Elucidation of the Mechanistic Pathways of the Hydroxyl Radical Scavenging Reaction by Daidzein Using Hybrid QM/MM Dynamics

A critical appraisal of geroprotective activities of flavonoids in terms of their bio-accessibility and polypharmacology

Flavonoids, a commonly consumed natural product, elicit health-benefits such as antioxidant, anti-inflammatory, antiviral, anti-allergic, hepatoprotective, anti-carcinogenic and neuroprotective activities. Several studies have reported the beneficial role of flavonoids in improving memory, learning, and cognition in clinical settings. Their mechanism of action is mediated through the modulation of multiple signalling cascades. This polypharmacology makes them an attractive natural scaffold for designing and developing new effective therapeutics for complex neurological disorders like Alzheimer's disease and Parkinson's disease. Flavonoids are shown to inhibit crucial targets related to neurodegenerative disorders (NDDs), including acetylcholinesterase, butyrylcholinesterase, β-secretase, γ-secretase, α-synuclein, Aβ protein aggregation and neurofibrillary tangles formation. Conserved neuro-signalling pathways related to neurotransmitter biogenesis and inactivation, ease of genetic manipulation and tractability, cost-effectiveness, and their short lifespan make Caenorhabditis elegans one of the most frequently used models in neuroscience research and high-throughput drug screening for neurodegenerative disorders. Here, we critically appraise the neuroprotective activities of different flavonoids based on clinical trials and epidemiological data. This review provides critical insights into the absorption, metabolism, and tissue distribution of various classes of flavonoids, as well as detailed mechanisms of the observed neuroprotective activities at the molecular level, to rationalize the clinical data. We further extend the review to critically evaluate the scope of flavonoids in the disease management of neurodegenerative disorders and review the suitability of C. elegans as a model organism to study the neuroprotective efficacy of flavonoids and natural products.

Antiviral Flavonoids: A Natural Scaffold with Prospects as Phytomedicines against SARS-CoV2

Flavonoids are vital candidates to fight against a wide range of pathogenic microbial infections. Due to their therapeutic potential, many flavonoids from the herbs of traditional medicine systems are now being evaluated as lead compounds to develop potential antimicrobial hits. The emergence of SARS-CoV-2 caused one of the deadliest pandemics that has ever been known to mankind. To date, more than 600 million confirmed cases of SARS-CoV2 infection have been reported worldwide. Situations are worse due to the unavailability of therapeutics to combat the viral disease. Thus, there is an urgent need to develop drugs against SARS-CoV2 and its emerging variants. Here, we have carried out a detailed mechanistic analysis of the antiviral efficacy of flavonoids in terms of their potential targets and structural feature required for exerting their antiviral activity. A catalog of various promising flavonoid compounds has been shown to elicit inhibitory effects against SARS-CoV and MERS-CoV proteases. However, they act in the high-micromolar regime. Thus a proper leadoptimization against the various proteases of SARS-CoV2 can lead to high-affinity SARS-CoV2 protease inhibitors. To enable lead optimization, a quantitative structure-activity relationship (QSAR) analysis has been developed for the flavonoids that have shown antiviral activity against viral proteases of SARS-CoV and MERS-CoV. High sequence similarities between coronavirus proteases enable the applicability of the developed QSAR to SARS-CoV2 proteases inhibitor screening. The detailed mechanistic analysis of the antiviral flavonoids and the developed QSAR models is a step forward toward the development of flavonoid-based therapeutics or supplements to fight against COVID-19.

Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics

Molecular insight into electronic rearrangements and structural trajectories arising from oxidative damages to DNA backbone is of crucial importance in understanding the effect of ionizing radiation, developing DNA biosensors and designing effective DNA cleaving molecules. Employing a Density Functional Theory based multi-scale Quantum-Mechanical-Molecular-Mechanical (QM/MM) simulation and a suitable partitioning of the Hamiltonian on solvated nucleotide, and single-, and double-stranded DNA, we mimic hydrogen transfer reactions from the backbone by OH radicals and report structural trajectories arising from on-the-fly electronic charge- and spin-density redistribution in these three different structural topologies of DNA. Trajectories reveal that H4′ abstraction can disrupt the deoxyribose moiety through the formation of C4′=O4′ ketone and a π-bond with base at C1′-N9 in a nucleotide versus only partial ketone formation in single- and double-stranded DNA, where the orientation of the base is topologically restrained. However, H5′ abstraction can lead DNA cleavage at 5′ end through the formation of C5′=O5′ ketone and breakage of P-O5′ bond. Results demonstrate that structural damages from oxidative reactions are restrained by base stacking and base-pair hydrogen bonding. The methodology can be suitably used to study targeted DNA and RNA damages from radicals and radiomimetic drugs to design DNA cleaving molecules for chemotherapy.

The beneficial and deleterious role of dietary polyphenols on chronic degenerative diseases by regulating gene expression

Dietary polyphenols, a natural component in many kinds of foods such as fruits and vegetables, play essential roles in a wide range of plant functions. Importantly, the discovery of the functions of polyphenols including anti-oxidant, anti-carcinogenic and anti-inflammatory has been appealing to researchers' attentions. Dietary polyphenols have shown protective effects on chronic degenerative diseases (CDD) such as cardiovascular diseases, cancers, and neurodegenerative diseases by regulating gene expression. Dietary polyphenols also affect the composition and activity of gut microbiota, in reverse, gut microbiota influences the bioavailability and physiological activity of dietary polyphenols. However, not all kinds of dietary polyphenols are beneficial for human health. The potential deleterious effects of several dietary polyphenols have been reported by inducing DNA damage and gene mutants. This review summarizes the potential therapeutic effects of dietary polyphenols on chronic degeneration diseases, the polyphenols-gut microbiota interactions, and the potential dangers of individual dietary polyphenols on human health.

Multi-functional neuroprotective activity of neohesperidin dihydrochalcone: a novel scaffold for Alzheimer's disease therapeutics identified via drug repurposing screening

Multi-target screening identifies neohesperidin dihydrochalcone for Alzheimer's disease therapeutics, which exhibits strong BACE1 and amyloid aggregation inhibition along with antioxidant activity.

Multi-response optimisation of the extraction solvent system for phenolics and antioxidant activities from fermented soy flour using a simplex-centroid design

A simplex-centroid design comprising three solvents (water, ethanol and methanol) was used to optimise the extraction mixture for phenolics and antioxidant activities from defatted soy flour fermented with Monascus purpureus or Aspergillus oryzae. Total phenolics were more efficiently extracted using only water for both samples. The highest antioxidant activities by the DPPH and ABTS methods were obtained using extraction mixtures containing at least 75 wt% water. Specific water:ethanol:methanol ratios promoted the joint optimisation of the total phenolic and isoflavone contents as well as antioxidant activities: 0.5:0.375:0.125 (wt/wt/wt) and 0.5:0.3:0.2 (wt/wt/wt) from defatted soy flour fermented with M. purpureus or A. oryzae, respectively. However, a water:ethanol ratio of 0.5:0.5 (wt/wt) was deemed optimal because it is comprised of green solvents and yielded results that were greater than 90% of the multi-response maximum values. Both the solvents and the sample matrix strongly influenced the extractability of total phenolics and isoflavones.

Flavonol–carbon nanostructure hybrid systems: a DFT study on the interaction mechanism and UV/Vis features

The properties of flavonol–carbon nanosystem hybrid materials are analyzed using computational chemistry.