The rational design of the vector‒host system and the conditions for its use is the key to its most effective use as a biocatalyst for obtaining valuable products or for testing potential bioregulators. In this work, we will consider examples of such solutions for some yeasts from the literature over the past 5 years and our experience in optimizing the reactions of 17α-hydroxylation of pregnanes with recombinant strains of the yeast S. cerevisiae and Y. lipolytica. Thus, it was known that pregnenolone and its product pregnenolone and the products of its transformation by cytochrome P450 17α-hydroxylase/17,20-lyase (P450c17) ‒ 17 hydroxypregnenolone, dehydroepiandrosterone ‒ undergo 3-O-acetylation by the Atf2p enzyme of the yeast Saccharomyces cerevisiae. We have found that adding isoamyl or amyl alcohol to the cultivation medium significantly reduced the formation of 3-O-acetylated products by both uninduced and induced cells of transgenic yeast S. cerevisiae GRF18 YEp5117α expressing P450c17 under the control of the GAL10 promoter. In this case, the Atf2p substrate competition model was applied. A more effective solution was to use a different host microorganism and an expression promoter. The analysis of the genome of the yeast Y. lipolytica using the BLAST program showed the absence of potential analogues of Atf2p, which was confirmed by the absence of pregnenolone acetylation products. Selecting the optimal host organism is an alternative to using a strain with a deleted gene.

BODIPY fluorescent dyes is a versatile class of molecules with a wide spectrum of applications, particularly in biological imaging and sensing. For these applications, lipophilicity is a critical factor that influences the compound's solubility, biodistribution, and biological interactions. This study investigated the synthesis and lipophilicity characterization of a series of BODIPY fluorescent dyes. The lipophilicity of the compounds was determined by high-performance liquid chromatography and compared to the predictions of theoretical methods. The results demonstrated the effectiveness of some fragment-based methods in BODIPY's lipophilicity calculation. The role of hydrophobic surface area in molecular lipophilicity was also investigated. The findings of this study provide insights into the structure-property relationships of BODIPY dyes and can be used to design derivatives with desired lipophilicity for specific applications.

Inhibition of quorum sensing is considered to be an effective strategy of control and treatment of a wide range of acute and persistent infections. Pseudomonas aeruginosa is an opportunistic bacterium with a high adaptation potential that contributes to healthcare-associated infections. In the present study, the effects of the synthesized hybrid structures bearing sterically hindered phenolic and heterocyclic moieties in a single scaffold on the production of virulence factors by P. aeruginosa were determined. It has been shown that the obtained compounds significantly reduce both pyocyanin and alginate production and stimulate the biosynthesis of siderophores in vitro, which may be attributed to their iron-chelating properties. The results of docking-based inverse high-throughput virtual screening indicate that transcription regulator LasR and Cu-transporter OPRC could be potential molecular targets for these compounds. Investigation of the impact small molecules exert on the molecular mechanisms of the production of bacterial virulence factors may pave the way for the design and development of novel antibacterial agents.

In a previous work, we reported the synthesis of four novel indole steroids and their effect on rat C6 glioma proliferation in vitro. The steroid derived from dehydroepiandrosterone and tryptamine (IS-1) was the most active (52 % inhibition at 10 mu M), followed by one of the epimers derived from pregnenolone and tryptamine (IS -3, 36 % inhibition at 10 mu M). By contrast, the steroid derived from estrone and tryptamine (IS-2) showed negligible activity at 10 mu M. No necrosis, increase in intracellular calcium or ROS levels was observed. In this work, the effect of compounds on C6 glioma apoptosis and autophagy is examined by fluorimetry and fluorescent microscopy. The IS-3 epimers disrupt the mitochondrial membrane potential and induce apoptosis in vitro moderately whereas IS-1 and IS-2 do not. However, IS-1 produces a large increase in monodansylcadaverine-positive autophagic vesicles over 24 h. The antiproliferative effect of indole steroids is ameliorated by auto-phagy inhibitor hydroxychloroquine, suggesting an autophagy-dependent mechanism of cell death.

The work covers synthesis and lipophilicity estimation of several BODIPY dyes. For these compounds, the distribution between 1-octanol and water layers is experimentally described and the corresponding partition coefficients LogP are calculated. The experimental LogP values are compared with popular fragment-based methods XLopP3, ALogPS, WLogP, SILICOS-IT and MLogP. Additionally, the hydrophobic and polar surface areas are found with quantum-mechanical calculations. That allowed to find a correlation between the LogP coefficient and the molecular surface topology, as well as to determine the corresponding incremental values of the methyl, acetyl, and phenyl substituents.

A 3-acetyl analogue of 5-hydroxyindole was synthesised and evaluated for its effects on rat C6 glioma cell functions. It was found that 3-acetyl-5-hydroxy-2-methylindole at 10 μmol/L led to a sharp reduction of mitochondrial membrane potential, induction of autophagy and decrease of proliferation of C6 glioma cells. The compound’s effect was comparable to that of rotenone, an inhibitor of cell respiration.

4-methyl-7-methoxycoumarin (CumOMe) has been synthesized and in silico calculations demonstrated localization of methoxy group within 0.4 nm from Fe ion of hem groups for some structures of human CYP19 & CYP46 as well as CYP152 S. paucimobilis , CYP158 St. coelicolor , HMUO C. diphtheriae , XPLA R. rhodochrous , CYP199A4 Rh. palustris , CYP101A1 Ps. putida and CYP51 M. tuberculosis .

An efficient procedure has been developed for the synthesis of 1,4-dihydropyridines containing aliphatic and 2-(1-hydroxycyclopropyl)methyl substituents via multicomponent Hantzsch reaction using europium(III) chloride hexahydrate as catalyst. The synthesized compounds were evaluated for their potential biological activity by simulation of phospholipid bilayer permeability and molecular docking against human protein kinase and cytochrome P450. Study of the effect of the synthesized compounds on the growth of the yeasts Yarrowia lipolytica and Saccharomyces cerevisiae showed the absence of acute toxicity.

Two fluorescent sterol-like molecules have been synthesized, namely, a derivative of 7-nitrobenzofurazan (NBD) with 17-(methylamino)-androst-5-en-3beta-ol (DAM-NBD) and NBD-piperazine conjugate with cholesteryl chloroformate (NBD-pip-CCF). In silico docking and plasma membrane simulations have shown ability of the compounds to penetrate the lipid bilayer, as well as to bind affinely of the yellow fever mosquito SCP-2 protein structure (code PDB: 3BDQ; binding energy about −11.9 kcal/mol). Also docking with AlphaFOLD-predicted insect Neverland protein structure demonstrated DAM-NBD binding with a similar affinity. The theoretical results indicate perspectives of the fluorescent steroid usage to study insect protein-sterol interactions.

In this work we examined the synthesized N-alkynyl-17-aminosteroids and N-alkynyl-20-aminosteroids (based on dehydroepiandrosterone and pregnenolone, respectively) for their effect on C6 rat glioma cell functions. At 10 μM, the compounds had an insignificant effect on C6 glioma mitochondrial membrane potential, but increased cell autophagy by 70-90%, comparable to the known autophagy inducer dexamethasone. Docking simulations predict a potential high-affinity interaction between N-alkynylaminosteroids and Keap1 and the Hedgehog pathway protein, Smoothened, which are involved in autophagy regulation. The possible mechanisms of observed processes are discussed.

The article provides the route to trifluoroacetylated fluorescent boron dipyrromethene dye (2). The compound performs intensive absorption and emission bands in near-red wavelength region. Photophysical properties of 2 are investigated in different solvents. A notable increase of fluorescence quantum yield after trifluoroacetyl group insertion connected with a change in intramolecular interactions parameters. The role of molecular geometry aspects in observed photophysical properties and molecular fragments rotation energy barriers are explained by quantum-mechanical calculations. 2 performs considerable antimycobacterial activity. According to molecular docking simulations, 2 is capable of affinity binding in the active sites of mycobacterial MycP1 and MycP3 serine proteases. The geometries of final ligand-protein complexes show the possibility of protein active site covalent modification at the serine residue of the catalytic triad. At lower concentrations, 2 can act as a fluorescent dye for microscopy analysis and corresponding staining patterns are shown for Mycobacterium smegmatis and Staphylococcus aureus cells.

Two new fluorescent NBD-piperazine derivatives with lipophilic substituents of formylcholesterol and hexanoic acid (compounds 2 and 3, respectively) were synthesized. Using in silico calculations, their abilities to permeate through lipid bilayer and to be bound affinely with some cytochromes P450 of human (2 with lanosterol 14α-demethylase CYP51, 3 with drug-metabolizing CYP1A1, CYP2D6, CYP3A4; energy of binding E bind from –14.4 to –10 kcal/mol) and of mycobacteria (2 with sterol 27-hydroxylase CYP125, 3 with “orphan” CYP164; E bind from –13.3 to –9.1 kcal/mol) were demonstrated. The synthesized compounds and calculated computational data will contribute to prioritization of in vitro investigations aiming to revealing properties of the proteins.

Polylactide (PLA) is one of the most promising biodegradable and biocompatible polymer materials. Estimation of hydrolytic destruction of PLA is of high importance for their applications both at planning and at real-time exploitation. This paper reports on synthesis and applicability of fluorescein-O-dihexanoate as a pro-fluorescent marker of hydrolytic destruction of two types of PLA-based materials. Fluorescence enhancement correlated with adequately more fast destruction of poly-D,L-lactide as well as less stability to alkaline hydrolysis. Thus, applicability of fluorescein-O-dihexanoate for fluorescence-based estimation of hydrolytic destruction of PLA-based materials is shown in quite real time mode.

Abstract Computer-aided docking-based inverse high-throughput virtual screening (inv HTVS) was applied for a quick evaluation of compounds as new affine ligands for SARS-CoV-2 proteins. We performed Autodock Vina-based inv HTVS using more than 450 structures of the virus proteins from Protein Data Bank (PDB) and totally ~ 2000 structures of compound with electrophilic motifs (mainly, α,β-unsaturated carbonyls) from Pubchem (CID codes) or Biogem databases. The inv HTVS calculations were semi-automatically organized, run and analyzed using our helper program tool composed of Python scripts and Excel files with macroses. Criteria for binding energy (Ebind, kcal/mol) values (no more than 6.9), distance between thiol groups of cysteine residues and electrophilic groups of the compounds within 0.4 nm (distance criterium) and total number of structures meeting the criteria were used. New in silico interactions were found for Mpro in the cases of such phytochemicals as peperomine E, 15-oxosteviol, zambesiacolactone B, isodehydroeupatundin, 2deoxycucurbitacin and jatrophone. Analogously, potential covalent ligands for NSP12 were found to include ixerin D, xindongnin C, rabdosin B, epinodosin as well as such ligands for NSP16 were found to include anhydroverlotolin-like compound CID325147, mexicanin E, insulicolide B and geoditin A. These and others hits are discussed with respect to their availability and biological properties. Thus, a set of natural compounds were pointed out as potential new covalent inhibitors of SARS-CoV-2 proteins Mpro, Nsp12 and Nsp16. This information could be used for further evaluations as prophylaxis tools or drugs against COVID-19.

A fluorescent molecular rotor (FMR) based on boron dipyrromethene core was obtained. Fluorescence emission properties of the compound strongly depend on the medium viscosity. The emission intensity increases 27 times after viscosity changing from ethanol to glycerol medium. At the same time, the compound appeared almost insensitive to solvatochromic effects. Obtained FMR also can affinely bind with the bovine serum albumin protein active sites followed by noticeable emission intensity growth. Possible ligand binding cites and main amino acid surrounding were described with molecular docking simulations and are in an agreement with experimental data. The results can be used for further design and synthesis of novel fluorescent viscosity and protein-ligand interactions censors suitable for implementation in biosystems in vitro and in vivo.

Zn-containing proteins play essential roles in the viability and virulence of bacteria, so are considered to be possible molecular new drug targets. Based on literature data about N-acyl-o-phenylenediamine and 2-pycolylamine as warheads of drugs and molecular probes for Zn-bearing enzymes like histone deacetylases, we guessed that N-(7-nitrobenzofurazan-4-y)-o-phenylenediamine (NBD-OPD), 2-pycolyl-(N-(7-nitrobenzofurazan-4-amine)) and ciprofloxacin 2-pycolylamide (CPF-Pic2) are potential fluorescent inhibitors of such enzymes. Molecular docking was performed for estimate affinity of the compounds to a set of bacterial enzymes, and photochemical and electrochemical properties were calculated in silico using DFT.

The search for new antibacterial drugs has continued to be an urgent matter. One of the approaches is the development of covalent inhibitors using biochemoinformatics at the initial stages. In this work, structures of a few plant-derived substances with electrophilic unsaturated carbonyl and structures of small synthetic compounds suitable for fragment-based drug discovery (FBDD) with -CH2-Br group were selected as ligands for sets of structures of bacterial proteins. The theoretical assessment was carried out using the Autodock Vina program for calculation and FYTdock for the organization of the process and the analysis of results. Natural Ixerine D as well as synthetic 4-(4-(2-bromoethyl)piperazin-1-yl)-7-nitrobenzofurazan demonstrated the most promising results as potential Cys-targeted inhibitors.

S-Allylation of 4-pentyl- and 4-[(1-acetoxycyclopropyl)methyl]-3,4-dihydropyrimidine-2(1H)-thiones with 2-functionalized allyl bromides available from cyclopropanol intermediates has been reported for the first time. New unique heterocyclic compounds structurally related to 3rd generation calcium channel blockers have been synthesized in high yields.

Our computer-aided protein-ligand docking test using Autodock Vina software allowed to reveal the potential of few α- and β-diketones from plants and alternative living organisms as covalent ligands for few proteins of coronavirus SARS-CoV-2 – a causative agent of COVID-19. It has been established that values for energy of binding (docking score, Ebind, kcal/mol) less than –7.5 and for distances of ligands’ carbonyl groups to side chain nitrogens of arginine residues of some coronaviral enzymes within 0.4 nm have been true for β-diketones 6-gingerdione (Pubchem code CID162952), 8-gingerdione (CID14440537), tetrahydrocurcumine (CID124072) as well as α-diketone wallitaxane E (CID132967478). The in silico revealed interactions are interesting to be verified in vitro and they point out a possibility of investigation of the compounds and related natural materials as tools for struggle against coronaviral infections.