Discovery and mechanism of action of Thonzonium bromide from an FDA-approved drug library with potent and broad-spectrum inhibitory activity against main proteases of human coronaviruses

The effect of para-substituted benzaldehyde derivatives with push/pull electron groups on the conformation of bovine serum albumin and its toxicity investigation in Brachionus calyciflorus Pallas (rotifers)

As intermediates widely used in the synthesis of industrial compounds, excessive ingestion of 4-hydroxybenzaldehyde (4-HBzH) and 4-nitrobenzaldehyde (4-NBzH) may induce potentially irreversible damage in organisms. The potential toxicological of 4-HBzH and 4-NBzH were investigated through a multi-disciplinary approach involving density functional theory (DFT), multispectral techniques and molecular docking, with bovine serum albumin (BSA) employed as the model protein of the study. The interaction mechanism between 4-NBzH/4-HBzH and BSA involved static quenching, and the affinity of 4-NBzH for BSA was stronger than that of 4-HBzH as shown by the Ka value (4-NBzH: 6.30 × 104 M-1 ＞ 4-HBzH: 5.96 × 104 M-1), which is also confirmed by DFT calculations. The binding of 4-HBzH/4-NBzH to BSA is mainly through hydrogen bonding and hydrophobic interactions, to which van der Waals forces also contribute, as supported by molecular simulations. Furthermore, the toxicity test based on the Brachionus calyciflorus Pallas (Rotifers) showed that the LC50 of 4-NBzH (8.36 mg/L) was significantly lower than that of 4-HBzH (12.13 mg/L). Interestingly, the electron-withdrawing group-substituted benzaldehyde derivatives may be more hazardous than the electron donor-substituted benzaldehyde derivatives. The findings of this study elucidate toxicological information on the action of 4-HBzH/4-NBzH with BSA and rotifers and offer theoretical foundation for the prevention of the hazards from benzaldehyde derivatives.

Molecular simulations guided drugs repurposing to inhibit human GPx1 enzyme for cancer therapy

Overexpression of the antioxidant enzyme glutathione peroxidase-1 (GPx1) is associated with different cancer types. Inhibitors of GPx1, including mercaptosuccinic acid and pentathiepins derivatives, have been proposed previously and investigated as potent drugs to combat cancer. However, these compounds often lack specificity and demonstrate off-target effects, which necessitates the need for more targeted, non-toxic, and effective GPx1 inhibitors. This study utilized molecular docking and dynamic simulations based computational pipeline to repurpose drugs, approved by The Food and Drug Administration [1], as potent GPx1 inhibitors from a library containing 1615 synthetic compounds. The drug suitability and stability of the selected compounds were further investigated using ADMET, bioactivity probability, Molecular Mechanics-Generalized Born Surface Area (MM-GBSA), and Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) analyses. Initially, 13 compounds were virtually screened based on the Triangle Matcher algorithm, docking modules, and GBVI/WSA dG scoring function. Of these 13 screened compounds, three compounds, including dronedarone, nilotinib, and thonzonium, were rigorously selected based on their ADMET profiles, physicochemical properties, drug suitability, and stability and were subjected to Molecular Dynamic (MD) simulations. MD simulations further validated the stability of the dronedarone, nilotinib, and thonzonium complexes with GPx1 and provided further insights into the mechanism of their interaction. The in-silico approaches used herein revealed thonzonium, dronedarone, and nilotinib as potent GPx1 inhibitors.

Identifying Exifone as a Dual-Target Agent Targeting Both SARS-CoV-2 3CL Protease and the ACE2/S-RBD Interaction Among Clinical Polyphenolic Compounds

The ongoing emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has led to resistance against multiple coronavirus disease 2019 (COVID-19) vaccines and therapeutic medications, making the development of effective therapeutics against SARS-CoV-2 a high priority. Studies have shown that bioactive polyphenols, particularly those with triphenol groups, can effectively inhibit the activity of SARS-CoV-2 3-chymotrypsin-like protease (3CLpro). However, the structural instability of polyphenols necessitates further research. To address this, we conducted a literature review to identify triphenol compounds that are either approved or currently undergoing clinical trials, assessing their potential to inhibit SARS-CoV-2 3CLpro. Exifone and benserazide hydrochloride were identified as the inhibitors of SARS-CoV-2 3CLpro among these compounds, using a fluorescence resonance energy transfer (FRET)-based assay. Benserazide hydrochloride was confirmed as a covalent binder to SARS-CoV-2 3CLpro through time-dependent inhibition and kinetic analysis, with its binding mode elucidated by molecular docking. Notably, exifone not only inhibited the protease activity but also blocked the interaction between the host cell receptor angiotensin-converting enzyme 2 (ACE2) and the SARS-CoV-2 spike protein receptor binding domain (S-RBD), as identified by surface plasmon resonance (SPR) and flow cytometry. Additionally, exifone demonstrated antiviral activity against various SARS-CoV-2-S pseudovirus variants. In conclusion, the discovery of exifone and benserazide hydrochloride underscores the potential of polyphenols in developing conserved 3CLpro inhibitors for coronaviruses, offering new strategies for the rapid development of effective drugs against both current and future coronavirus pandemics.

Systematic Reevaluation of Repurposed Drugs Against the Main Protease of SARS-CoV-2 via Combined Experiments

The main protease (Mpro) of SARS-CoV-2 is an attractive drug target for antivirals, as this enzyme plays a key role in virus replication. Drug repurposing is a promising option for the treatment of coronavirus disease 2019 (COVID-19). Recently, a number of FDA-approved drugs have been identified as Mpro inhibitors, but stringent hit validation is lacking. In this study, we rigorously reevaluated the in vitro inhibition of the Mpro enzyme by repurposed drugs via combined experiments, including the fluorescence resonance energy transfer (FRET) assay, fluorescence polarization (FP) assay, and protease biosensor cleavage assay. Our results from a set of in vitro assays revealed that boceprevir is a potential Mpro inhibitor, but other repurposed drugs, including atazanavir, dipyridamole, entrectinib, ethacridine, glecaprevir, hydroxychloroquine, ivermectin, meisoindigo, pelitinib, raloxifene, roxatidine acetate, saquinavir, teicoplanin, thonzonium bromide, and valacyclovir, are not. Our research highlights that the use of candidate Mpro inhibitors from primary screening warrants further comprehensive studies before the reporting of new findings.

Enantioselective effects of chiral profenofos on the conformation for human serum albumin

Profenofos, as a typical chiral organophosphorus pesticide, can cause various environmental problems and even endanger human health when used in excess. The toxicity of chiral profenofos was investigated through multispectral analysis, molecular docking, and density functional theory (DFT), employing human serum albumin (HSA) as the model protein. Fluorescence titration and lifetime measurements demonstrated that the interaction between chiral profenofos and HSA involves static quenching. Chiral profenofos forms a 1:1 complex with HSA at site II (subdomain IIIA), primarily driven by hydrophobic interactions and hydrogen bonds. Notably, the binding efficacy diminishes as temperature increases. Spectroscopic analyses confirm that chiral profenofos alters the microenvironment and structure of HSA, with the R-enantiomer exerting a greater impact than the S-enantiomer. Consequently, the toxicological implications of the R-profenofos is significantly more pronounced. Investigating the molecular-level toxic effects of chiral pesticides enhances the thoroughness of pesticide assessments, aids in understanding their distribution, metabolism, and associated risks, and facilitates the development of mitigation strategies.

Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.

On Inactivation of the Coronavirus Main Protease

A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.

Danshensu inhibits SARS-CoV-2 by targeting its main protease as a specific covalent inhibitor and discovery of bifunctional compounds eliciting antiviral and anti-inflammatory activity

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to human. Since there are still no effective treatment options against the new emerging variants of SARS-CoV-2, it is necessary to devote a continuous endeavor for more targeted drugs and the preparation for the next pandemic. Salvia miltiorrhiza and its active ingredients possess wide antiviral activities, including against SARS-CoV-2. Danshensu, as one of the most important active ingredients in Salvia miltiorrhiza, has been reported to inhibit the entry of SARS-CoV-2 into ACE2 (angiotensin-converting enzyme 2)-overexpressed HEK-293T cells and Vero-E6 cells. However, there is a paucity of information regarding its detailed target and mechanism against SARS-CoV-2. Here, we present Danshensu as a covalent inhibitor of 3-chymotrypsin-like protease (3CLpro) against SARS-CoV-2 by the time-dependent inhibition assay (TDI) and mass spectrometry analysis. Further molecular docking, site-directed mutagenesis, circular dichroism (CD) and fluorescence spectra revealed that Danshensu covalently binds to C145 of SARS-CoV-2 3CLpro, meanwhile forming the hydrogen bonds with S144, H163 and E166 in the S1 site. Structure-based optimization of Danshensu led to the discovery of the promising compounds with good inhibitory activity and microsomal stability in vitro. Due to Danshensu inhibiting lung inflammation in the mouse model, we found that Danshensu derivatives also showed better anti-inflammatory activity than Danshensu in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophage cells. Thus, our study provides not only the clue of the efficacy of Salvia miltiorrhiza against SARS-CoV-2, but also a detailed mechanistic insight into the covalent mode of action of Danshensu for design of covalent inhibitors against SARS-CoV-2 3CLpro, highlighting its potential as a bifunctional molecule with antivirus and anti-inflammation.

Enantioselective effect of chiral prothioconazole on the conformation of bovine serum albumin

As a typical chiral triazole fungicide, the enantioselective toxicity of prothioconazole to environmental organisms is of increasing concern. Herein, the binding mechanism of chiral PTCs to BSA was investigated by multi-spectral technique and molecular docking. Fluorescence titration and fluorescence lifetime experiments fully established that quenching BSA fluorescence by chiral PTCs is static quenching and could spontaneously bind to BSA. Hydrophobic interactions dominate the binding process of chiral PTCs to BSA. Differently, although both chiral PTCs and BSA have a primary binding site, the difference in chiral isomerism leads to a stronger binding ability of S-PTC than R-PTC. Both configurations of PTC can change the conformation of BSA and induce changes in the microenvironment around its amino acid residues, and the effect of S-PTC is more significant. Overall, S-PTC exhibited a more substantial effect on BSA structure relative to R-PTC. That is, S-PTC may lead to more potent potential toxicological effects on environmental organisms. This study provides a comprehensive assessment of the environmental behavior of chiral pesticides and their potential toxicity to environmental organisms at the molecular level and provides a theoretical basis for the screening of highly effective and biologically less toxic enantiomers of chiral pesticides.