In-Cell Testing of Zinc-Dependent Histone Deacetylase Inhibitors in the Presence of Class-Selective Fluorogenic Substrates: Potential and Limitations of the Method.

The development of anticancer drugs based on zinc-dependent histone deacetylase inhibitors (HDACi) has acquired great practical significance over the past decade. The most important HDACi characteristics are selectivity and strength of inhibition since they determine the mechanisms of therapeutic action. For in-cell testing of the selectivity of de novo-synthesized HDACi, Western blot analysis of the level of acetylation of bona fide protein substrates of HDACs of each class is usually used.

Effects of natural polymorphisms in SARS-CoV-2 RNA-dependent RNA polymerase on its activity and sensitivity to inhibitors in vitro.

SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is the key enzyme required for viral replication and mRNA synthesis. RdRp is one of the most conserved viral proteins and a promising target for antiviral drugs and inhibitors. At the same time, analysis of public databases reveals multiple variants of SARS-CoV-2 genomes with substitutions in the catalytic RdRp subunit nsp12.

Selective Inhibition of HDAC Class I Sensitizes Leukemia and Neuroblastoma Cells to Anticancer Drugs.

The acquired resistance of neuroblastoma (NB) and leukemia cells to anticancer therapy remains the major challenge in the treatment of patients with these diseases. Although targeted therapy, such as receptor tyrosine kinase (RTK) inhibitors, has been introduced into clinical practice, its efficacy is limited to patients harboring mutant kinases. Through the analysis of transcriptomic data of 701 leukemia and NB patient samples and cell lines, we revealed that the expression of RTK, such as KIT, FLT3, AXL, FGFR3, and NTRK1, is linked with HDAC class I.

Pre-Senescence Induction in Hepatoma Cells Favors Hepatitis C Virus Replication and Can Be Used in Exploring Antiviral Potential of Histone Deacetylase Inhibitors.

Recent evidence suggests that fibrotic liver injury in patients with chronic hepatitis C correlates with cellular senescence in damaged liver tissue. However, it is still unclear how senescence can affect replication of the hepatitis C virus (HCV). In this work, we report that an inhibitor of cyclin-dependent kinases 4/6, palbociclib, not only induced in hepatoma cells a pre-senescent cellular phenotype, including G1 arrest in the cell cycle, but also accelerated viral replicon multiplication.

Electron-Vibrational Spectra and Dynamics of the Lutein Molecule.

The carotenoid molecules such as lutein play an important role in the absorption of light and the following transfer of energy during photosynthesis. However, the study of these processes by the experimental methods only is quite difficult because some of the transitions between the electronic states of carotenoids are optically forbidden and the effect of vibrational states change also must be taken into account. In the present work, electronic-vibrational states of the lutein molecule in the LHCII complex of higher plants and in the diethyl ether solution were described using the methods.

Structural isomers of cinnamic hydroxamic acids block HCV replication via different mechanisms.

A set of ortho-, meta- and para-substituted cinnamic hydroxamic acids (CHAs) was synthesized. In each series of structural isomers, a phenyl substituent was linked to an aromatic ring of the parent cinnamic acid via a linker of one to four atoms in length. Using a cell test system with the full-length replicon of hepatitis C virus (HCV), we established a relationship between the suppression of HCV replicon propagation and the inhibition of class I/IIb histone deacetylases (HDACs).

Synthesis of N'-propylhydrazide analogs of hydroxamic inhibitors of histone deacetylases (HDACs) and evaluation of their impact on activities of HDACs and replication of hepatitis C virus (HCV).

N'-Propylhydrazide analogs of hydroxamic inhibitors of histone deacetylases (HDACs), including tubastatin A, vorinostat and belinostat, were synthesized. All prepared compounds inhibited HDAC1/2/3, but not HDAC6, except for one hydrazide analog of HDAC4/5/7 inhibitor that was completely inactive. A novel 4-substituted derivative of N'-propylbenzohydrazide with extremely high anti-HCV activity was discovered.

Rhodium(III) Complex with a Bulky Cyclopentadienyl Ligand as a Catalyst for Regioselective Synthesis of Dihydroisoquinolones through C-H Activation of Arylhydroxamic Acids.

Catalytic reaction of arylhydroxamic acids with alkenes represents a convenient method for preparation of biologically active dihydroisoquinolones. Here, the rhodium(III) complex [(C H tBu CH tBu)RhCl ] , which allows one to carry out such reactions with high regioselectivity to obtain 4-substituted dihydroisoquinolones in 72-97 % yields, is described. The regioselectivity is provided by the bulky cyclopentadienyl ligand of the catalyst, which is formed through a [2+2+1] cyclotrimerization of tert-butylacetylene.

Calculation of the excited states properties of LH1 complex of Thermochromatium tepidum.

Calculation of the excited states properties of pigment complexes is one of the key problems in the photosynthesis research. The excited states of LH1 complex of Thermochromatium tepidum were studied by means of the high-precision quantum chemistry methods. The influence of different parameters of the calculation procedure was examined.

Pyridine hydroxamic acids are specific anti-HCV agents affecting HDAC6.

Recently we reported benzohydroxamic acids (BHAs) as potent and selective inhibitors of hepatitis C virus (HCV) replicon propagation. In this work 12 pyridine hydroxamic acids (PHAs) were synthesized and tested in full-genome replicon assay. It was found that PHAs possessed very similar anti-HCV properties compared to BHAs.

Self-trapped leaky waves in lattices: discrete and Bragg soleakons.

We propose lattice soleakons: self-trapped waves that self-consistently populate slowly-attenuating leaky modes of their self-induced defects in periodic potentials. Two types, discrete and Bragg, lattice soleakons are predicted. Discrete soleakons that are supported by combination of self-focusing and self-defocusing nonlinearities propagate robustly for long propagation distances.

Benzohydroxamic acids as potent and selective anti-HCV agents.

A diverse collection of 40 derivatives of benzohydroxamic acid (BHAs) of various structural groups were synthesized and tested against hepatitis C virus (HCV) in full-genome replicon assay. Some of these compounds demonstrated an exceptional activity, suppressing viral replication at sub-micromolar concentrations. The compounds were inactive against key viral enzymes NS3, and NS5B in vitro assays, suggesting host cell inhibition target(s).

Finite element simulation of a perturbed axial-symmetric whispering-gallery mode and its use for intensity enhancement with a nanoparticle coupled to a microtoroid.

We present an optical mode solver for a whispering gallery resonator coupled to an adjacent arbitrary shaped nano-particle that breaks the axial symmetry of the resonator. Such a hybrid resonator-nanoparticle is similar to what was recently used for bio-detection and for field enhancement. We demonstrate our solver by parametrically studying a toroid-nanoplasmonic device and get the optimal nano-plasmonic size for maximal enhancement.

Reactive rifampicin derivative able to damage transcription complex.

Rifampicin (Rif) is powerful broad spectrum antibiotic that targets bacterial RNA polymerase (RNAP) by blocking the transcript exit channel. The performance of the drug can be further enhanced by tagging with active chemical groups that produce collateral damage. We explored this principle by tethering Rif to Fe(2+)-EDTA chelate.

New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling.

A variety of contemporary analytical platforms, utilized in technical and biological applications, take advantage of labeling the objects of interest with fluorescent tracers-compounds that can be easily and sensitively detected. Here we describe the synthesis of new fluorescent quinoline and quinolone compounds, whose light emission can be conveniently tuned by simple structural modifications. Some of these compounds can be used as sensitizers for lanthanide emission in design of highly sensitive luminescent probes.

Attosecond pulses with sophisticated spatio-spectral waveforms: spatio-spectral Airy and auto-focusing beams.

We propose a scheme for producing attosecond pulses with sophisticated spatio-spectral waveforms. The profile of a seed attosecond pulse is modified and its central frequency is up-converted through interaction with an infrared pump pulse. The transverse profile of the infrared beam and a spatiotemporal shift between the seed and infrared pulses are used for manipulating the spatio-spectral waveform of the generated pulse beam.

Sawtooth grating-assisted phase-matching.

We show that a sawtooth phase-modulation is the optimal profile for grating assisted phase matching (GAPM). Perfect (sharp) sawtooth modulation fully corrects the phase-mismatch, exhibiting conversion equal to conventional phase matching, while smoothened, approximate sawtooth structures are more efficient than sinusoidal or square GAPM modulations that were previously studied. As an example, we demonstrate numerically optically-induced sawtooth GAPM for high harmonic generation.

Luminescent probes for ultrasensitive detection of nucleic acids.

Novel amino-reactive derivatives of lanthanide-based luminescent labels of enhanced brightness and metal retention were synthesized and used for the detection of cDNA oligonucleotides by molecular beacons. Time-resolved acquisition of the luminescent signal that occurs upon hybridization of the probe to the target enabled the avoidance of short-lived background fluorescence, markedly enhancing the sensitivity of detection, which was less than 1 pM. This value is about 50 to 100 times more sensitive than the level achieved with conventional fluorescence-based molecular beacons, and is 10 to 60 times more sensitive than previously reported for other lanthanide-based hybridization probes.

Homogeneous fluorescent assay for RNA polymerase.

A new method for determination of RNA polymerase (RNAP) activity is presented. The method uses nucleoside tri- and tetraphosphate derivatives carrying 4-methylumbelliferone residue at the terminal phosphate. Incorporation of such compounds in RNA by RNA polymerase is accompanied by release of di- and triphosphate derivatives of 4-methylumbelliferone.

Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.

During transcription elongation, RNA polymerase (RNAP) occasionally loses its grip on the growing RNA end and backtracks on the DNA template. Prokaryotic Gre factors rescue the backtracked ternary elongating complex through stimulation of an intrinsic endonuclease activity, which removes the disengaged 3' RNA segment. By using RNA-protein crosslinking in defined ternary elongating complexes, site-directed mutagenesis, discriminative biochemical assays, and docking of the two protein structures, we show that Gre acts by providing two carboxylate residues for coordination of catalytic Mg2+ ion in the RNAP active center.