A detailed DFT-based study of the free radical scavenging activity and mechanism of daphnetin in physiological environments

In vitro and in vivo studies of the therapeutic potential of Tinospora crispa extracts in osteoarthritis: Targeting oxidation, inflammation, and chondroprotection

ETHNOPHARMACOLOGICAL RELEVANCE

The increasing incidence of osteoarthritis (OA), especially among the elderly population, highlights the need for more efficacious treatments that go beyond mere symptomatic relief. Tinospora crispa (L.) Hook. f. & Thomson (TC) boasts a rich traditional heritage, widespread use in Ayurveda, traditional Chinese medicine (TCM), and diverse indigenous healing practices throughout Southeast Asia for treating arthritis, rheumatism, fever, and inflammation.

AIM OF THE STUDY

This study investigates the anti-inflammatory and chondroprotective potential of TC stem extracts, including ethanolic TC extract (ETCE) and aqueous TC extract (ATCE), in modulating OA pathogenesis through in vitro and in vivo approaches.

MATERIALS AND METHODS

The study utilized LC-MS/MS to identify key compounds in TC stem extracts. In vitro experiments assessed the antioxidative and anti-inflammatory properties of ETCE and ATCE in activated macrophages, while an in vivo monoiodoacetate (MIA)-induced OA rat model evaluated the efficacy of ETCE treatment. Key markers of oxidative stress, such as superoxide dismutase (SOD) and catalase (CAT), were assessed alongside pro-inflammatory cytokines TNF-α and IL-1β, and matrix-degrading enzymes, matrix metalloproteinase (MMP 13 and MMP 3), to evaluate the therapeutic effects of TC stem extracts on OA.

RESULTS

Chemical profiling of the extracts was conducted using LC-MS/MS in positive ionization, identifying seven compounds, including pseudolaric acid B, stylopine, and reticuline, which were reported for the first time in this species. The study utilized varying concentrations of TC stem extracts, specifically 6.25-25 μg/mL for in vitro assays and 500 mg/kg for in vivo studies. Our findings also revealed that both ETCE and ATCE exhibit dose-dependent reduction in reactive oxygen species (41%-52%) and nitric oxide (NO) levels (50% and 72%), with ETCE displaying superior antioxidative efficacy and marked anti-inflammatory properties, significantly reducing TNF-α and IL-6 at concentrations above 12.5 μg/mL. In the MIA-induced OA rat model, ETCE treatment notably outperformed ATCE, markedly lowering TNF-α (1.91 ± 0.37 pg/mL) and IL-1β (26.30 ± 3.68 pg/mL) levels and effectively inhibiting MMP 13 and MMP 3 enzymes. Furthermore, macroscopic and histopathological assessments, including ICRS scoring and OARSI grading, indicate that TC stem extracts reduce articular damage and proteoglycan loss in rat knee cartilage. These results suggest that TC stem extracts may play a role in preventing cartilage degradation and potentially alleviating inflammation and pain associated with OA, though further studies are needed to confirm these effects.

CONCLUSION

This study highlights the potential of TC stem extracts as a novel, chondroprotective therapeutic avenue for OA management. By targeting oxidative stress, pro-inflammatory cytokines, and cartilage-degrading enzymes, TC stem extracts promise to prevent cartilage degradation and alleviate inflammation and pain associated with OA.

The inhibitory potential of 4,7-dihydroxycoumarin derivatives on ROS-producing enzymes and direct HOO•/o2• - radical scavenging activity - a comprehensive kinetic DFT study

This study examined the antiradical activity of three synthesized coumarin derivatives: (E)-3-(1-((2-hydroxyphenyl)amino)ethylidene)-2,4-dioxochroman-7-yl acetate (A1-OH), (E)-3-(1-((3-hydroxyphenyl)amino)ethylidene)-2,4-dioxochroman-7-yl acetate (A2-OH), and (E)-3-(1-((4-hydroxyphenyl)amino)ethylidene)-2,4-dioxochroman-7-yl acetate (A3-OH) against HOO•/O2•- radical species. The investigation included electron spin resonance (ESR) measurements and a DFT kinetic study. Thermodynamic and kinetic parameters of antiradical mechanisms-Formal Hydrogen Atom Transfer (f-HAT), Radical Adduct Formation (RAF), Sequential Proton Loss followed by Electron Transfer (SPLET), and Single-Electron Transfer followed by Proton Transfer (SET-PT)-were evaluated using the Quantum Mechanics-based test for Overall Free Radical Scavenging Activity (QM-ORSA) under physiological conditions. ESR results indicated antiradical activity decreased in the sequence A1-OH (58.7%) > A2-OH (57.5%) > A3-OH (53.1%). Kinetic analysis revealed the f-HAT mechanism dominated HOO• inactivation. A newly formulated Sequential Proton Loss followed by Radical Adduct Formation (SPL-RAF) mechanism described interactions with O2•-. The activity toward O2•- was A2-OH (1.26 × 106 M-1s-1) > A3-OH (7.71 × 105 M-1s-1) > A1-OH (4.22 × 105 M-1s-1). Molecular docking and dynamics studies tested inhibitory capability against enzymes producing reactive species: Lipoxygenase (LOX), Myeloperoxidase (MPO), NAD(P)H oxidase (NOX), and Xanthine Oxidase (XOD). Affinity to enzymes decreased in the order: XOD > LOX > NOX > MPO.

On the dual role of (+)-catechin as primary antioxidant and inhibitor of viral proteases

Natural antioxidants have become the subject of many investigations due to the role that they play in the reduction of oxidative stress. Their main scavenging mechanisms concern the direct inactivation of free radicals and the coordination of metal ions involved in Fenton-like reactions. Recently, increasing attention has been paid to non-covalent inhibition of enzymes involved in different diseases by the antioxidants. Here, a computational investigation on the primary antioxidant power of (+)-catechin against the •OOH radical has been performed in both lipid-like and aqueous environments, taking into account the relevant species present in the simulated acid-base equilibria at the physiological pH. Hydrogen Atom Transfer (HAT), Single Electron Transfer (SET), and Radical Adduct Formation (RAF) mechanisms were studied, and relative rate constants were estimated. The potential inhibitory activity of the (+)-catechin towards the most important proteases from SARS-CoV-2, 3C-like (Mpro) and papain-like (PLpro) proteases was also investigated by MD simulations to provide deeper atomistic insights on the binding sites. Based on the antioxidant and antiviral properties also unravelled by comparison with other molecules having similar chemical scaffold, our results propose that (+)-CTc satisfies can explicate a dual action as antioxidant and antiviral in particular versus Mpro from SARS-CoV-2.

The molecular effects underlying the pharmacological activities of daphnetin

As an increasingly well-known derivative of coumarin, daphnetin (7,8-dithydroxycoumarin) has demonstrated various pharmacological activities, including anti-inflammation, anti-cancer, anti-autoimmune diseases, antibacterial, organ protection, and neuroprotection properties. Various studies have been conducted to explore the action mechanisms and synthetic methods of daphnetin, given its therapeutic potential in clinical. Despite these initial insights, the precise mechanisms underlying the pharmacological activities of daphnetin remain largely unknown. In order to address this knowledge gap, we explore the molecular effects from the perspectives of signaling pathways, NOD-like receptor protein 3 (NLRP3) inflammasome and inflammatory factors; and try to find out how these mechanisms can be utilized to inform new combined therapeutic strategies.

Primary Antioxidant Power and Mpro SARS-CoV-2 Non-Covalent Inhibition Capabilities of Miquelianin

The antioxidant power of quercetin-3-O-glucuronide (miquelianin) has been studied, at the density functional level of theory, in both lipid-like and aqueous environments. In the aqueous phase, the computed pKa equilibria allowed the identification of the neutral and charged species present in solution that can react with the ⋅OOH radical. The Hydrogen Atom Transfer (HAT), Single Electron Transfer (SET) and Radical Adduct Formation (RAF) mechanisms were considered, and the individual, total and fraction corrected rate constants were obtained. Potential non-covalent inhibition of Mpro from SARS-CoV-2 by miquelianin has been also evaluated.

Comparison of Cu3, Cu5, and Cu7 clusters as potential antioxidants: A theoretical quest

CONTEXT

Herein, we compare and contrast the dual roles of Cun clusters (n = 3, 5, and 7 atoms) in scavenging or generating RO• free radicals from ROH at the theoretical levels (where R = H, methyl, ethyl, n-propyl, i-propyl, n-butyl, t-butyl, and phenyl). This investigation is performed in water media to mimic the actual environment in the biological system. In the presence of the Cun clusters, bond dissociation energy (BDE) of RO-H and R-OH is reduced. This is clear evidence for the increased possibility of both the RO-H and R-OH bonds breakage and scavenging of RO• radicals. The nature of anchoring bonds responsible for the interaction of Cun clusters with ROH and RO• are interpreted using the quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) analysis. The DFT results indicate that the O•⋅⋅⋅•Cu bond is stronger and has more covalent character in RO•⋅⋅⋅•Cun radical complexes than in ROH⋅⋅⋅•Cun. Therefore, the interactions of Cun clusters with RO• radicals (antioxidant) are more pronounced than their interactions with ROH non-radicals (pro-oxidant).

METHODS

The GAMESS software package was utilized in this paper. The B3LYP and M06 functions with the 6-311 +  + G(d,p), and LANL2DZ/SDD basis sets was used to perform the important geometrical parameters of RO•⋅⋅⋅•Cun and ROH⋅⋅⋅•Cun, binding energy (Eb), and bond dissociation energy (BDE).

Computational assessment of the primary and secondary antioxidant potential of alkylresorcinols in physiological media

Alkylresorcinols are a group of natural phenolic compounds found in various foods such as whole grain cereals, bread, and certain fruits. They are known for their beneficial health effects, such as anti-inflammatory and anti-cancer properties. This study aimed to evaluate the antioxidant activity of two typical alkylresorcinols namely olivetol and olivetolic acid (Oli and OliA) under physiological conditions. The free radical scavenging capacity of Oli and OliA toward oxygenated free radicals (HO˙ and HOO˙ radicals) was investigated using thermodynamic and kinetic calculations. The results revealed that Oli and OliA are potent scavengers of HO˙ radical in both polar and lipid media, acting exclusively via the FHT (formal hydrogen transfer) mechanism. Moreover, they demonstrated excellent scavenging activity toward HOO˙ radical in water via the SET (single electron transfer) mechanism, outperforming the common antioxidant BHT. In lipid media, Oli and OliA showed moderate scavenging activity toward HOO˙ radical via the FHT mechanism. Significant prooxidant potential of OliA- was also demonstrated through the formation of complexes with copper ions. Additionally, docking studies indicate that the compounds exhibited a good affinity for ROS-producing enzymes, including myeloperoxidase (MP), cytochrome P450 (CP450), lipoxygenase (LOX), and xanthine oxidase (XO), highlighting their potential as natural antioxidants with promising therapeutic applications.

The chemical ecology of coumarins and phenazines affects iron acquisition by pseudomonads

Secondary metabolites are important facilitators of plant-microbe interactions in the rhizosphere, contributing to communication, competition, and nutrient acquisition. However, at first glance, the rhizosphere seems full of metabolites with overlapping functions, and we have a limited understanding of basic principles governing metabolite use. Increasing access to the essential nutrient iron is one important, but seemingly redundant role performed by both plant and microbial Redox-Active Metabolites (RAMs). We used coumarins, RAMs made by the model plant Arabidopsis thaliana, and phenazines, RAMs made by soil-dwelling pseudomonads, to ask whether plant and microbial RAMs might each have distinct functions under different environmental conditions. We show that variations in oxygen and pH lead to predictable differences in the capacity of coumarins vs phenazines to increase the growth of iron-limited pseudomonads and that these effects depend on whether pseudomonads are grown on glucose, succinate, or pyruvate: carbon sources commonly found in root exudates. Our results are explained by the chemical reactivities of these metabolites and the redox state of phenazines as altered by microbial metabolism. This work shows that variations in the chemical microenvironment can profoundly affect secondary metabolite function and suggests plants may tune the utility of microbial secondary metabolites by altering the carbon released in root exudates. Together, these findings suggest that RAM diversity may be less overwhelming when viewed through a chemical ecological lens: Distinct molecules can be expected to be more or less important to certain ecosystem functions, such as iron acquisition, depending on the local chemical microenvironments in which they reside.

Insights on the antiradical capacity and mechanism of phytocannabinoids: H-abstraction and electron transfer processes in physiological media and the influence of the acid-base equilibrium

Phytocannabinoids are natural products primarily isolated from Cannabis sativa that exhibit the typical C21 terpenophenolic skeleton. This class of compounds has been shown to be effective in the treatment of various oxidation-related diseases, which has made their antioxidant properties the focus of increasing interest. In the present contribution, the primary antioxidant properties of eight representative phytocannabinoids have been systematically studied against a variety of biologically significant radical species using the density functional theory (DFT) method. The findings demonstrated that phytocannabinoids, in water at physiological pH, exhibit excellent radical scavenging capacity, mainly exerted by the single electron transfer (SET) process from the deprotonated state. In contrast, phytocannabinoids are moderate radical scavengers in non-polar environment via the formal hydrogen atom transfer (fHAT) process. Among the compounds examined, cannabichromene (CBC) and cannabifuran (CBF) had the greatest free radical scavenging capacity in water, surpassing even common antioxidants like BHT and Trolox. CBF is expected to have potent antiradical action toward peroxyl radicals, alkoxy radicals, and nitrogen dioxide in water at physiological pH. These results provide supporting evidence that phytocannabinoids may be useful in scavenging harmful free radicals in physiological environments.

Computational investigation on the antioxidant activities and on the Mpro SARS-CoV-2 non-covalent inhibition of isorhamnetin

In the present work, we report a computational study on some important chemical properties of the flavonoid isorhamnetin, used in traditional medicine in many countries. In the course of the study we determined the acid-base equilibria in aqueous solution, the possible reaction pathways with the •OOH radical and the corresponding kinetic constants, the complexing capacity of copper ions, and the reduction of these complexes by reducing agents such as superoxide and ascorbic anion by using density functional level of theory Density Functional Theory. Finally, the non-covalent inhibition ability of the SARS-CoV-2 main protease enzyme by isorhamnetin was examined by molecular dynamics (MD) and docking investigation.

Computational design of new tacrine analogs: an in silico prediction of their cholinesterase inhibitory, antioxidant, and hepatotoxic activities

Tacrine, the first drug approved for the treatment of Alzheimer's disease (AD), is a non-competitive cholinesterase inhibitor withdrawn due to its acute hepatotoxicity. However, new non-hepatotoxic forms of tacrine have been actively researched. Moreover, several recent reports have shown that oxidative stress is the cause of damage and plays a role in the pathogenesis of several neurodegenerative diseases including AD. The aim of the present study is the design of new easily synthesized tacrine analogs with less hepatotoxicity and potent antioxidant activity. In this context, a library of 34 novel tacrine analogs bearing an antioxidant fragment was designed and evaluated for its hepatotoxicity as well as anticholinesterase and antioxidant activities using computational methods. As a result, six new tacrine analogs have been proposed as potential inhibitors of cholinesterase with antioxidant activity and low or no hepatotoxicity. Furthermore, ADME calculations suggest that these compounds are promising oral drug candidates. Communicated by Ramaswamy H. Sarma.

Daphnetin: A bioactive natural coumarin with diverse therapeutic potentials

Daphnetin (DAP), a coumarin derivative extracted from Daphne species, is biologically active phytochemical with copious bioactivities including anti-inflammatory, anti-oxidant, neuroprotective, analgesic, anti-pyretic, anti-malarial, anti-bacterial, anti-arthritic, neuroprotective, hepatoprotective, nephroprotective, and anti-cancer activities. A wide range of studies have been conducted exploring the significance and therapeutic potential of DAP. This study reviewed various databases such as NCBI, PubMed, Web of Science, Scopus and Google Scholar for published research articles regarding the sources, synthesis, and various bioactivities of DAP using different key words, including but not limited to “pharmacological activities,” “sources,” “neuroprotective effect,” “synthesis,” “cancer,” “anti-inflammatory effect” of “daphnetin.” Furthermore, this review encompasses both in-vivo and in-vitro studies on DAP for treating various diseases. A comprehensive review of the literature revealed that the DAP had a promising pharmacological and safety profile, and could be employed as a pharmaceutical moiety to treat a variety of illnesses including microbial infections, cancer, arthritis, hepatic damage, inflammation and neurological anomalies. The current review intends to provide an in-depth focus on all pharmacological activities and therapeutic approaches for the pharmaceutical and biomedical researchers.

Probing the Potential Mechanism of Quercetin and Kaempferol against Heat Stress-Induced Sertoli Cell Injury: Through Integrating Network Pharmacology and Experimental Validation

Quercetin and kaempferol are flavonoids widely present in fruits, vegetables, and medicinal plants. They have attracted much attention due to their antioxidant, anti-inflammatory, anticancer, antibacterial, and neuroprotective properties. As the guarantee cells in direct contact with germ cells, Sertoli cells exert the role of support, nutrition, and protection in spermatogenesis. In the current study, network pharmacology was used to explore the targets and signaling pathways of quercetin and kaempferol in treating spermatogenic disorders. In vitro experiments were integrated to verify the results of quercetin and kaempferol against heat stress-induced Sertoli cell injury. The online platform was used to analyze the GO biological pathway and KEGG pathway. The results of the network pharmacology showed that quercetin and kaempferol intervention in spermatogenesis disorders were mostly targeting the oxidative response to oxidative stress, the ROS metabolic process and the NFκB pathway. The results of the cell experiment showed that Quercetin and kaempferol can prevent the decline of cell viability induced by heat stress, reduce the expression levels of HSP70 and ROS in Sertoli cells, reduce p-NF-κB-p65 and p-IκB levels, up-regulate the expression of occludin, vimentin and F-actin in Sertoli cells, and protect cell structure. Our research is the first to demonstrate that quercetin and kaempferol may exert effects in resisting the injury of cell viability and structure under heat stress.

The radical scavenger capacity and mechanism of prenylated coumestan-type compounds: a DFT analysis

The antiradical capacity and mechanisms of two representative coumestan-type compounds, namely isosojagol (Iso) and phaseoul (Pha), were examined using quantum chemistry calculations and computational kinetics methods. From a thermodynamic point of view, the 18CH groups of the prenyl substituent have been found to be the most suitable sites for radical attacks via the formal hydrogen transfer (FHT) mechanism. However, the kinetic study revealed that the reaction at these CH groups is slow and does not contribute to the overall reactivity of these compounds, which the phenolic groups mainly define. The kinetic study also revealed that the studied compounds are good free radical scavengers with overall rate coefficients as high as recognized antioxidants such as carnosic acid, artepillin C, thymol, and rosefuran.

Insights on the kinetics and mechanisms of the peroxyl radical scavenging capacity of caftaric acid: the important role of the acid–base equilibrium

Considering the acid–base equilibrium, caftaric acid has been shown to be one of the best antioxidants among phenolic acids in the aqueous physiological environment.

Is cannabidiolic acid an overlooked natural antioxidant? Insights from quantum chemistry calculations

The radical scavenging capacity of CBDA is moderate in lipid media but it is very important in water via the SET mechanism.

Mechanism of Antiradical Activity of Newly Synthesized 4,7-Dihydroxycoumarin Derivatives-Experimental and Kinetic DFT Study

Coumarin derivatives have proven beneficial biological activities, but the mechanism of their radical scavenging potency is not fully understood. In this study, the antiradical capacity of two newly synthesized 4,7-dihydroxycoumarin derivatives: (E)-3-(1-((3-hydroxy-4-methoxyphenyl)amino)-ethylidene)-2,4-dioxochroman-7-yl acetate (A-3OH) and (E)-3-(1-((4-hydroxy-3-methoxyphenyl)amino)ethylidene)-2,4-dioxochroman-7-yl acetate (A-4OH) towards HO• were examined by Electron Paramagnetic Resonance (EPR) Spectroscopy and Density Functional Theory (DFT). The compounds were fully characterized by the elemental microanalysis, IR, and NMR spectroscopies. The effect of pH on the acid-base equilibria is separately discussed and the predominant species at the physiological pH were determined. Several common mechanisms (Hydrogen Atom Transfer (HAT), Single-Electron Transfer followed by Proton Transfer (SET-PT), Sequential Proton Loss followed by Electron Transfer (SPLET), Radical Adduct Formation (RAF), and Intramolecular Hydrogen Atom Abstraction (iHAA)) of radical scavenging were investigated based on thermodynamic and kinetic parameters. EPR results indicated that both compounds significantly reduce the amount of present HO•. The results of the kinetic DFT study demonstrated that both compounds predominantly exhibit antiradical capacity through HAT and SPLET mechanisms. The estimated overall rate constants (koverall) proved that A-4OH shows better antioxidant capacity than A-3OH which is well-correlated with the results obtained by EPR measurement.

Modeling the peroxyl radical scavenging behavior of Carnosic acid: Mechanism, kinetics, and effects of physiological environments

Carnosic acid (CA), a phenolic diterpene and abietane-type compound, is a potent natural antioxidant with medical benefits. The present paper elucidates, for the first time, the kinetics and the exact mechanism of the peroxyl radical scavenging activity of CA in the gas phase and under physiological conditions. According to the obtained results, the reaction of CA with HOO^• is significantly faster in aqueous solution than in the gas phase and nonpolar environments. The abstraction of the hydrogen atom from 2-OH is the decisive mechanism in the gas phase and nonpolar media, while both hydrogen abstraction (15%) and electron transfer (85%) mechanisms can take place in aqueous solution. The overall rate coefficient in water (4.73 × 10⁶ M^-1 s^-1) is about 36 times higher than that of the reference antioxidant Trolox (1.30 × 10⁵ M^-1 s^-1), suggesting that CA is a potent scavenger of peroxyl radicals in polar media.

Antioxidant Activity of Natural Samwirin A: Theoretical and Experimental Insights

Samwirin A (SW), a natural compound isolated from Sambucus williamsii or Rourea harmandiana, is known to exhibit potent antiosteoporosis activity and promote cell proliferation in rat osteoblast-like UMR 106 cells. Antiosteoporosis activity suggests that the compound must also exhibit antioxidant activity but this has not been studied thus far. In the present study, the antioxidant activity of SW was examined by experimental and computational studies. It was found that SW exhibits good hydroperoxyl scavenging activity, particularly in water at physiological pH (k overall = 1.01 × 107 M-1 s-1). The single-electron transfer mechanism defines the HOO• + SW reaction in water, while the activity in the lipid medium is moderate and it follows the formal hydrogen transfer mechanism. The rate constant of the HOO• scavenging reaction in the aqueous solution is about 78 times higher than the reference compound Trolox. The computational results are in line with experimental data underscoring that SW is a promising radical scavenger in aqueous media at physiological pH.