificity of proton transfer in fold type I (S)-selective TAs. Moreover, BCATs are the only (S)-selective enzymes within fold type IV TAs. Dual substrate recognition in BCATs is implemented via the "lock and key" mechanism without side-chain rearrangements of the active site residues. Another feature of the active site organization in BCATs is the binding of the substrate α-COOH group on the P-side of the active site near the PLP phosphate group. Close localization of two charged groups seems to increase the effectiveness of external aldimine formation in BCAT catalysis. In this review, the structure-function features and the substrate specificity of bacterial and archaeal BCATs are analyzed. These BCATs differ from eukaryotic ones in the wide substrate specificity, optimal temperature, and reactivity toward pyruvate as the second substrate. The prospects of biotechnological application of BCATs in stereoselective synthesis are discussed.