Stancho Stanchev

Rhomboid proteases are ubiquitous intramembrane serine proteases that can cleave transmembrane substrates within lipid bilayers. They exhibit many and diverse functions, such as but not limited to, growth factor signaling, immune and inflammatory response, protein quality control, and parasitic invasion. Human rhomboid protease RHBDL4 has been demonstrated to play a critical role in removing misfolded proteins from the Endoplasmic Reticulum and is implicated in severe diseases such as various cancers and Alzheimer’s disease. Therefore, RHBDL4 is expected to constitute an important therapeutic target for such devastating diseases. Despite its critical role in many biological processes, the enzymatic properties of RHBDL4 remain largely unknown. To enable a comprehensive characterization of RHBDL4’s kinetics, catalytic parameters, substrate specificity, and binding modality we expressed and purified recombinant RHBDL4, and employed it in a Förster Resonance Energy Transfer-based cleavage assay. Until now, kinetic studies have been limited mostly to bacterial rhomboid proteases. Our in vitro platform offers a new method for studying RHBDL4’s enzymatic function and substrate preferences. Furthermore, we developed and tested potential inhibitors using our assay and successfully identified peptidyl α-ketoamide inhibitors of RHBDL4 that are highly effective against recombinant RHBDL4. We utilize ensemble docking and molecular dynamics (MD) simulations to explore the binding modality of substrate-derived peptides bound to RHBDL4. Our analysis focused on key interactions and dynamic movements within RHBDL4’s active site that contributed to binding stability, offering valuable insights for optimizing the non-prime side of RHBDL4 ketoamide inhibitors. In summary, our study offers fundamental insights into RHBDL4’s catalytic activities and substrate preferences, laying the foundation for downstream applications such as drug inhibitor screenings and structure-function studies, which will enable the identification of lead drug compounds for RHBDL4.

The mechanisms of intramembrane proteases are incompletely understood due to the lack of structural data on substrate complexes. To gain insight into substrate binding by rhomboid proteases, we have synthesised a series of novel peptidyl‐chloromethylketone (CMK) inhibitors and analysed their interactions with Escherichia coli rhomboid GlpG enzymologically and structurally. We show that peptidyl‐CMKs derived from the natural rhomboid substrate TatA from bacterium Providencia stuartii bind GlpG in a substrate‐like manner, and their co‐crystal structures with GlpG reveal the S1 to S4 subsites of the protease. The S1 subsite is prominent and merges into the ‘water retention site’, suggesting intimate interplay between substrate binding, specificity and catalysis. Unexpectedly, the S4 subsite is plastically formed by residues of the L1 loop, an important but hitherto enigmatic feature of the rhomboid fold. We propose that the homologous region of members of the wider rhomboid‐like protein superfamily may have similar substrate or client‐protein binding function. Finally, using molecular dynamics, we generate a model of the Michaelis complex of the substrate bound in the active site of GlpG. ![][1] Despite valuable insights from inhibitor‐bound rhomboid proteases, full understanding of intramembrane proteolysis requires structural views of protease‐substrate complexes. Direct insights into substrate binding and catalytic mechanism of an intramembrane protease now come from X‐ray structures of the bacterial rhomboid protease GlpG complexed to substrate‐derived peptide inhibitors. The EMBO Journal (2014) 33: 2408–2421 [1]: pending:yes

The antimicrobial 40-amino-acid-peptide lucifensin was synthesized by native chemical ligation (NCL) using N-acylbenzimidazolinone (Nbz) as a linker group. NCL is a method in which a peptide bond between two discreet peptide chains is created. This method has been applied to the synthesis of long peptides and proteins when solid-phase synthesis is imcompatible. Two models of ligation were developed: [15 + 25] Ala-Cys and [19 + 21] His-Cys. The [19 + 21] His-Cys method gives lower yield because of the lower stability of 18-peptide-His-Nbz-CONH₂ peptide, as suggested by density functional theory calculation. Acetamidomethyl-deprotection and subsequent oxidation of the ligated linear lucifensin gave a mixture of lucifensin isomers, which differed in the location of their disulfide bridges only. The dominant isomer showed unnatural pairing of cysteines [C1−6], [C3−5], and [C2−4], which limits its ability to form α-helical structure. The activity of isomeric lucifensin toward Bacillus subtilis, Staphylococcus aureus, and Micrococcus luteus was lower than that of the natural lucifensin. The desired product native lucifensin was prepared from this isomer using a one-pot reduction with dithiotreitol and subsequent air oxidation in slightly alkaline medium. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.

Nine biologically active theophylline derivatives were investigated using quantum chemical methods (density functional theory level). All calculations were performed at B3LYP/6‐31G** level of theory. The electrostatic potential charges, highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) gap, dipole moment, vibration frequencies, and electronic spectra were calculated. Log P was determined by Ghose‐Crippen method. All of the compounds under study are polar and negatively charged, which is necessary for their interaction with the receptors/enzymes. Majority of the compounds are lipophilic and they can easily diffuse through the cell membrane. The observed differences between the calculated and the experimental vibration frequencies in the Fourier Transform Infrared Spectroscopy (FTIR) spectra are established to be mainly in NH and OH bands, due to hydrogen bonds formation. The discrepancies between theoretical and experimental electronic spectra may be due to vibration effects and H‐bonding with the solvent molecules. The obtained results show that this type of spectrum is formed mainly by the xanthine fragment of the molecule, especially in the fingerprint region. All calculated properties could be useful for future qualitative‐structure activity relationship (QSAR) analysis.

New tubular host molecules, which are composed of two β-cyclodextrin macrocycles that are connected through two disulfide bonds, have been prepared by the air-promoted oxidation of 6^I,6^IV-dideoxy-6^I,6^IV-disulfanyl-β-cyclodextrin in aqueous solution. This reaction leads to three products: monomeric intramolecular disulfide and two dimeric species, which are termed as “non-eclipsed” and “eclipsed” cyclodextrin duplexes. Oxidation at a concentration of the starting thiol of 0.1 mM gave the intramolecular disulfide as the major product whereas a concentration in the millimolar range afforded the dimeric species as the dominant products. The tubular structure of the “non-eclipsed” isomer was unequivocally determined by X-ray analysis. The binding affinities of the duplexes to a wide range of compounds, including fluorescent dyes and clinically used drugs Imatinib and Esomeprazol, were studied in water by ITC. For most guest compounds, the experimentally determined K_a values were in the range 10⁷–10⁸ M⁻¹. These binding affinities are significantly higher than those found in the literature for analogous complexes with native cyclodextrins. In cases of binding of neutral or anionic guest molecules cyclodextrin duplexes outperformed cucurbiturils. A complex between a duplex and Nile blue was used to investigate its ability to penetrate the cytoplasmic membrane of HeLa cells. We found that the complex accumulated in the cell membrane but did not pass into cytosol. Importantly, the complex did not decompose to a significant extent under high dilution in the cellular environment.

Curcumin (1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5- dione) is a natural biological active substance with an antioxidant activity. The ability of curcumin to inhibit the free radical mechanisms can be used in a prevention of diseases such as cancer and coronary heart disease. The UV-VIS spectrophotometric and chemiluminescent dynamic methods for determination of antioxidant activity of curcumin were developed. The spectrophotometric method includes investigation of the interaction between DNA, isolated from HL-60 cells, and curcumin. The decreasing of the absorption of curcumin in the presence of HL-60 DNA against the blank sample can be a measurement for some complex formation between curcumin and DNA. The chemiluminescent method involves three tests for detection of luminol - depending chemiluminescence on the base of model systems which generate superoxide, hydroxide and hypochlorite radicals. The strongest decay of chemilunimescence was registered at the highest concentration of curcumin (100 ?mol/L).

Six novel 4-hydroxycoumarin derivatives were rationally synthesized, verified, and characterized by molecular docking using crystal HIV-1 protease. Molecular docking studies predicted antiprotease activity of (7) and (10). The most significant functional groups, responsible for the interaction with HIV-1 protease by hydrogen bonds formation are pyran oxygen, atom, lactone carbonyl oxygen and one of the hydroxyl groups. The newly synthesized compounds were biologically tested in MT-4 cells for inhibiting HIV-1 replication, exploring the protection of cells from the cytopathic effect of HIV measured by cell survival in MTT test. One derivative −7 showed 76–78% inhibition of virus infectivity with IC₅₀ = 0.01 nM, much less than the maximal nontoxic concentration (1 mM). Antiprotease activity of 7 in two different concentrations was detected to be 25%. Nevertheless, the results of study of (7) encourage using it as a pharmacophore for further synthesis and evaluation of anti-HIV activity.