Promising Drug Fondaparinux for the Treatment of COVID-19: an In Silico Analysis of Low Molecular Weight Heparin, Direct Oral Anticoagulant, and Antiplatelet Drug Interactions with Host Protease Furin.

PURPOSE: As of July 2022, the COVID-19 pandemic has affected over 555 million worldwide confirmed cases and caused more than 6.3 million deaths. The studies showed that the D-dimer levels were increased in non-survivors compared to survivors and heparin treatment has begun to be administered to the patients in severe clinics. As we knew that the entrance of SARS-CoV-2 to the host cell needs to be facilitated by host proteases; we published our hypothesis that heparin as a serine protease inhibitor may block the interaction between spike protein receptor-binding domain and host proteases. In our study, we aimed to investigate the interactions between not only heparins but also other antiplatelet and anticoagulant drugs including fondaparinux. METHODS: In this study, docking studies were carried out to evaluate the interactions between low molecular weight heparins (LMWHs) (enoxaparin, dalteparin, tinzaparin), direct oral anticoagulant, and antiplatelet drugs with host proteases. Molecular docking studies were performed by using Schrödinger molecular modeling software. 3D structures of the ligands were obtained from the 2D structures by assigning the OPLS-2005 force field using the Maestro 12.7. The 3D crystal structure of the furin complexed with an inhibitor, 2,5-dideoksistreptamin derivative, was extracted from the Protein Data Bank (PDB ID: 5MIM). Docking studies were carried out using the Grid-based Ligand Docking with Energetics module of the Schrödinger Software. RESULTS: The docking studies revealed that fondaparinux was the most relevant molecule to interact with furin with a docking score of - 12.74. It showed better interaction than the natural ligand of furin with an increased score compared to the docking score of - 8.155 of the natural ligand. AnaGA*IsA structure representing LMWH structure has shown a docking score of - 11.562 which was also better than the score of the natural ligand of furin. CONCLUSION: Our findings have shown that LMWHs and fondaparinux can be used for their possible antiviral effects in COVID-19 patients. Our results have shown that in accordance with heparin and LMWH, fondaparinux can also be a candidate for "drug repurposing" in COVID-19 therapy, not only because of their anticoagulant but also possible antiviral effects.

Biological activity and ADME/Tox prediction of some 2-substituted benzoxazole derivatives.

In this study, we mainly focused on some in vitro biological activities of a series of (5 or 6)-amino-2- (substituted phenyl and benzyl) benzoxazole derivatives. For this purpose, we tested cytotoxic and genotoxic activities of them on cancer cell lines and their topoisomerase inhibitory activities. We also tested their cytotoxic and genotoxic activities on non-cancerous cells (L929) and their mutagenic activities by Ames test to evaluate their effects on healthy cells. Only TD5 was found cytotoxic on all the tested cancer cell lines and did not exhibit either cytotoxic or genotoxic activities against healthy cells, whereas TD1, TD2, TD3 and TD7 were more cytotoxic against only HeLa cells. Only TD4 was found as mutagenic derivative. None of the compounds had any topoisomerase inhibitory activities nevertheless some of them caused inhibition of topoisomerase II activity. Additionally, we used an in silico model to predict the drug-like properties of them to evaluate their bioavailability to the QikProp Properties Predictions. All the calculated properties were found in a permissible range. According to the data obtained from biological activity studies, it can be concluded that the methylene bridge at the position 2 of benzoxazole ring decreases cytotoxic activity on cancer cells and inhibitory activity on DNA topoisomerases.

Discovery of 5-(or 6)-benzoxazoles and oxazolo[4,5-b]pyridines as novel candidate antitumor agents targeting hTopo IIα.

Discovery of novel anticancer drugs which have low toxicity and high activity is very significant area in anticancer drug research and development. One of the important targets for cancer treatment research is topoisomerase enzymes. In order to make a contribution to this field, we have designed and synthesized some 5(or 6)-nitro-2-(substitutedphenyl)benzoxazole (1a-1r) and 2-(substitutedphenyl)oxazolo[4,5-b]pyridine (2a-2i) derivatives as novel candidate antitumor agents targeting human DNA topoisomerase enzymes (hTopo I and hTopo IIα). Biological activity results were found very promising for the future due to two compounds, 5-nitro-2-(4-butylphenyl)benzoxazole (1i) and 2-(4-butylphenyl)oxazolo[4,5-b]pyridine (2i), that inhibited hTopo IIα with 2 µM IC50 value. These two compounds were also found to be more active than reference drug etoposide. However, 1i and 2i did not show any satisfactory cyctotoxic activity on the HeLa, WiDR, A549, and MCF7 cancer cell lines. Moreover, molecular docking and molecular dynamic simulations studies for the most active compounds were applied in order to understand the mechanism of inhibition activity of hTopo IIα. In addition, in silico ADME/Tox studies were performed to predict drug-likeness and pharmacokinetic properties of all the tested compounds.

Head-to-head bisbenzazole derivatives as antiproliferative agents: design, synthesis, in vitro activity, and SAR analysis.

In the present work, a series of bisbenzazole derivatives were designed and synthesized as antiproliferative agents. The antiproliferative activity of these compounds was investigated using MTT assay. Bisbenzazole derivatives showed significant antiproliferative activity against all the four tested cancer cell lines. Among the various bisbenzazole derivatives, bisbenzoxazole derivatives exhibited the most promising anticancer activity followed by bisbenzimidazole and bisbenzothiazole derivatives. All the derivatives were found to be less toxic as compared to methotrexate (positive control) in normal human cells, indicating selective and efficient antiproliferative activity of these bisbenzazole derivatives. The structure-activity relationships of heteroaromatic systems and linkers present in bisbenzazole derivatives were analyzed in detail. In silico ADMET prediction revealed that bisbenzazole is a drug-like small molecule with a favorable safety profile. Compound 31 is a potential antiproliferative hit compound that exhibits unique cytotoxic activity distinct from methotrexate. Twenty-one bisbenzoxazole derivatives have been designed synthesized and evaluated to be an antiproliferative activity against four human tumor cell lines.

Fenoterol and dobutamine as SARS-CoV-2 main protease inhibitors: A virtual screening study.

Global health is under heavy threat by a worldwide pandemic caused by a new type of coronavirus (COVID-19) since its rapid spread in China in 2019 [1]. Currently, there are no approved specific drugs and effective treatment for COVID-19 infection, but several available drugs are known to facilitate tentative treatment. Since drug design, development and testing procedures are time-consuming [2], [1], [2], [3], virtual screening studies with the aid of available drug databases take the initiative at this point and save the time. Besides, drug repurposing strategies promises to identify new agents for the novel diseases in a time-critical fashion. In this study, we used structure based virtual screening method on FDA approved drugs and compounds in clinical trials. As a result of this study we choose three most prominent compounds for further studies. Here we show that these three compounds (dobutamine and its two derivatives) can be considered as promising inhibitors for SARS-CoV-2 main protease and results also demonstrate the possible interactions of dobutamine and its derivatives with SARS-CoV-2 main protease (6W63) [6]. Our efforts in this work directly address current urgency of a new drug discovery against COVID-19.

In Silico Design of Novel Sirtuin 1 Enzyme Activators for the Treatment of Age-related Diseases and Life Span.

AIM: The aim of the study was to develop new SIRT1 activator compounds, for this aim, we used virtual screening and molecular dynamics methods, which have been important tools for new hit compound searches. BACKGROUND: Recently, with the progress of computing technology, it has been possible to obtain higher efficiency and lower costs for drug discovery. With in silico research and drug design, there is a reduction in time-consuming and expensive experimental work. An NAD+ dependent histone deacetylase enzyme, Sirtuin 1 (SIRT1), is involved in a variety of human disorders such as type II diabetes, cancer, obesity, and aging. Activation of SIRT1 could be useful for longevity and treating metabolic disorders. OBJECTIVE: We used computational methods to develop new SIRT1 activator compounds. METHODS: Firstly, virtual screening studies on the human SIRT1 enzyme were carried out. We used approximately 150.000 commercially available compounds from the Zinc database, which include FDA-approved drugs. According to virtual screening results, we selected seven potent activators. Then we compared these hit compounds with known activators by using docking methods. One of these hit compounds, acebutolol, is an FDA-approved drug, and was selected for additional studies using molecular dynamics simulations. RESULTS: Seven hit compounds were identified with database screening. Each showed strong interactions with SIRT1, and acebutolol formed H-bonds with the important active site residues, Asn226 and/or Glu230 during the dynamics simulation. CONCLUSION: Based on our in silico studies, the seven most promising compounds, especially acebutolol, showed promising SIRT1 activator potency. The results may be used to design new selective and more potent SIRT1 activator drugs.

Towards a Better Understanding of Computational Models for Predicting DNA Methylation Effects at the Molecular Level.

Human DNA is a very sensitive macromolecule and slight changes in the structure of DNA can have disastrous effects on the organism. When nucleotides are modified, or changed, the resulting DNA sequence can lose its information, if it is part of a gene, or it can become a problem for replication and repair. Human cells can regulate themselves by using a process known as DNA methylation. This methylation is vitally important in cell differentiation and expression of genes. When the methylation is uncontrolled, however, or does not occur in the right place, serious pathophysiological consequences may result. Excess methylation causes changes in the conformation of the DNA double helix. The secondary structure of DNA is highly dependent upon the sequence. Therefore, if the sequence changes slightly the secondary structure can change as well. These slight changes will then cause the doublestranded DNA to be more open and available in some places where large adductions can come in and react with the DNA base pairs. Computer models have been used to simulate a variety of biological processes including protein function and binding, and there is a growing body of evidence that in silico methods can shed light on DNA methylation. Understanding the anomeric effect that contributes to the structural and conformational flexibility of furanose rings through a combination of quantum mechanical and experimental studies is critical for successful molecular dynamic simulations.

Synthesis and molecular docking studies of some novel antimicrobial benzamides.

Common use of classical antibiotics has caused to the growing emergence of many resistant strains of pathogenic bacteria. Therefore, we aimed to synthesize a number of N-(2-hydroxy-(4 or 5)-nitrophenyl)benzamide derivatives as a new class of antimicrobial compounds. Moreover, our second goal is to predict the interaction between active structures and enzymes (DNA -gyrase and FtsA) in the binding mode. In this study, thirteen N-(2-hydroxy-(4 or 5-nitrophenyl)-substituted-benzamides were synthesized and determined for their antimicrobial activity using the microdilution method. According to this work, none of the compounds showed any activity against Candida albicans and its clinical isolate. Some of the benzamides (4N1, 5N1, 5N2) displayed very significant activity against Staphylococcus aureus and MSSA with <4 µg/ml MIC value, even they were found to be more potent than ceftazidime. 4N1 was also found to be more effective than gentamicin against Enterococcus faecalis clinical isolate. Molecular docking studies revealed that 4N1, 5N1, and 5N2 showed a good interactions with DNA-gyrase. Moreover, 5N1 has interacted with FtsA enzyme in the binding mode, as well. Only compound 5N4 displayed very good activity against Escherichia coli ATCC 25922. These findings showed us that 4N1, 5N1, 5N2, and 5N4 could be lead compounds to discover new antibacterial candidates against multidrug-resistant strains.

4-Thiazolidinone Derivatives as MMP Inhibitors in Tissue Damage: Synthesis, Biological Evaluation and Docking Studies.

Nine 2-(1,2-benzothiazol-3-yl)-N-(4-oxo-2-phenyl-1,3-thiazolidin-3-yl)propanamides combining a benzisothiazole and 4-thiazolidinone in one framework were designed and synthesized. The aim of the study was to verify their effectiveness to affect the inflammatory/oxidative process in which free oxygen and nitrite (ROS and RNS) radicals, inflammatory mediators, such as nuclear factor κB (NF-κB), and matrix metalloproteinases (MMPs) are involved. Docking studies of all the compounds were performed in order to explore their binding mode at the MMP-9 protein. An appreciable anti-inflammatory/potential wound healing effects of the tested compounds was highlighted. Derivative 23, bearing a 4-carboxyphenyl substituent at C2 of the 4-thiazolidinone ring, exhibited the highest activity, being able to inhibit MMP-9 at nanomolar level(IC50 = 40 nM).

Biological evaluation and pharmacophore modeling of some benzoxazoles and their possible metabolites.

A series of benzoxazole derivatives and some possible primary metabolites were evaluated as anticancer agents. In vitro anti-proliferative activities of the compounds were tested using the SRB assay on cancerous (HeLa) and non-cancerous (L929) cell lines. It was found that 17 of 21 tested compounds had cytotoxic activity on HeLa cells and the cytotoxic activities of the compounds were 15-700 times higher than on L929 cells. We generated two distinct pharmacophore models for the cytotoxic activities of the compounds on HeLa and L929 cells. While active compounds such as camptothecin and X8 fitted the two models generated for both cell lines, selective cytotoxic compounds such as XT3B fitted only the model generated for HeLa cells. Evaluation of the genotoxic activities of the cytotoxic compounds with the alkaline comet assay revealed that compounds X17 and XT3 showed strong genotoxic effects against HeLa cells at low concentrations whereas they had no genotoxic effect on L929 cells. Due to the selective ability for inducing DNA strand breaks only on cancerous cells, the compounds were identified as effective derivatives for anticancer candidates.

Determination of the Apoptotic Effect and Molecular Docking of Benzamide Derivative XT5 in K562 Cells.

BACKGROUND: The tyrosine kinase inhibitor, imatinib, used as a first line treatment in Chronic Myeloid Leukemia (CML) patients, may lead to resistance and failure to therapy. Novel combinations of imatinib with other drugs is a strategy to improve treatment efficiency. OBJECTIVE: In this study, the antileukemic and apoptotic effects of a benzamide derivative XT5 and benzoxazole derivative XT2B and their combination with imatinib were investigated in imatinib-sensitive (K562S) and imatinib-resistant (K562R) CML cells. METHODS: In vitro cytotoxicity was determined by MTT assay. Then, apoptotic effect of XT5 on CML cell lines was tested by Annexin V flow cytometry, caspase activation and RT-PCR. Docking calculation was performed using AutoDock Vina in PyMOL environment using AutoDock/Vina plugin for PyMOL. RESULTS: According to our MTT assay data, XT5 indicated significant antiproliferative effect on cell lines, therefore we investigated apoptotic effects of XT5. Treatment of K562 cell lines with a combination of XT5 and imatinib-XT5 increased cytotoxicity, the Annexin V binding and caspase 3/7 activation. In addition to apoptosis assays, we observed an increase in the expression levels of the pro-apoptotic (BAX, BAD and BIM) genes in XT5 treated K562R and K562S cells. Molecular modelling experiments showed that XT5 showed hydrogenbonding interactions with important amino acids of BCR-ABL kinase receptor; however XT2B did not show any hydrogen bond interaction. CONCLUSION: Our results indicate that XT5 could be a potential candidate to be used as a new anticancer drug and XT5 combination with imatinib as an alternate treatment strategy for overcoming imatinib resistance.

Design and synthesis of 2-substituted-5-(4-trifluoromethylphenyl-sulphonamido)benzoxazole derivatives as human GST P1-1 inhibitors.

The glutathione transferases (GSTs) are a family of widely distributed Phase II detoxification enzymes. GST P1-1 is frequently overexpressed in rat and human tumours. It is suggested that overexpression of hGST P1-1 by human tumor cells may play a role in resistance to cancer chemotherapy. Hence, hGST P1-1 can be a promising target for cancer treatment. In this study, new hGST P1-1 inhibitors, 2-(4-substitutedphenyl/benzyl)-5-(4-trifluoromethylphenylsulphonamido) benzoxazole derivatives (Va-Vk) have been designed and synthesized. Surprisingly, in vitro hGST P1-1 enzyme inhibition studies demonstrated that all of the tested compounds except Vj had better activity than the reference drug EA and it is also correlated with the docking results. Additionally we compared the interactions with hGST P1-1 enzyme of newly synthesized compound Vh (bearing CF3 group) and previously synthesized compound 5f (bearing NO2 group). According to the docking results, compound Vh bound to the hGST P1-1 enzyme with a higher affinity compared to 5f. Therefore, we can consider that these data make a sense and can explain its higher activity. The compounds that obtained from this research could be used as scaffolds in design of new potent hGST P1-1 inhibitors useful in the treatment of the resistance of cancer chemotherapy.

Antitumor activities on HL-60 human leukemia cell line, molecular docking, and quantum-chemical calculations of some sulfonamide-benzoxazoles.

We previously synthesized some novel benzoxazole derivatives-containing sulfonamide. In this study, the compounds were investigated for their antitumor activities against the HL-60 human leukemia cells, using the MTT assay. Moreover, quantum chemical calculations using the DFT methods were applied for understanding the difference in antitumor activity. Additionally, molecular docking into active site of the DNA Topo II enzyme was performed on 3QX3. PDB file in order to find out possible mechanism of antitumor effect. According to all obtained results showed that compounds 1b, 1c, and 1d could be potential drug candidates as new antitumor agents, and are promising for cancer therapy.

Generated 3D-common feature hypotheses using the HipHop method for developing new topoisomerase I inhibitors.

The continued interest in designing novel topoisomerase I (Topo I) inhibitors and the lack of adequate ligand-based computer-aided drug discovery efforts combined with the drawbacks of structure-based design prompted us to explore the possibility of developing ligand-based three-dimensional (3D) pharmacophore(s). This approach avoids the pitfalls of structure-based techniques because it only focuses on common features among known ligands; furthermore, the pharmacophore model can be used as 3D search queries to discover new Topo I inhibitory scaffolds. In this article, we employed the HipHop module using Discovery Studio to construct plausible binding hypotheses for clinically used Topo I inhibitors, such as camptothecin, topotecan, belotecan, and SN-38, which is an active metabolite of irinotecan. The docked pose of topotecan was selected as a reference compound. The first hypothesis (Hypo 01) among the obtained 10 hypotheses was chosen for further analysis. Hypo 01 had six features, which were two hydrogen-bond acceptors, one hydrogen-bond donor, one hydrophob aromatic and one hydrophob aliphatic, and one ring aromatic. Our obtained hypothesis was checked by using some of the aromathecin derivatives which were published for their Topo I inhibitory potency. Moreover, five structures were found to be possible anti-Topo I compounds from the DruglikeDiverse database. From this research, it can be suggested that our model could be useful for further studies in order to design new potent Topo I-targeting antitumor drugs.

Synthesis and biological evaluation of 2-substituted-5-(4-nitrophenylsulfonamido)benzoxazoles as human GST P1-1 inhibitors, and description of the binding site features.

Glutathione-S-transferases (GSTs) are enzymes involved in cellular detoxification by catalyzing the nucleophilic attack of glutathione (GSH) on the electrophilic center of numerous of toxic compounds and xenobiotics, including chemotherapeutic drugs. Human GST P1-1, which is known as the most prevalent isoform of the mammalian cytosolic GSTs, is overexpressed in many cancers and contributes to multidrug resistance by directly conjugating to chemotherapeutics. It is suggested that this resistance is related to the high expression of GST P1-1 in cancers, thereby contributing to resistance to chemotherapy. In addition, GSTs exhibit sulfonamidase activity, thereby catalyzing the GSH-mediated hydrolysis of sulfonamide bonds. Such reactions are of interest as potential tumor-directed prodrug activation strategies. Herein we report the design and synthesis of some novel sulfonamide-containing benzoxazoles, which are able to inhibit human GST P1-1. Among the tested compounds, 2-(4-chlorobenzyl)-5-(4-nitrophenylsulfonamido)benzoxazole (5 f) was found as the most active hGST P1-1 inhibitor, with an IC50 value of 10.2 µM, showing potency similar to that of the reference drug ethacrynic acid. Molecular docking studies performed with CDocker revealed that the newly synthesized 2-substituted-5-(4-nitrophenylsulfonamido)benzoxazoles act as catalytic inhibitors of hGST P1-1 by binding to the H-site and generating conjugates with GSH to form S-(4-nitrophenyl)GSH (GS-BN complex) via nucleophilic aromatic substitution reaction. The 4-nitrobenzenesulfonamido moiety at position 5 of the benzoxazole ring is essential for binding to the H-site and for the formation of the GST-mediated GSH conjugate.

IR, Raman and SERS spectra of 2-phenoxymethylbenzothiazole.

The FT-IR and FT-Raman spectra of 2-phenoxymethylbenzothiazole were recorded and analyzed. The surface enhanced Raman scattering (SERS) spectrum was recorded in a silver colloid. The vibrational wavenumbers of the compound have been computed using the Hartree-Fock/6-31G* basis and compared with the experimental values. The appearance of the Ag-O stretching mode at 237cm(-1) in the SERS spectrum along with theoretically calculated atomic charge density, leads us to suggest that the molecule is adsorbed through the oxygen atom with the molecular plane tilted on the colloidal silver surface. The direction of charge transfer contribution to SERS has been discussed from the frontier orbital theory.