The quasi-irreversible inactivation of cytochrome P450 enzymes by paroxetine: a computational approach

Molecular Insights Into β-Glucuronidase Inhibition by Alhagi Graecorum Flavonoids: A Computational and Experimental Approach

In this study, we aimed to investigate the inhibitory mechanisms of β-glucuronidase by flavonoids derived from Alhagi graecorum through both experimental and computational approaches. The activity of β-glucuronidase was assessed using an in vitro enzyme inhibition assay, where myricetin and chrysoeriol were identified as potent inhibitors based on their low IC50 values. Kinetic studies were conducted to determine the inhibition type, revealing that both compounds exhibit noncompetitive inhibition of β-glucuronidase-catalyzed hydrolysis of PNPG. Molecular docking was employed to explore the binding affinities of the flavonoids, showing that myricetin formed the highest number of polar interactions with the enzyme. Additionally, molecular dynamics (MD) simulations were performed to evaluate the stability of the enzyme-inhibitor complexes, demonstrating consistent trajectory behavior for both compounds, with significant energy stabilization. Interaction energy analyses highlighted the dominant role of electrostatic forces in myricetin's inhibition mechanism, while Van der Waals forces were more prominent for chrysoeriol. The MM/PBSA method was used to calculate the binding free energies, with myricetin and chrysoeriol exhibiting the lowest values. Potential energy landscape analysis further revealed that β-glucuronidase adopts a more closed conformation when bound to these inhibitors, limiting substrate access. These findings suggest that flavonoids from Alhagi graecorum hold promise for clinical applications, particularly in managing drug-induced enteropathy.

Unraveling the mechanism of carbonic anhydrase IX inhibition by alkaloids from Ruta chalepensis: A synergistic analysis of in vitro and in silico data

Due to the pivotal role of carbonic anhydrase IX (CA IX) in pathological conditions, there's a pressing need for novel inhibitors to improve patient outcomes and clinical management. Herein, we investigated the inhibitory efficacy of six alkaloids from Ruta chalepensis against CA IX through in vitro inhibition assay and computational modeling. Skimmianine and maculosidine displayed significant inhibitory activity in vitro, with low IC50 values of 105.2 ± 3.2 and 295.7 ± 14.1 nM, respectively. Enzyme kinetics analyses revealed that skimmianine exhibited a mixed inhibition mode, contrasting with the noncompetitive inhibition mechanism observed for the reference drug (acetazolamide), as indicated by intersecting lines in the Lineweaver-Burk plots. The findings of docking calculations revealed that skimmianine and maculosidine exhibited extensive polar interactions with the enzyme. These alkaloids demonstrate substantial binding interactions and occupy identical binding site as acetazolamide, thereby enhancing their efficacy as inhibitors of CA IX. Utilizing a 100 ns molecular dynamics (MD) simulation, the dynamic interactions between isolated alkaloids and CA IX were intensively assessed. Analysis of diverse MD parameters revealed that skimmianine and maculosidine displayed consistent trajectories and notable energy stabilization during their interaction with CA IX. The findings of MM/PBSA analysis depicted the minimum binding free energy for skimmianine and maculosidine. In addition, the Potential Energy Landscape (PEL) analysis revealed distinct and stable conformational states for the CA IX-ligand complexes, with Skimmianine showing the most stable and lowest energy configuration. These computational findings align with experimental results, emphasizing the potential efficacy of skimmianine and maculosidine as inhibitors of CA IX.

Dynamic interactions and inhibitory mechanisms of Artemisia annua terpenoids with carbonic anhydrase IX

This study evaluates the inhibitory potential of terpenoids isolated from Artemisia annua against carbonic anhydrase IX (CAIX), a crucial enzyme overexpressed in hypoxic tumor environments. Employing a multidisciplinary approach, we utilized in vitro assays, enzyme kinetics, molecular docking, and molecular dynamics (MD) simulations to comprehensively assess the efficacy of these compounds. Among the terpenoids tested, manool emerged as the most potent inhibitor, exhibiting the lowest IC50 value of 160.2 ± 15.2 nM. This was followed by labda-8(17),12-diene-15,16-dial with an IC50 of 297.9 ± 8.84 nM. Enzyme kinetics revealed a mixed inhibition mode for both compounds. Molecular docking aligned well with in vitro data, showing extensive polar and hydrophobic interactions within the CAIX binding site. Further insights were gained through 300 ns MD simulations, which highlighted the dynamic interactions and stability of these complexes. Manool demonstrated the most significant stabilization of CAIX, as evidenced by favorable RMSD, Rg, SASA profiles, and the strongest hydrogen bonding interactions. Additionally, MM/PBSA calculations confirmed manool's superior binding affinity. These findings underscore the therapeutic potential of manool as a potent CAIX inhibitor, providing a foundation for the development of effective anticancer agents targeting hypoxic tumor environments. ADMET analysis revealed favorable pharmacokinetic profiles for the terpenoids, with manool demonstrating high lipophilicity and BBB permeability, though potential CYP-mediated interactions were noted.

Bridging in silico and in vitro perspectives to unravel molecular mechanisms underlying the inhibition of β-glucuronidase by coumarins from Hibiscus trionum

Unraveling the intricacies of β-glucuronidase inhibition is pivotal for developing effective strategies in applications specific to gastrointestinal health and drug metabolism. Our study investigated the efficacy of some Hibiscus trionum phytochemicals as β-glucuronidase inhibitors. The results showed that cleomiscosin A and mansonone H emerged as the most potent inhibitors, with IC50 values of 3.97 ± 0.35 μM and 10.32 ± 1.85 μM, respectively. Mechanistic analysis of β-glucuronidase inhibition indicated that cleomiscosin A and the reference drug EGCG displayed a mixed inhibition mode against β-glucuronidase, while mansonone H exhibited noncompetitive inhibition against β-glucuronidase. Docking studies revealed that cleomiscosin A and mansonone H exhibited the lowest binding affinities, occupying the same site as EGCG, and engaged significant key residues in their binding mechanisms. Using a 30 ns molecular dynamics (MD) simulation, we explored the interaction dynamics of isolated compounds with β-glucuronidase. Analysis of various MD parameters showed that cleomiscosin A and mansonone H exhibited consistent trajectories and significant energy stabilization with β-glucuronidase. These computational insights complemented experimental findings, underscoring the potential of cleomiscosin A and mansonone H as β-glucuronidase inhibitors.

Phytochemical Analysis, and Antioxidant and Hepatoprotective Activities of Chamaerops humilis L. Leaves; A Focus on Xanthine Oxidase

Chamaerops humilis L. is clumping palm of the family Arecaceae with promising health-promoting effects. Parts of this species are utilized as food and employed in folk medicine to treat several disorders. This study investigated the phytochemical constituents of C. humilis leaves and their antioxidant and xanthine oxidase (XO) inhibitory activities in vitro and in vivo in acetaminophen (APAP)-induced hepatotoxicity in rats. The chemical structure of the isolated phytochemicals was determined using data obtained from UV, MS, IR, and 1H-, 13C-NMR spectroscopic tools as well as comparison with authentic markers. Eleven compounds, including tricin 7-O-β-rutinoside, vicenin, tricin, astragalin, borassoside D, pregnane-3,5,6,16-tetrol, oleanolic acid, β-sitosterol and campesterol were isolated from C. humilis ethanolic extract (CHEE). CHEE and the butanol, n-hexane, and dichloromethane fractions exhibited in vitro radical scavenging and XO inhibitory efficacies. The computational findings revealed the tendency of the isolated compounds towards the active site of XO. In vivo, CHEE ameliorated liver function markers and prevented tissue injury induced by APAP in rats. CHEE suppressed hepatic XO, decreased serum uric acid and liver malondialdehyde (MDA), and enhanced reduced glutathione (GSH), superoxide dismutase (SOD), and catalase in APAP-treated rats. CHEE ameliorated serum tumor necrosis factor alpha (TNF-α) and interleukin (IL)-1β in APAP-treated rats. Thus, C. humilis is rich in beneficial phytochemicals that possess binding affinity towards XO. C. humilis exhibited potent in vitro antioxidant and XO inhibitory activities, and prevented APAP hepatotoxicity by attenuating tissue injury, oxidative stress and inflammation.

Dissecting molecular mechanisms underlying the inhibition of β-glucuronidase by alkaloids from Hibiscus trionum: Integrating in vitro and in silico perspectives

β-Glucuronidase, a crucial enzyme in drug metabolism and detoxification, represents a promising target for therapeutic intervention due to its potential to modulate drug pharmacokinetics and enhance therapeutic efficacy. Herein, we assessed the inhibitory potential of phytochemicals from Hibiscus trionum against β-glucuronidase. Grossamide and grossamide K emerged as the most potent β-glucuronidase inhibitors with IC50 values of 0.73 ± 0.03 and 1.24 ± 0.03 μM, respectively. The investigated alkaloids effectively inhibited β-glucuronidase-catalyzed PNPG hydrolysis through a noncompetitive inhibition mode, whereas steppogenin displayed a mixed inhibition mechanism. Molecular docking analyses highlighted grossamide and grossamide K as inhibitors with the lowest binding free energy, all compounds successfully docked into the same main binding site occupied by the reference drug Epigallocatechin gallate (EGCG). We explored the interaction dynamics of isolated compounds with β-glucuronidase through a 200 ns molecular dynamics (MD) simulation. Analysis of various MD parameters revealed that grossamide and grossamide K maintained stable trajectories and demonstrated significant energy stabilization upon binding to β-glucuronidase. Additionally, these compounds exhibited the lowest average interaction energies with the target enzyme. The MM/PBSA calculations further supported these findings, showing the lowest binding free energies for grossamide and grossamide K. These computational results are consistent with experimental data, suggesting that grossamide and grossamide K could be potent inhibitors of β-glucuronidase.

Deciphering molecular mechanisms underlying the inhibition of β-glucuronidase by xanthones from Centaurium spicatum

Herein, we scrutinized the inhibitory potential of five xanthones and a flavonoid, sourced from Centaurium spicatum, against β-glucuronidase activity. The results showed that gentisin and azaleatin emerged as the most potent inhibitors, with significantly lower IC50 values of 0.96 ± 0.10 and 0.57 ± 0.04 μM, respectively. The evaluation of enzyme kinetics unveiled that the isolated xanthones manifested inhibition of β-glucuronidase through a mixed inhibition mode, whereas azaleatin exhibited a noncompetitive inhibition mechanism. The findings from molecular docking analysis unveiled that the compounds under investigation, particularly azaleatin, displayed comparatively diminished binding affinities towards β-glucuronidase. Furthermore, the tested drugs were shown to occupy a common binding site as the employed reference drug. Our comprehensive Molecular Dynamics (MD) simulations analysis revealed consistent trajectories for the investigated drugs, wherein azaleatin and gentisin demonstrated notable stabilization of energy levels. Analysis of various MD parameters revealed that drugs with the lowest IC50 values maintained relatively stable interactions with β-glucuronidase. These drugs were shown to exert notable alterations in their conformation or flexibility upon complexation with the target enzyme. Conversely, the flexibility and accessibility of β-glucuronidase was reduced upon drug binding, particularly with azaleatin and gentisin, underscoring the stability of the drug-enzyme complexes. Analysis of Coul-SR and LJ-SR interaction energies unveiled consistent and stable interactions between certain isolated drugs and β-glucuronidase. Azaleatin notably displayed the lowest average Coul-SR interaction energy, suggesting strong electrostatic interactions with the enzyme's active site and significant conformational variability during simulation. Remarkably, LJ-SR interaction energies across different xanthones complexes were more negative than their Coul-SR counterparts, emphasizing the predominant role of van der Waals interactions, encompassing attractive dispersion and repulsive forces, in stabilizing the drug-enzyme complexes rather than electrostatic interactions.

Mechanistic insights into the metabolic pathways of vanillin: unraveling cytochrome P450 interaction mechanisms and implications for food safety

Vanillin, a key flavor compound found in vanilla beans, is widely used in the food and pharmaceutical industries for its aromatic properties and potential therapeutic benefits. This study presents a comprehensive quantum chemical analysis to elucidate the interaction mechanisms of vanillin with CYP450 enzymes, with a focus on mechanism-based inactivation. Three potential inactivation pathways were evaluated: aldehyde deformylation, methoxy dealkylation, and acetal formation. Aldehyde deformylation was identified as the most energy-efficient, involving the removal of the aldehyde group from vanillin and leading to the formation of benzyne intermediates that could react with the iron porphyrin moiety of CYP450, potentially resulting in enzyme inactivation. Further investigation into the interactions of vanillin with CYP2E1 and CYP1A2 was conducted using molecular docking and molecular dynamics (MD) simulation. The docking analyses supported the findings from DFT studies, wherein vanillin revealed high binding affinities with the studied isozymes. Moreover, vanillin occupied the main binding site in both isozymes, as evidenced by the inclusion of the heme moiety in their binding mechanisms. Employing a 100 ns molecular dynamics simulation, we scrutinized the interaction dynamics between vanillin and the two isozymes of CYP450. The assessment of various MD parameters along with interaction energies revealed that vanillin exhibited stable trajectories and substantial energy stabilization during its interaction with both CYP450 isozymes. These insights can guide future research and ensure the safe application of vanillin, especially in scenarios where it may interact with CYP450 enzymes.

Unveiling the tyrosinase inhibitory potential of phenolics from Centaurium spicatum: Bridging in silico and in vitro perspectives

Phenolics, abundant in plants, constitute a significant portion of phytoconstituents consumed in the human diet. The phytochemical screening of the aerial parts of Centaurium spicatum led to the isolation of five phenolics. The anti-tyrosinase activities of the isolated compounds were assessed through a combination of in vitro experiments and multiple in silico approaches. Docking and molecular dynamics (MD) simulation techniques were utilized to figure out the binding interactions of the isolated phytochemicals with tyrosinase. The findings from molecular docking analysis revealed that the isolated phenolics were able to bind effectively to tyrosinase and potentially inhibit substrate binding, consequently diminishing the catalytic activity of tyrosinase. Among isolated compounds, cichoric acid displayed the lowest binding energy and the highest extent of polar interactions with the target enzyme. Analysis of MD simulation trajectories indicated that equilibrium was reached within 30 ns for all complexes of tyrosinase with the isolated phenolics. Among the five ligands studied, cichoric acid exhibited the lowest interaction energies, rendering its complex with tyrosinase the most stable. Considering these collective findings, cichoric acid emerges as a promising candidate for the design and development of a potential tyrosinase inhibitor. Furthermore, the in vitro anti-tyrosinase activity assay unveiled significant variations among the isolated compounds. Notably, cichoric acid exhibited the most potent inhibitory effect, as evidenced by the lowest IC50 value (7.92 ± 1.32 µg/ml), followed by isorhamnetin and gentiopicrin. In contrast, sinapic acid demonstrated the least inhibitory activity against tyrosinase, with the highest IC50 value. Moreover, cichoric acid exhibited a mixed inhibition mode against the hydrolysis of l-DOPA catalyzed by tyrosinase, with Ki value of 1.64. Remarkably, these experimental findings align well with the outcomes of docking and MD simulations, underscoring the consistency and reliability of our computational predictions with the actual inhibitory potential observed in vitro.

Deciphering the Molecular Mechanisms of Reactive Metabolite Formation in the Mechanism-Based Inactivation of Cytochrome p450 1B1 by 8-Methoxypsoralen and Assessing the Driving Effect of phe268

This study provides a comprehensive computational exploration of the inhibitory activity and metabolic pathways of 8-methoxypsoralen (8-MP), a furocoumarin derivative used for treating various skin disorders, on cytochrome P450 (P450). Employing quantum chemical DFT calculations, molecular docking, and molecular dynamics (MD) simulations analyses, the biotransformation mechanisms and the active site binding profile of 8-MP in CYP1B1 were investigated. Three plausible inactivation mechanisms were minutely scrutinized. Further analysis explored the formation of reactive metabolites in subsequent P450 metabolic processes, including covalent adduct formation through nucleophilic addition to the epoxide, 8-MP epoxide hydrolysis, and non-CYP-catalyzed epoxide ring opening. Special attention was paid to the catalytic effect of residue Phe268 on the mechanism-based inactivation (MBI) of P450 by 8-MP. Energetic profiles and facilitating conditions revealed a slight preference for the C4'=C5' epoxidation pathway, while recognizing a potential kinetic competition with the 8-OMe demethylation pathway due to comparable energy demands. The formation of covalent adducts via nucleophilic addition, particularly by phenylalanine, and the generation of potentially harmful reactive metabolites through autocatalyzed ring cleavage are likely to contribute significantly to P450 metabolism of 8-MP. Our findings highlight the key role of Phe268 in retaining 8-MP within the active site of CYP1B1, thereby facilitating initial oxygen addition transition states. This research offers crucial molecular-level insights that may guide the early stages of drug discovery and risk assessment related to the use of 8-MP.

Multi-target action of Garcinia livingstonei extract and secondary metabolites against fatty acid synthase, α-glucosidase, and xanthine oxidase

Garcinia livingstonei is a traditional herbal medicine that showed beneficial health effects and bioactivities. Four compounds have been isolated from the plant leaves and were elucidated as lupeol, betulin, podocarpusflavone A, and amentoflavone. The inhibitory activities of G. livingstonei extract and isolated metabolites against fatty acid synthase (FAS), α-glucosidase, and xanthine oxidase (XO) were investigated in vitro. The affinity of the compounds toward the studied enzymes was investigated in silico. The plant extract inhibited FAS, α-glucosidase, and XO with IC50 values of 26.34, 67.88, and 33.05 µg/mL, respectively. Among the isolated metabolites, betulin exhibited the most inhibitory activity against α-glucosidase and XO with IC50 values of 38.96 and 30.94 µg/mL, respectively. Podocarpusflavone A and betulin were the most potent inhibitors of FAS with IC50 values of 24.08 and 27.96 µg/mL, respectively. Computational studies corroborated these results highlighting the interactions between metabolites and the enzymes. In conclusion, G. livingstonei and its constituents possess the potential to modulate enzymes involved in metabolism and oxidative stress.

Mechanistic aspects of reactive metabolite formation in clomethiazole catalyzed biotransformation by cytochrome P450 enzymes

Clomethiazole (CLM), a sedative and anticonvulsant drug, is commonly employed for the treatment of alcohol withdrawal syndrome because it suppresses cytochrome P450 (P450) activity associated with the generation of free radicals and liver damage. The catalyzed biotransformation of thiazole-containing drugs by P450 is known to afford reactive metabolites. These metabolites can alter the biological functions of macromolecules and result in toxicity and adverse drug interactions. Multitargeted molecular modeling and quantum chemical DFT calculations were performed to explore the binding modes and molecular mechanisms underlying the mechanism-based inactivation (MBI) of P450 by CLM. The mechanistic details associated with reactive metabolite formation from further metabolic processes were extensively assessed. Seven possible routes were proposed for CLM-P450 biotransformation including CLM hydroxylation, sulfoxidation, N-oxidation, CN epoxidation (oxaziridine formation), and CC epoxidation. The results revealed a degree of preference for the C-N epoxidation pathway because of the low energy requirements of its rate-determining step (8.74 and 10.07 kcal mol-1 for LS and HS states, respectively). A kinetic competition for the CLM-methyl hydroxylation pathway was detected because the H-abstraction energy barrier was relatively comparable to the thermodynamically prevailing oxaziridine formation rate-determining step (12.58 and 14.52 kcal mol-1 for quartet and doublet states, respectively). Our studies assessed the mechanisms of covalent nucleophilic epoxide adduct formation through nucleophilic addition, hydrolysis of epoxidation products, and nonenzymatic degradation. CLM was shown to display P450-inhibitory activity by forming covalent adducts rather than further metabolization to reactive metabolites. The outcomes of molecular docking allowed assessing the binding profile of CLM with three human P450 isozymes, namely, CYP2E1, CYP3A4, and CYP2D6.

Multitargeted molecular modelling of alginic acid modified with 4-aminophenol dopped with silver nanoparticles as a potent cytotoxic agent

The activity of alginic acid as a cytotoxic agent was improved by structure modification using 4-aminophenol (4-AP) through condensation and polymerization processes. Then, silver nanoparticles were employed through doping to further enhance the cytotoxic activity of the modified polymer. The structure of the prepared materials was characterized by FT-IR, ¹HNMR, UV spectroscopy, X-ray diffraction, and electron microscopy, and the thermal behavior of all synthesized materials was intensively studied. The cytotoxicity of the prepared compounds against cell lines of human hepatocellular (HepG-2) and lung (A-549) carcinomas was investigated. Alginic acid modified with 4-AP (Alg-4-AP₃) showed the highest activity against HepG-2 and A-549 among all tested materials with IC₅₀ values of 3.0 ± 0.19 μg/mL and 3.63 ± 0.23 μg/mL, respectively. Multitargeted molecular docking was employed to explore the binding modes of our compounds with the receptors EGFR, HER2, and VEGFR 2. The results revealed the inhibitory activity of our tested compounds against the proposed protein receptors, findings coincided with the in vitro results. In conclusion, the modification of alginic acid with 4-AP improved its cytotoxic activity against HepG-2 and A-549 cancer cells. In addition, doping the new materials with silver nanoparticles (AgNPs) further enhanced the cytotoxic activity.

Molecular modeling and DFT studies on the antioxidant activity of Centaurea scoparia flavonoids and molecular dynamics simulation of their interaction with β-lactoglobulin

Plants of the genus Centaurea have been widely used as natural therapeutics in different countries. This study investigated the antioxidant-structure activity relationship of eight flavonoids isolated from Centaurea scoparia using DFT studies and in vitro radical scavenging and xanthine oxidase (XO) inhibition assays, and to correlate the theoretical values with the experimental findings. Docking analysis was carried out to explore the binding modes of the isolated phytochemicals with XO and bovine β-lactoglobulin (BLG). Interactions of the isolated compounds with BLG were studied using molecular dynamics (MD) simulations which revealed the involvement of hydrogen bonding. The root-mean-square deviation (RMSD) of BLG and BLG-flavonoid complexes reached equilibrium and fluctuated during the 10 ns MD simulations. The radius of gyration (Rg) and solvent accessible surface area (SASA) revealed that various systems were stabilized at approximately 2500 ps. In addition, the RMS fluctuations profile indicated that the ligand's active site exerted rigidity behavior during the simulation. The hydrogen atom transfer (HAT) and the energies of hydrogen abstractions were estimated by calculating the bond dissociation enthalpy (BDE) of O-H in gas phase and water. The isolated compounds showed radical scavenging and XO inhibitory activities along with binding affinity with XO as revealed in silico. The BDE was linked to the radical scavenging processes occurring in polar solvents. These processes are single electron transfer followed by proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET). Our calculations indicated the agreement between the calculated results and the experimentally measured antioxidant activity of the flavonoids isolated from C. scoparia.

Identification of the metabolite of ophiopogonanone A by liquid chromatography/quadrupole time-of-flight mass spectrometry

RATIONALE

Ophiopogonanone A (OPA) is one of the representative homoisoflavonoids isolated from Ophiopogonis Radix. The aim of this study was to identify and characterize the metabolites of OPA generated in the liver microsomes and hepatocytes of rats and humans.

METHODS

The metabolites were generated by incubating OPA (5 μM) with liver microsomes or hepatocytes at 37°C. To trap the reactive metabolites, glutathione (GSH, 5mM) was added into microsomal incubations. The metabolite identification and profiling were performed using ultra-high-performance liquid chromatography combined with photo-diode array detector and quadrupole time-of-flight tandem mass spectrometry (LC-Q/TOF-MS). The acquired mass data were processed by MetaboLynx software. The structures of the metabolites were tentatively characterized in terms of their accurate masses, product ions, and retention times.

RESULTS

Under the present conditions, a total of nine metabolites were detected and their structures were tentatively identified. Among these metabolites, M8 (OPA catechol) was the most abundant metabolite both in rat and human liver microsomes. M7 (glucuronidation product of M8) was the major metabolite both in rat and human hepatocytes. The metabolic pathways of OPA include demethylenation, dehydrogenation, hydroxylation, methylation and glucuronidation and GSH conjugation.

CONCLUSION

Our results provided valuable information regarding the in vitro metabolism of OPA, which would help us understand the mechanism of the elimination of OPA and in turn the effectiveness and potential toxicity.

Methysticin Acts as a Mechanism-Based Inactivator of Cytochrome P450 2C9

Methysticin is one of the naturally occurring bioactive constituents extracted from Piper methysticum Forst. In the present study, we intended to investigate the inhibitory effect of methysticin on cytochrome P450 (P450) enzymes. Methysticin exhibited time-, concentration-, and NADPH-dependent inhibition on CYP2C9 using diclofenac as a probe substrate. Approximately 85% of CYP2C9 activity was inhibited by methysticin at 50 μM after a 30 min preincubation with human liver microsomes in the presence of NADPH. The kinetic parameters K_I, k_inact, and t_1/2,inact were 13.32 ± 1.35 μM, 0.054 ± 0.005 min^-1, and 12.83 ± 3.23 min, respectively. Sulfaphenazole (competitive inhibitor of CYP2C9) displayed a significant protective effect on methysticin-induced CYP2C9 inactivation. However, the inclusion of catalase/superoxide dismutase or glutathione (GSH) showed no such protection. A carbene intermediate was postulated to be involved in methysticin-induced CYP2C9 inactivation as K₃Fe(CN)₆ recovered 14.96% of CYP2C9 activity. A methysticin-derived ortho-quinone intermediate dependent on NADPH was trapped by GSH, and this intermediate was believed to be involved in CYP2C9 inactivation. CYP1A2, 2C9, and 3A4 were the major enzymes responsible for methysticin bioactivation. Taken together, the present work demonstrated that methysticin was a mechanism-based inactivator of CYP2C9. Both ortho-quinone and carbene intermediates appeared to be involved in the inactivation of CYP2C9 induced by methysticin.

Energy Decomposition Analysis of the Nature of Coordination Bonding at the Heme Iron Center in Cytochrome P450 Inhibition

Drug compounds or their metabolic intermediates (MIs) sometimes inhibit the function of cytochrome P450 enzymes (P450s) by forming a coordination bond with the Fe(III) heme or Fe(II) heme of P450s. Such inhibition is one of the major causes of drug-drug interactions (DDIs), a subject of longstanding academic and practical interest. However, such coordination bonding is not fully understood at the quantum mechanical level, thus hampering rational improvement of the accuracy of DDI-related predictions. In this work, we employed density functional theory (DFT) and the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme to investigate the nature of the coordination bonding formed in the reversible and quasi-irreversible inhibition of P450s. The GKS-EDA results highlighted a previously unrecognized role of the electron correlation effect in P450 inhibition. The correlation effect tends to be larger in Fe(II) complexes of MI-type inhibitors and is particularly prominent for the nitrosoalkane ligand. An additional natural bond orbital (NBO) analysis provided insight into the relative significance of the σ donation and π backdonation effects in various heme-inhibitor complexes.

Pogostone inhibits the activity of CYP3A4, 2C9, and 2E1 in vitro

CONTEXT

Pogostone possesses various pharmacological activities, which makes it widely used in the clinic. Its effect on the activity of cytochrome P450 enzymes (CYP450s) could guide its clinical combination.

OBJECTIVE

To investigate the effect of pogostone on the activity of human CYP450s.

MATERIALS AND METHODS

The effect of pogostone on the activity of CYP450s was evaluated in human liver microsomes (HLMs) compared with blank HLMs (negative control) and specific inhibitors (positive control). The corresponding parameters were obtained with 0-100 μM pogostone and various concentrations of substrates.

RESULTS

Pogostone was found to inhibit the activity of CYP3A4, 2C9, and 2E1 with the IC₅₀ values of 11.41, 12.11, and 14.90 μM, respectively. The inhibition of CYP3A4 by pogostone was revealed to be performed in a non-competitive and time-dependent manner with the K_i value of 5.69 μM and the KI/K_inact value of 5.86/0.056/(μM/min). For the inhibition of CYP2C9 and 2E1, pogostone acted as a competitive inhibitor with the K_i value of 6.46 and 7.67 μM and was not affected by the incubation time.

DISCUSSION AND CONCLUSIONS

The inhibitory effect of pogostone on the activity of CYP3A4, 2C9, and 2E1 has been disclosed in this study, implying the potential risk during the co-administration of pogostone and drugs metabolized by these CYP450s. The study design provides a reference for further in vivo investigations to validate the potential interaction.

Water biocatalytic effect attenuates cytochrome P450-mediated carcinogenicity of diethylnitrosamine: A computational insight

The mechanism-based mutagenicity and carcinogenicity of diethylnitrosamine (DEN) are believed to act through interactions with cytochrome P450 (P450) enzymes. DFT calculations to explore the conceivable mechanisms underlying the reaction of P450 with DEN with and without water as a biocatalyst were performed. The results shed light on the biocatalytic role of water in lowering the H-abstraction energy barriers because of the electrostatic effect driven by hydrogen bonding. Our DFT analysis revealed how metabolites are formed in the dealkylation (toxification) and denitrosation (detoxification) pathways. Also, our findings uncovered the active position of DEN vulnerable to P450 interactions. Two factors control the toxification and detoxification rates: the stability of denitrosation products and the HS rebound barrier of the α-pathway. Thus, water biocatalytic attenuation of DEN carcinogenicity was attained by stabilizing denitrosation products and slowing the α-HS rebound process. Docking and MD simulations were performed to assess the binding modes of DEN to P450's active site and to inspect the denitrosation and dealkylation processes, respectively.

Visnagin prevents isoproterenol-induced myocardial injury by attenuating oxidative stress and inflammation and upregulating Nrf2 signaling in rats

Oxidative tissue injury and inflammatory responses play major roles in cardiovascular diseases and heart failure. Visnagin (VIS) is a natural bioactive component of Ammi visnaga, with promising radical scavenging and anti-inflammatory activities. This study explored the protective effect of VIS against isoproterenol (ISO)-induced acute myocardial injury and oxidative stress in rats. VIS was supplemented for 14 days, and the rats received ISO (100 mg/kg) twice at an interval of 24 h. ISO-induced myocardial injury was characterized by elevated serum CK-MB, LDH, and troponin-I associated with increased heart weight and several histopathological changes. ISO increased reactive oxygen species (ROS), malondialdehyde (MDA), NF-κB p65, TNF-α, IL-6, and decreased glutathione and antioxidant enzymes in rats' hearts. VIS prevented myocardial injury and ameliorated the cardiac function markers, ROS, MDA, NF-κB p65, and pro-inflammatory cytokines in ISO-intoxicated rats. In addition, VIS decreased Bax mRNA and caspases, and upregulated Nrf2, HO-1, Bcl-2, and PPARγ. Molecular docking simulations revealed the binding method of VIS to NF-κB, Keap1, and PPARγ. In conclusion, VIS protects against ISO-induced acute myocardial injury by attenuating oxidative tissue injury and reducing key inflammatory and apoptosis markers. In vivo and in silico results showed that activation of Nrf2/HO-1 signaling and PPARγ mediates the cardioprotective effect of VIS.

Galangin Attenuates Liver Injury, Oxidative Stress and Inflammation, and Upregulates Nrf2/HO-1 Signaling in Streptozotocin-Induced Diabetic Rats

Chronic hyperglycemia increases the risk of liver damage. Oxidative stress and aberrant inflammatory response are entangled in diabetes-associated liver injury. This study evaluated the protective effect of the flavonoid galangin (Gal) on glucose intolerance, liver injury, oxidative stress, inflammatory response, and Nrf2/HO-1 signaling in diabetic rats. Diabetes was induced by streptozotocin (STZ), and the rats received Gal for six weeks. STZ-induced rats showed glucose intolerance, hypoinsulinemia, elevated glycated hemoglobin (HbA1c), and decreased liver glycogen. Gal ameliorated glucose intolerance, reduced HbA1c%, increased serum insulin and liver glycogen and hexokinase activity, and suppressed glycogen phosphorylase, glucose-6-phosphatase and fructose-1,6-biphosphatase in diabetic rats. Circulating transaminases, ALP and LDH, and liver ROS, MDA, TNF-α, IL-1β, and IL-6 were increased and GSH, SOD, and CAT were diminished in diabetic rats. In addition, diabetic rats exhibited multiple histopathological alterations and marked collagen deposition. Treatment with Gal mitigated liver injury, prevented histopathological alterations, decreased ROS, MDA, pro-inflammatory cytokines, Bax and caspase-3, and enhanced cellular antioxidants and Bcl-2. Gal downregulated hepatic Keap1 in diabetic rats and upregulated Nrf2 and HO-1 mRNA as well as HO-1 activity. Molecular modeling studies revealed the ability of Gal to bind to and inhibit NF-κB and Keap1, and also showed its binding pattern with HO-1. In conclusion, Gal ameliorates hyperglycemia, glucose intolerance, oxidative stress, inflammation, and apoptosis in diabetic rats. Gal improved carbohydrate metabolizing enzymes and upregulated Nrf2/HO-1 signaling.

Geminal Diheteroatomic Motifs: Some Applications of Acetals, Ketals, and Their Sulfur and Nitrogen Homologues in Medicinal Chemistry and Drug Design

Acetals and ketals and their nitrogen and sulfur homologues are often considered to be unconventional and potentially problematic scaffolding elements or pharmacophores for the design of orally bioavailable drugs. This opinion is largely a function of the perception that such motifs might be chemically unstable under the acidic conditions of the stomach and upper gastrointestinal tract. However, even simple acetals and ketals, including acyclic molecules, can be sufficiently robust under acidic conditions to be fashioned into orally bioavailable drugs, and these structural elements are embedded in many effective therapeutic agents. The chemical stability of molecules incorporating geminal diheteroatomic motifs can be modulated by physicochemical design principles that include the judicious deployment of proximal electron-withdrawing substituents and conformational restriction. In this Perspective, we exemplify geminal diheteroatomic motifs that have been utilized in the discovery of orally bioavailable drugs or drug candidates against the backdrop of understanding their potential for chemical lability.

Paroxetine-Overview of the Molecular Mechanisms of Action

In the 21st century and especially during a pandemic, the diagnosis and treatment of depression is an essential part of the daily practice of many family doctors. It mainly affects patients in the age category 15–44 years, regardless of gender. Anxiety disorders are often diagnosed in children and adolescents. Social phobias can account for up to 13% of these diagnoses. Social anxiety manifests itself in fear of negative social assessment and humiliation, which disrupts the quality of social functioning. Treatment of the above-mentioned disorders is based on psychotherapy and pharmacotherapy. Serious side effects or mortality from antidepressant drug overdose are currently rare. Recent studies indicate that paroxetine (ATC code: N06AB), belonging to the selective serotonin reuptake inhibitors, has promising therapeutic effects and is used off-label in children and adolescents. The purpose of this review is to describe the interaction of paroxetine with several molecular targets in various points of view including the basic chemical and pharmaceutical properties. The central point of the review is focused on the pharmacodynamic analysis based on the molecular mechanism of binding paroxetine to various therapeutic targets.