Sulforaphane prevents and reverses allergic airways disease in mice via anti-inflammatory, antioxidant, and epigenetic mechanisms.

Sulforaphane has been investigated in human pathologies and preclinical models of airway diseases. To provide further mechanistic insights, we explored L-sulforaphane (LSF) in the ovalbumin (OVA)-induced chronic allergic airways murine model, with key hallmarks of asthma. Histological analysis indicated that LSF prevented or reversed OVA-induced epithelial thickening, collagen deposition, goblet cell metaplasia, and inflammation. Well-known antioxidant and anti-inflammatory mechanisms contribute to the beneficial effects of LSF. Fourier transform infrared microspectroscopy revealed altered composition of macromolecules, following OVA sensitization, which were restored by LSF. RNA sequencing in human peripheral blood mononuclear cells highlighted the anti-inflammatory signature of LSF. Findings indicated that LSF may alter gene expression via an epigenetic mechanism which involves regulation of protein acetylation status. LSF resulted in histone and α-tubulin hyperacetylation in vivo, and cellular and enzymatic assays indicated decreased expression and modest histone deacetylase (HDAC) inhibition activity, in comparison with the well-known pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA). Molecular modeling confirmed interaction of LSF and LSF metabolites with the catalytic domain of metal-dependent HDAC enzymes. More generally, this study confirmed known mechanisms and identified potential epigenetic pathways accounting for the protective effects and provide support for the potential clinical utility of LSF in allergic airways disease.

In silico investigation of DNA minor groove binding bibenzimidazoles in the context of UVA phototherapy.

The versatility of DNA minor groove binding bibenzimidazoles extends to applications in cancer therapy, beyond their typical use as DNA stains. In the context of UVA phototherapy, a series of halogenated analogues designated ortho-, meta-, and para-iodoHoechst have been investigated. Phototoxicity involves dehalogenation of the ligands following exposure to UVA light, resulting in the formation of a carbon-centred radical. While the cytotoxic mechanisms have been well established, the nature and severity of DNA damage induced by the ortho-, meta-, and para-iodoHoechst isomers requires clarification. Our aims were to measure and compare the binding constants of iodoHoechst analogues, and to determine the proximity of the carbon-centred radicals formed following photodehalogenation to the C1', C4', and C5' DNA carbons. We performed molecular docking studies, as well as classical molecular dynamics simulations to investigate the interactions of Hoechst ligands with DNA including a well-defined B-DNA dodecamer containing the high affinity AATT minor groove binding site. Docking highlighted the binding of Hoechst analogues to AATT regions in oligonucleotides, nucleosomes, and origami DNA helical bundles. Further, MD simulations demonstrated the stability of Hoechst ligands in the AATT-containing minor groove over microsecond trajectories. Our findings reiterate that the efficiency of dehalogenation per se, rather than the proximity of the carbon-centred radicals to the DNA backbone, is responsible for the extreme phototoxicity of the ortho- isomer compared to the meta- and para-iodoHoechst isomers. More generally, our analyses are in line with the potential utility of ortho-iodoHoechst in DNA-targeted phototherapy, particularly if combined with a cell-specific delivery system.

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity.

Announced on December 31, 2019, the novel coronavirus arising in Wuhan City, Hubei Province resulted in millions of cases and lives lost. Following intense tracking, coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of COVID-19 and the continuous evolution of the virus has given rise to several variants. In this review, a comprehensive analysis of the response to the pandemic over the first three-year period is provided, focusing on disease management, development of vaccines and therapeutics, and identification of variants. The transmissibility and pathogenicity of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron are compared. The binding characteristics of the SARS-CoV-2 spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor and reproduction numbers are evaluated. The effects of major variants on disease severity, hospitalisation, and case-fatality rates are outlined. In addition to the spike protein, open reading frames mutations are investigated. We also compare the pathogenicity of SARS-CoV-2 with SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Overall, this study highlights the strengths and weaknesses of the global response to the pandemic, as well as the importance of prevention and preparedness. Monitoring the evolution of SARS-CoV-2 is critical in identifying and potentially predicting the health outcomes of concerning variants as they emerge. The ultimate goal would be a position in which existing vaccines and therapeutics could be adapted to suit new variants in as close to real-time as possible.

Identification of dietary compounds that interact with the circadian clock machinery: Molecular docking and structural similarity analysis.

The molecular clock is vital for regulating circadian rhythms in various physiological processes, and its dysregulation is associated with multiple diseases. As such, the use of small molecule modulators to regulate the molecular clock presents a promising therapeutic approach. In this study, we generated a homology model of the human circadian locomotor output cycles kaput (CLOCK) protein to evaluate its ligand binding sites. Using molecular docking, we obtained further insights into the binding mode of the control compound CLK8 and explored a selection of dietary compounds. Our investigation of dietary compounds was guided by their potential interactions with the retinoic acid-related orphan receptors RORα/γ, which are involved in circadian regulation. Through the molecular similarity and docking analyses, we identified oleanolic acid demethyl, 3-epi-lupeol, and taraxasterol as potential ROR-interacting compounds. These compounds may exert therapeutic effects through their modulation of RORα/γ activity and subsequently influence the molecular clock. Overall, our study highlights the potential of small molecule modulators in regulating the molecular clock and the importance of exploring dietary compounds as a source of such modulators. Our findings also provide insights into the binding mechanisms of CLK8 and shed light on potential compounds that can interact with RORs to regulate the molecular clock. Future investigations could focus on validating the efficacy of these compounds in modulating the molecular clock and their potential use as therapeutic agents.

EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals.

Antiviral drugs are important for the coronavirus disease 2019 (COVID-19) response, as vaccines and antibodies may have reduced efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Antiviral drugs that have been made available for use, albeit with questionable efficacy, include remdesivir (Veklury®), nirmatrelvir-ritonavir (Paxlovid™), and molnupiravir (Lagevrio®). To expand the options available for COVID-19 and prepare for future pandemics, there is a need to investigate new uses for existing drugs and design novel compounds. To support these efforts, we have created a comprehensive library of 750 molecules that have been sourced from in vitro, in vivo, and in silico studies. It is publicly available at our dedicated website (https://epimedlab.org/crl/). The EpiMed Coronabank Chemical Collection consists of compounds that have been divided into 10 main classes based on antiviral properties, as well as the potential to be used for the management, prevention, or treatment of COVID-19 related complications. A detailed description of each compound is provided, along with the molecular formula, canonical SMILES, and U.S. Food and Drug Administration approval status. The chemical structures have been obtained and are available for download. Moreover, the pharmacokinetic properties of the ligands have been characterised. To demonstrate an application of the EpiMed Coronabank Chemical Collection, molecular docking was used to evaluate the binding characteristics of ligands against SARS-CoV-2 nonstructural and accessory proteins. Overall, our database can be used to aid the drug repositioning process, and for gaining further insight into the molecular mechanisms of action of potential compounds of interest.

Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 variant (Omicron), represents a significant deviation in genetic makeup and function compared to previous variants. Following the BA.1 sublineage, the BA.2 and BA.3 Omicron subvariants became dominant, and currently the BA.4 and BA.5, which are quite distinct variants, have emerged. Using molecular dynamics simulations, we investigated the binding characteristics of the Delta and Omicron (BA.1) variants in comparison to wild-type (WT) at the interface of the spike protein receptor binding domain (RBD) and human angiotensin converting enzyme-2 (ACE2) ectodomain. The primary aim was to compare our molecular modelling systems with previously published observations, to determine the robustness of our approach for rapid prediction of emerging future variants. Delta and Omicron were found to bind to ACE2 with similar affinities (-39.4 and -43.3 kcal/mol, respectively) and stronger than WT (-33.5 kcal/mol). In line with previously published observations, the energy contributions of the non-mutated residues at the interface were largely retained between WT and the variants, with F456, F486, and Y489 having the strongest energy contributions to ACE2 binding. Further, residues N440K, Q498R, and N501Y were predicted to be energetically favourable in Omicron. In contrast to Omicron, which had the E484A and K417N mutations, intermolecular bonds were detected for the residue pairs E484:K31 and K417:D30 in WT and Delta, in accordance with previously published findings. Overall, our simplified molecular modelling approach represents a step towards predictive model systems for rapidly analysing arising variants of concern.

Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNet™ library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity.

BACKGROUND: As highlighted in the OliveNet™ library, Olea europaea consists of a diverse collection of chemical compounds. We have classified over 600 compounds into 13 main classes and 47 subclasses. Various compounds, including oleuropein and hydroxytyrosol, have been investigated for their potential beneficial effects in multiple human pathologies. However, the vast majority of compounds remain largely unexplored and approximately 50% are currently non-commercially available. METHOD: Here, we utilise conventional software to characterise the absorption, distribution, metabolism, excretion, and toxicity profile of OliveNet™ compounds. Molecular docking was performed for assessment of P-glycoprotein (P-gp) inhibition and interactions with the human ether-à-go-go-related gene (hERG) channel. Potential hERG ion channel inhibition was calibrated using in vitro patch clamp assays and steered molecular dynamics (SMD) simulations were used to examine membrane permeability of a subset of compounds. RESULTS: Our findings indicated that 313 out of 675 olive compounds were predicted to be absorbed by the gastrointestinal tract. Hydroxytyrosol required the least amount of force to pass through the lipid bilayer compared to elenolic acid diglucoside in SMD simulations. Based on the ADMET and molecular docking data, the hERG inhibitory activities of verbascoside, oleuropein, and hydroxytyrosol were investigated using patch clamp assays and they were identified as non-inhibitors. CONCLUSIONS: While the favourable properties of well-known compounds were confirmed, we identified oleuropein aglycone decarboxymethyl dialdehyde acetal form, decarboxymethyl elenolic acid dialdehyde, acetal of decarboxymethyl elenolic acid dialdehyde, methyl malate-ß-hydroxytyrosol ester, hydroxytyrosil elenolate, D-(+)-erythro-1-(4-hydroxy-3-methoxy)-214-phenyl-1,2,3-propantriol, (+)-1-acetoxypinoresinol-4″-O-methyl ether, and 3-[1-(hydroxymethyl)-(E)-1-propenyl] glutaric acid as potential candidates for synthesis and further evaluation.