Milan Senćanski

Zn(II) complex with 2-quinolinecarboxaldehyde selenosemicarbazone: synthesis, structure, interaction studies with DNA/HSA, molecular docking and caspase-8 and -9 independent apoptose induction

A new Zn(II)-based potential chemotherapeutic agent was synthesized from the ligand 2-quinolinecarboxaldehyde selenosemicarbazone (Hqasesc). Single crystal X-ray diffraction analysis showed that the Zn(II) complex consists of a cation [Zn(Hqasesc)2]2+, two perchlorate anions and one ethanol solvent molecule. The interaction of calf thymus (CT) DNA and human serum albumin (HSA) with the Zn(II) complex was explored using absorption and emission spectral methods, and also has been supported by molecular docking studies. The complex has more affinity to minor DNA groove than major, with no significant intercalation. The HSA interaction studies of the complex revealed the quenching of the intrinsic fluorescence of the HSA through a static quenching mechanism. The antitumor activity of the ligand and the complex against pancreatic adenocarcinoma cell line (AsPC-1) and acute monocytic leukemia (THP-1) cells was evaluated. Both compounds are strong concentration-dependent apoptosis inducers in THP-1 cells. While Hqasesc in AsPC-1 cells induces apoptosis only at the highest concentration, treatment with the Zn complex shows a concentration-dependent apoptotic response, where the treated cells are arrested in the G1-to-S phase accompanied with extensive activation of caspase-8 and -9. These results indicate that the ligand and Zn(II) complex display cell phenotype specific activity.

In silico analysis suggests interaction between Ebola virus and the extracellular matrix.

The worst Ebola virus (EV) outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trend lines in this crisis are grave, and now represents a global public health threat concern. Limited therapeutic and/or prophylactic options are available for people suffering from Ebola virus disease (EVD) and further complicate the situation. Previous studies suggested that the EV glycoprotein (GP) is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM) was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs) are involved in interaction between GP and ECM. This finding could contribute to a better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.

Arginase Flavonoid Anti-Leishmanial in Silico Inhibitors Flagged against Anti-Targets

Arginase, a drug target for the treatment of leishmaniasis, is involved in the biosynthesis of polyamines. Flavonoids are interesting natural compounds found in many foods and some of them may inhibit this enzyme. The MetIDB database containing 5667 compounds was screened using an EIIP/AQVN filter and 3D QSAR to find the most promising candidate compounds. In addition, these top hits were screened in silico versus human arginase and an anti-target battery consisting of cytochromes P450 2a6, 2c9, 3a4, sulfotransferase, and the pregnane-X-receptor in order to flag their possible interactions with these proteins involved in the metabolism of substances. The resulting compounds may have promise to be further developed for the treatment of leishmaniasis.

Theoretical insight into sulfur–aromatic interactions with extension to D2 receptor activation mechanism

Contacts between aromatic rings and sulfur-containing amino acids are frequent in proteins. However, little is known about the nature of their interactions particularly if substituents are present on aromatic ring. In this paper, DFT quantum chemical calculations were used to study substituted benzenes in complex with hydrogen sulfide (H2S), methanethiol (CH3SH), and (Methylsulfanyl)methane (CH3SCH3). It was found that SH···π interaction is more stabilizing than the S···π interaction in the case of benzene, but this is changed with increasing electronegativity of the substituent on benzene ring. Although the change of energy of SH···π and S···π interaction follows the conventional model of substituent effect, where S···π interactions are maximized and SH···π interactions are diminished with electron-withdrawing substituent on benzene as a result of changes in the aryl π-system, it was found that it is mainly a consequence of direct electrostatic interaction between substituent and the sulfur-containing molecule. We also investigated the model system of Cys···Trp interaction, adjacent to a cluster of aromatic amino acids, in proteins, using explicit membrane molecular dynamics simulations results of D3 dopamine receptor crystal structure as starting point. It was found that fluorination in aromatic cluster enhances the Cys···Trp interaction. The effect is maximized when transferred through the rest of aromatic system suggesting possible explanation for frequent contacts between sulfur-containing and aromatic amino acids in proteins and their effects on protein folding and stabilization.

Molecular Modeling of 5HT2A Receptor – Arylpiperazine Ligands Interactions

In this paper, we report the molecular modeling of the 5HT2A receptor and the molecular docking of arylpiperazine‐like ligands. The focus of the research was on explaining the effects the ligand structure has on the binding properties of the 5HT2A receptor and on the key interactions between the ligands and the receptor‐binding site. To see what the receptor–ligand interactions were, various substituents were introduced in one part of the ligand, keeping the rest unchanged. In this way, using a docking analysis on the proposed 5HT2A receptor model, we identified key receptor–ligand interactions and determined their properties. Those properties were correlated with experimentally determined binding affinities in order to determine the structure to activity relationship of the examined compounds.

Ni(II) complex with bishydrazone ligand: synthesis, characterization, DNA binding studies and pro-apoptotic and pro-differentiation induction in human cancerous cell lines

A new Ni(II) complex, [Ni(L)(H2O)] (1), with diethyl 3,3′-(2,2′-(1,1′-(pyridine-2,6-diyl)bis(ethan-1-yl-1-ylidene))bis(hydrazin-1-yl-2-ylidene))bis(3-oxopropanoate) ligand (H2L) was synthesized as a potential chemotherapeutic agent. Polidentate ligand was coordinated to Ni(II) NNN-tridentately, in dianionic form, while monodentate water coordination completed square-planar geometry around metal. Structure in the solution was determined by NMR spectroscopy and the same coordination mode was observed in the solid state using IR spectroscopy and further verified by DFT calculations and electrochemical studies. Thermal stability of 1 was determined in both air and nitrogen atmosphere. Anticancer activity of 1 was investigated on acute monocytic leukemia (THP-1) and pancreatic adenocarcinoma (AsPC-1) cell lines. On THP-1 cells 1 induced powerful apoptotic response (ED50 = 10 ± 3 μM), which was revealed to be only partially caspase-dependent, with activation of caspase-8 as the dominant course. This suggested that experimentally validated covalent binding of 1 to DNA is not the only mechanism responsible for programmed cell death. This was supported with experiments on AsPC-1 cells. Although treatment of those cells with 1 resulted in poor apoptotic response, cell cycle changes showed concentration-dependent shifts indicating a dual mechanism of activity. This study also reviews the results of preliminary biological screening, which demonstrates that 1 displays a unique pattern of anticancer activity with at least two mechanisms involved.

Pro-apoptotic and pro-differentiation induction by 8-quinolinecarboxaldehyde selenosemicarbazone and its Co(III) complex in human cancer cell lines

8-Quinolinecarboxaldehyde selenosemicarbazone (H8qasesc) and its octahedral Co(III) complex were characterized by single crystal X-ray diffraction analysis, spectroscopy methods and cyclic voltammetry. The antineoplastic activity of the ligand and the complex has been assessed on an acute monocytic leukemia cell line (THP-1) and AsPC-1 cancer stem cell (CSC) line derived from a patient suffering from pancreatic adenocarcinoma, with cisplatin (CDDP) as a reference compound. Evaluation involved determination of pro-apoptotic activity, changes in cell cycle distribution, the role of caspase activation in the process of cell death, and the ability of the investigated compounds to challenge reprogramming of the CSC phenotype. Compared to CDDP, treatment with H8qasesc induced a higher apoptotic response in both investigated cell lines. Apoptosis triggered by H8qasesc was highly caspase-dependent but did not include activation of either caspase-8 or -9. According to cell cycle changes H8qasesc delayed the transition of cells during DNA replication but in a manner different from that of CDDP. The ligand did not show nuclease activity on pUC19 plasmid, while docking studies disclosed that it does not have intercalating properties. Treatment of THP-1 cells with the Co(III) complex resulted in a strong toxic response, whereas cell death in the treated AsPC-1 line was not achieved for 24 h. Additionally, the complex concentration-dependently digested plasmid DNA which might be the cause of its cytotoxic activity. Finally, H8qasesc successfully initiated reprogramming of the CSC phenotype in the AsPC-1 cell line.

In silico analysis suggests repurposing of ibuprofen for prevention and treatment of EBOLA virus disease

The large 2014/2015 Ebola virus outbreak in West Africa points out the urgent need to develop new preventive and therapeutic approaches that are effective against Ebola viruses and can be rapidly utilized. Recently, a simple theoretical criterion for the virtual screening of molecular libraries for candidate inhibitors of Ebola virus infection was proposed. Using this method the ‘drug space’ was screened and 267 approved and 382 experimental drugs as candidates for treatment of the Ebola virus disease (EVD) have been selected. Detailed analysis of these drugs revealed the non-steroidal anti-inflammatory drug ibuprofen as an inexpensive, widely accessible and minimally toxic candidate for prevention and treatment of EVD. Furthermore, the molecular mechanism underlying this possible protective effect of ibuprofen against EVD is suggested in this article.

In Silico Study of the Structurally Similar ORL1 Receptor Agonist and Antagonist Pairs Reveal Possible Mechanism of Receptor Activation

Abstract An opioid receptor like (ORL1) receptor is a member of a family of G-protein coupled receptors. It is a new pharmaceutical target with broad therapeutic potential in the regulation of important biological functions such as nociception, mood disorders, drug abuse, learning or cardiovascular control. The crystal structure of this receptor in complex with an antagonist was determined recently (PDB ID: 4EA3). By removing the ligand and subjecting the empty receptor to molecular dynamics simulation in a solvated lipid membrane we obtained an optimized ORL1 receptor structure which could be used in a subsequent docking study of two structurally similar agonist–antagonist ligand pairs. Ligands were docked to the empty ORL1 receptor (with and without the third intracellular loop, IC3) in different orientations, and the resulting complexes were monitored during molecular dynamics simulation in order to see how the subtle differences in structure of agonists and antagonists might affect ligand–receptor interactions and trigger receptor activation. It was established that agonists and antagonists bound to the same, relatively large, binding site in the receptor, created by residues from transmembrane helices TM2, TM3, TM5, TM6 and TM7 and close to the extra cellular end of the receptor bundle. The key difference between these two types of ligands is interaction with residue Val2836.55 and a flexibility of ligand molecules. Ligands that cannot easily avoid this interaction will initiate movement of the intracellular end of TM6 (by a mechanism which involves Met1343.36 and several aminoacids of TM5) and possibly activate the receptor when assisted by G-protein.

In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum

There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite’s respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1–UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum. The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.