Comparison of clinically approved molecules on SARS-CoV-2 drug target proteins: a molecular docking study

The new type of coronavirus, SARS-CoV-2 has affected more than 22.6 million people worldwide. Since the first day the virus was spotted in Wuhan, China, numerous drug design studies have been conducted all over the globe. Most of these studies target the receptor-binding domain of spike protein of SARS-CoV-2, which is known to bind to the human ACE2 receptor and SARS-CoV-2 main protease, vital for the virus’ replication. However, there might be a third target, human furin protease, which cleaves the virus’ S1-S2 domains playing an active role in its entry into the host cell. In this study, we docked five clinically used drug molecules, favipiravir, hydroxychloroquine, remdesivir, lopinavir, and ritonavir onto three target proteins, the receptor-binding domain of SARS-CoV-2 spike protein, SARS-CoV-2 main protease, and human furin protease. Results of molecular docking simulations revealed that human furin protease might be targeted by COVID-19. Remdesivir, a nucleic acid derivative, strongly bound to the active site of this protease, suggesting that this molecule can be used as a template for designing novel furin protease inhibitors to fight against the disease. Protein-drug interactions revealed in this study at the molecular level, can pave the way for better drug design for each specific target.     

In silico exploration of binding potentials of anti SARS-CoV-1 phytochemicals against main protease of SARS-CoV-2

The phytochemicals can play complementary medicine compared to synthetic drugs considering their natural origin, safety, and low cost. Phytochemicals hold a key position for the expansion of drug development against corona viruses and need better consideration to the agents that have already been shown to display effective activity against various strains of corona viruses. In this study, we performed molecular docking studies on potential forty seven phytochemicals which are SARS-CoV-1 M^pro inhibitors to identify potential candidate against the main proteins of SARS-CoV-2. In Silico Molecular docking studies revealed that phytochemicals 16 (Broussoflavan A), 22 (Dieckol), 31 (Hygromycin B), 45 (Sinigrin) and 46 (Theaflavin-3,3′-digallate) exhibited excellent SARS-CoV-2 M^pro inhibitors. Furthermore, supported by Molecular dynamics (MD) simulation analysis such as Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of gyration (Rg) and H-bond interaction analysis. We expect that our findings will provide designing principles for new corona virus strains and establish important frameworks for the future development of antiviral drugs.     

Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particular importance. A critical antiviral target is the SARS-CoV-2 main protease (M^pro), and our aim was to identify lead compounds with potential inhibitory effects. We performed an initial molecular docking screen of 300 small molecules, which included phenolic compounds and fatty acids from our OliveNet™ library (224), and an additional group of curated pharmacological and dietary compounds. The prototypical α-ketoamide 13b inhibitor was used as a control to guide selection of the top 30 compounds with respect to binding affinity to the M^pro active site. Further studies and analyses including blind docking were performed to identify hypericin, cyanidin-3-O-glucoside and SRT2104 as potential leads. Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M^pro active site. An enzyme-linked immunosorbent assay indicated that, albeit, not as potent as the covalent positive control (GC376), our leads inhibited the M^pro with activity in the micromolar range, and an order of effectiveness of hypericin and cyanidin-3-O-glucoside > SRT2104 > SRT1720. Overall, our findings, and those highlighted by others indicate that hypericin and cyanidin-3-O-glucoside are suitable candidates for progress to in vitro and in vivo antiviral studies.     

Isoelectric point determination by imaged CIEF of commercially available SARS-CoV-2 proteins and the hACE2 receptor

In order to contribute to the scientific research on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we have investigated the isoelectric points (pI) of several related proteins, which are commercially available: the receptor-binding domain (RBD) with His- and Fc-tag, the S1 subunit with His-tag, the S1/S2 subunits with His-tag and the human angiotensin-converting enzyme 2 (hACE2) with His-tag. First, the theoretical pI values, based on the amino acid (AA) sequences of the proteins, were calculated using the ProtParam tool from the Bioinformatics Resource Portal ExPASy. The proteins were then measured with the Maurice imaged CIEF system (native fluorescence detection), testing various measurement conditions, such as different ampholytes or ampholyte mixtures. Due to isoforms, we get sections with several peaks and not just one peak for each protein. The determined pI range for the RBD/Fc is 8.24–9.32 (theoretical pI: 8.55), for the RBD/His it is 7.36–9.88 (8.91) and for the S1/His it is 7.30–8.37 (7.80). The pI range of the S1/S2/His is 4.41–5.87 (no theoretical pI, AA sequence unknown) and for hACE2/His, the determined global range is 5.19–6.11 (5.60) for all experimental conditions chosen. All theoretically derived values were found within these ranges, usually close to the center. Therefore, we consider theoretical values as useful to make predictions about the isoelectric points of SARS-CoV-2 proteins. The experimental conditions had only a minor influence on the pI ranges obtained and mainly influenced the peak shapes.     

New N1-(4-aryloxybenzyl)uracils containing N3-positioned 4-(trimethyleneoxy)benzoic acid moiety,and study of their antiviral activity against SARS-CoV-2 and influenza virus

New title uracil derivatives, 4-{3-[2,6-dioxo-3-(4-aryl-oxybenzyl)-3,6-dihydropyrimidin-1(2H)-yl]propoxy}benzoic acids and their butoxy homologues, were obtained in three steps using 2,4-bis(trimethylsilyloxy)pyrimidine, 4-aryloxy-benzyl bromides and methyl 4-(ω-bromoalkoxy)benzoates as the key reactants. The compounds were studied as inhibitors of H1N1 influenza virus and SARS-CoV-2 R replication in MDCK and Vero E6 cell cultures, respectively, which revealed that the tested compounds had high levels of anti-SARS-CoV-2 activity.     

Native Structure-Based Peptides as Potential Protein–Protein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a positive-strand RNA virus that causes severe respiratory syndrome in humans, which is now referred to as coronavirus disease 2019 (COVID-19). Since December 2019, the new pathogen has rapidly spread globally, with over 65 million cases reported to the beginning of December 2020, including over 1.5 million deaths. Unfortunately, currently, there is no specific and effective treatment for COVID-19. As SARS-CoV-2 relies on its spike proteins (S) to bind to a host cell-surface receptor angiotensin-converting enzyme-2(ACE2), and this interaction is proved to be responsible for entering a virus into host cells, it makes an ideal target for antiviral drug development. In this work, we design three very short peptides based on the ACE2 sequence/structure fragments, which may effectively bind to the receptor-binding domain (RBD) of S protein and may, in turn, disrupt the important virus-host protein–protein interactions, blocking early steps of SARS-CoV-2 infection. Two of our peptides bind to virus protein with affinity in nanomolar range, and as very short peptides have great potential for drug development.     

Identification of SARS-CoV-2 Receptor Binding Inhibitors by In Vitro Screening of Drug Libraries

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global pandemic. The first step of viral infection is cell attachment, which is mediated by the binding of the SARS-CoV-2 receptor binding domain (RBD), part of the virus spike protein, to human angiotensin-converting enzyme 2 (ACE2). Therefore, drug repurposing to discover RBD-ACE2 binding inhibitors may provide a rapid and safe approach for COVID-19 therapy. Here, we describe the development of an in vitro RBD-ACE2 binding assay and its application to identify inhibitors of the interaction of the SARS-CoV-2 RBD to ACE2 by the high-throughput screening of two compound libraries (LOPAC^®1280 and DiscoveryProbeTM). Three compounds, heparin sodium, aurintricarboxylic acid (ATA), and ellagic acid, were found to exert an effective binding inhibition, with IC50 values ranging from 0.6 to 5.5 µg/mL. A plaque reduction assay in Vero E6 cells infected with a SARS-CoV-2 surrogate virus confirmed the inhibition efficacy of heparin sodium and ATA. Molecular docking analysis located potential binding sites of these compounds in the RBD. In light of these findings, the screening system described herein can be applied to other drug libraries to discover potent SARS-CoV-2 inhibitors.     

Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin,mutational spectrum and possible pathomechanism

As the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), rages across the world, killing hundreds of thousands and infecting millions, researchers are racing against time to elucidate the viral genome. Some Bangladeshi institutes are also in this race, sequenced a few isolates of the virus collected from Bangladesh. Here, we present a genomic analysis of these isolates. The analysis revealed that SARS-CoV-2 isolates sequenced from Dhaka and Chittagong were the lineage of Europe and India, respectively. Our analysis identified a total of 42 mutations, including three large deletions, half of which were synonymous. Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant difference was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh.     

Impact of TMPRSS2 Expression,Mutation Prognostics,and Small Molecule (CD,AD, TQ,and TQFL12) Inhibition on Pan-Cancer Tumors and Susceptibility to SARS-CoV-2

As a cellular protease, transmembrane serine protease 2 (TMPRSS2) plays roles in various physiological and pathological processes, including cancer and viral entry, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, we conducted expression, mutation, and prognostic analyses for the TMPRSS2 gene in pan-cancers as well as in COVID-19-infected lung tissues. The results indicate that TMPRSS2 expression was highest in prostate cancer. A high expression of TMPRSS2 was significantly associated with a short overall survival in breast invasive carcinoma (BRCA), sarcoma (SARC), and uveal melanoma (UVM), while a low expression of TMPRSS2 was significantly associated with a short overall survival in lung adenocarcinoma (LUAD), demonstrating TMPRSS2 roles in cancer patient susceptibility and severity. Additionally, TMPRSS2 expression in COVID-19-infected lung tissues was significantly reduced compared to healthy lung tissues, indicating that a low TMPRSS2 expression may result in COVID-19 severity and death. Importantly, TMPRSS2 mutation frequency was significantly higher in prostate adenocarcinoma (PRAD), and the mutant TMPRSS2 pan-cancer group was significantly associated with long overall, progression-free, disease-specific, and disease-free survival rates compared to the wild-type (WT) TMPRSS2 pan-cancer group, demonstrating loss of functional roles due to mutation. Cancer cell lines were treated with small molecules, including cordycepin (CD), adenosine (AD), thymoquinone (TQ), and TQFL12, to mediate TMPRSS2 expression. Notably, CD, AD, TQ, and TQFL12 inhibited TMPRSS2 expression in cancer cell lines, including the PC3 prostate cancer cell line, implying a therapeutic role for preventing COVID-19 in cancer patients. Together, these findings are the first to demonstrate that small molecules, such as CD, AD, TQ, and TQFL12, inhibit TMPRSS2 expression, providing novel therapeutic strategies for preventing COVID-19 and cancers.     

Ligand and Structure-Based In Silico Determination of the Most Promising SARS-CoV-2 nsp16-nsp10 2′-o-Methyltransferase Complex Inhibitors among 3009 FDA Approved Drugs

As a continuation of our earlier work against SARS-CoV-2, seven FDA-approved drugs were designated as the best SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (2′OMTase) inhibitors through 3009 compounds. The in silico inhibitory potential of the examined compounds against SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (PDB ID: (6W4H) was conducted through a multi-step screening approach. At the beginning, molecular fingerprints experiment with SAM (S-Adenosylmethionine), the co-crystallized ligand of the targeted enzyme, unveiled the resemblance of 147 drugs. Then, a structural similarity experiment recommended 26 compounds. Therefore, the 26 compounds were docked against 2′OMTase to reveal the potential inhibitory effect of seven promising compounds (Protirelin, (1187), Calcium folinate (1913), Raltegravir (1995), Regadenoson (2176), Ertapenem (2396), Methylergometrine (2532), and Thiamine pyrophosphate hydrochloride (2612)). Out of the docked ligands, Ertapenem (2396) showed an ideal binding mode like that of the co-crystallized ligand (SAM). It occupied all sub-pockets of the active site and bound the crucial amino acids. Accordingly, some MD simulation experiments (RMSD, RMSF, R_g, SASA, and H-bonding) have been conducted for the 2′OMTase—Ertapenem complex over 100 ns. The performed MD experiments verified the correct binding mode of Ertapenem against 2′OMTase exhibiting low energy and optimal dynamics. Finally, MM-PBSA studies indicated that Ertapenem bonded advantageously to the targeted protein with a free energy value of −43 KJ/mol. Furthermore, the binding free energy analysis revealed the essential amino acids of 2′OMTase that served positively to the binding. The achieved results bring hope to find a treatment for COVID-19 via in vitro and in vivo studies for the pointed compounds.     

Synthesis of indole-based oxadiazoles and their interaction with bacterial peptidoglycan and SARS-CoV-2 main protease: In vitro,molecular docking and in silico ADME/Tox study

In the present study, Indole-based-oxadiazole (1A-17A) compounds were successfully synthesized. The structures of all synthesized compounds were fully characterized by different sophisticated spectroscopic techniques such 1H NMR, 13C NMR, and HREI-MS. Further, the synthesized compounds were explored to investigate their broad-spectrum antibacterial and antibiofilm potential against multidrug resistant Pseudomonas aeruginosa (MDR-PA) and methicillin resistant Staphylococcus aureus (MRSA). The compounds possessed a broad spectrum of antibacterial activity having MIC values of values 1–8 mg/ml against the tested microorganisms. Compound A6 and A7 shows maximum antibacterial activity against MDR-PA, whereas A6, A7 and A11 shows highest activity against MRSA. Furthermore, antibiofilm assay shows that A6, A7 and A11 showed maximum inhibition of biofilm formation and it was found that at 4 mg/ml; A6, A7 and A11 inhibit MRSA biofilm formation by 81.1, 77.5 and 75.9%, respectively; whereas in case of P. aeruginosa; A6 and A7 showed maximum biofilm inhibition and inhibit biofilm formation by 81.5 and 73.7%, respectively. Molecular docking study showed that compounds A6, A7, A8, A10, and A11 had high binding affinity to bacterial peptidoglycan, indicating their potential inhibitory activity against tested bacteria, whereas A6 and A11 were found to be the most effective inhibitors of SARS CoV-2 main protease (3CLpro), with a binding affinity of ? 7.78 kcal/mol. Furthermore, SwissADME and pkCSM-pharmacokinetics online tools was applied to calculate the ADME/Tox profile of the synthesized compounds and the toxicity of these chemicals was found to be low. The Lipinski, Veber, Ghose, and Consensus LogP criteria were also used to predict drug-likeness levels of the compounds. Our findings imply that the synthesized compounds could be a useful for the preventing and treating biofilm-related microbial infection as well as SARS-CoV2 infections.     

In vitro corrosion study of different TiO2 nanotube layers on titanium in solution with serum proteins

Titanium oxide nanotubes prepared by anodization have received considerable attention in the biomaterials domain. The objective of this study was to demonstrate the electrochemical behavior of different diameter TiO(2) nanotube layers on titanium in phosphate buffered saline (PBS) and Dulbecco's minimum essential medium+10% fetal calf serum (D-FCS) using open circuit potentials (OCP), electrical impedance spectroscopy (EIS), and a potentiodynamic polarization test. The results showed that the nanotubes had higher OCP, higher resistance of the inter barrier layer (R(b)), and lower I(pass) in the two test solutions compared to the smooth Ti, especially the 30 nm diameter nanotubes. The corrosion resistance of the nanotubes in D-FCS was higher than in PBS because of protein adsorption from the D-FCS solution as suggested by scanning electron microscope (SEM) images. In addition, protein aggregates of 30 nm diameter nanotubes caused the model of EIS spectra to transform from two-layer to three-layer. The corrosion behavior of the nanotubes for use as a dental implant material is discussed.     

Synthesis of functional derivatives of 2-methylenecyclopentane and 2-methylenecyclohexane based on the allylborylation of imines,nitriles, isocyanates,and isothiocyanates by cycloalkenylmethyl(dipropyl)boranes

A study has been made of the allylborylation of imines, nitriles, isocyanates, and isothiocyanates by the action of cycloalkenylmethyl(dipropyl)boranes. Preparative methods have been developed for obtaining amines, phenylamides, and phenylthioamides of the 2-methylenecyclopentane and 2-methylenecyclohexane series.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117913 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 11, pp. 2597–2604, November, 1992.     

Lipophilicity determination of some nitrostyrene derivatives on RP-2, PR-8 and RP-18 layers

Summary The lipophilicity of 33 nitrostyrene derivatives was determined by reversed-phase thin-layer chromatography on RP-2, RP-8 and RP-18 layers using methanol as the organic phase. The R_M value of each compound linearly decreased with increasing concentration of the organic solvent. The retention strength of RP-2 layer was lower than that of RP-8 and RP-18 layers. Between the retention strength of RP-8 and RP-18 layers no significant difference was detected. Minor differences among the selectivities of the layers were also observed. The impact of the change of methanol concentration on the retention was higher on RP-2 than on RP-18 layers probably due to the sterically favourable interaction of methanol with the shorter alkyl groups on the silica surface.     

Organometallic complexes with biological molecules: V. In vivo cytotoxicity of diorganotin(IV)-amoxicillin derivatives in mitotic chromosomes of rutilus rubilio (pisces,cyprinidae)

In Order to test in vivo cytotoxicity of diorganotin(IV)-amoxicillin (amox) derivatives, mitotic chromosomes of Rutilus rubilio (Pisces, Cyprinidae) have been analyzed using two different chromosome-staining techniques. Results gathered after exposure of fish to the free amox · 3H₂O, R₂SnClamox · 2H₂O, and R₂Snamox · ₂ 2H₂O (R = methyl, butyl and phenyl; amox⁻ = 6-[D(−)-β-amino-p-hydroxyphenylacetamido]penicillinate) suggest that methyl derivatives seem to exert a lower cytotoxicity than butyl and phenyl ones and that R₂Snamox · ₂ 2H₂O deriva-tives are more toxic than R₂SnClamox · 2H₂O at both 10⁻⁵ and 10⁻⁷mol dm⁻³ concentrations. The following structural lesions have been iden-tified by comparative analysis of mitotic chromo-somes from untreated specimens (controls) and specimens treated with diorganotin(IV)-amoxicillin derivatives: (1) differentially stained chromosome areas; (2) granular deeply stained zones along the chromosomal body; (3) arm breakages; and (4) side-arm bridges (pseudochiasmata).     

Synthesis and anti-inflammatory and antimicrobial activities of some novel 2-methylquinazolin-4(3H)-one derivatives bearing urea,thiourea and sulphonamide functionalities

A variety of novel 2-methylquinazolin-4(3H)-one derivatives (1–29) bearing urea, thiourea and sulphonamide functionalities at position 3 of biological interest have been synthesized and screened for their anti-inflammatory (TNF-α and IL-6) and antimicrobial activities (antibacterial and antifungal). “Biological evaluation study revealed that the compounds 3, 4, 6, 9, 16 and 18 were found to have promising anti-inflammatory activity (up to 62–84% TNF-α and 73–92% IL-6 inhibitory activity) at concentration of 10 μM with reference to standard dexamethasone (75% TNF-α and 84% IL-6 inhibitory activities at 1 μM) and 7, 10, 12, 23, 25 and 28 have antimicrobial activity at MIC of 10–30 μg/mL against selected pathogenic bacteria and fungi.”     

Preparation of a novel,efficient, and recyclable magnetic catalyst,γ-Fe_2O_3@HAp-Ag nanoparticles,and a solvent- and halogen-free protocol for the synthesis of coumarin derivatives

In this protocol, Ag supported on the hydroxyapatite-core–shell magnetic γ-Fe_2O_3nanoparticles(γFe_2O_3@HAp-Ag NPs) as a novel, efficient, and magnetically recyclable catalyst is synthesized, and characterized by transmission electron microscopy(TEM), scanning electron microscopy(SEM), Fourier transform infrared spectroscopy(FT-IR), X-ray diffraction(XRD), and vibrating sample magnetometry(VSM). The use of the catalyst is described in the synthesis of coumarin derivatives by the Pechmann condensation of various phenols with β-ketoesters under solvent- and halogen-free conditions at 80℃.This novel and inexpensive method offers advantages, such as recyclability simple experimental protocol, short reaction time, minimal work-up procedure, and excellent yields of products, together with desirable, eco-friendly, green aspects by avoiding toxic elements and solvents, and ease of recovery from the reaction mixture using an external magnet.     

Design,synthesis of new novel quinoxalin-2(1H)-one derivatives incorporating hydrazone,hydrazine, and pyrazole moieties as antimicrobial potential with in-silico ADME and molecular docking simulation

A series of 6-(morpholinosulfonyl)quinoxalin-2(1H)-one based hydrazone, hydrazine, and pyrazole moieties were designed, synthesized, and evaluated for their in vitro antimicrobial activity. All the synthesized quinoxaline derivatives were characterized by IR, NMR (¹H /¹³C), and EI MS. The results displayed good to moderate antimicrobial potential against six bacterial, and two fungal standard strains. Among the tested derivatives, six quinoxalin-2(1H)-one derivatives 4a, 7, 8a, 11b, 13, and 16 exhibited a significant antibacterial activity with MIC values (0.97–62.5 µg/mL), and MBC values (1.94–88.8 µg/mL) compared with Tetracycline (MICs = 15.62–62.5 µg/mL, and MBCs = 18.74–93.75 µg/mL), and Amphotericin B (MICs = 12.49–88.8 µg/mL, and MFC = 34.62–65.62 µg/mL). In addition, according to CLSI standards, the most active quinoxalin-2(1H)-one derivatives demonstrated bactericidal and fungicidal behavior. Moreover, the most active quinoxaline derivatives showed a considerable antibacterial activity with bactericidal potential against multi-drug resistance bacteria (MDRB) strains with MIC values ranged between (1.95–15.62 µg/mL), and MBC values (3.31–31.25 µg/mL) near to standard Norfloxacin (MIC = 0.78–3.13 µg/mL, and MBC = 1.4–5.32 µg/mL. Further, in vitro S. aureus DNA gyrase inhibition activity were evaluated for the promising derivatives and displayed potency with IC₅₀ values (10.93 ± 1.81–26.18 ± 1.22 µM) compared with Ciprofloxacin (26.31 ± 1.64 µM). Interestingly, these derivatives revealed as good immunomodulatory agents by a percentage ranging between 82.8 ± 0.37 and 142.4 ± 0.98 %. Finally, some in silico ADME, toxicity prediction, and molecular docking simulation were performed and showed a promising safety profile with good binding mode.