Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther. 2013;138:103-141. [PMID: 23333322 DOI: 10.1016/j.pharmthera.2012.12.007]

Normal bronchial field basal cells show persistent methylome-wide impact of tobacco smoking, including in known cancer genes

Lung carcinogenesis is causally linked to cigarette smoking, in part by epigenetic changes. We tested whether accumulated epigenetic change in smokers is apparent in bronchial basal cells as cells of origin of squamous cell carcinoma. Using an EM-seq platform covering 53.8 million CpGs (96% of the entire genome) at an average of 7.5 sequencing reads per CpG site at a single base resolution, we evaluated cytology-normal basal cells bronchoscopically brushed from the in situ tobacco smoke-exposed 'bronchial epithelial field' and isolated by short-term primary culture from 54 human subjects. We found that mean methylation was globally lower in ever (former and current) smokers versus never smokers (p = 0.0013) across promoters, CpG shores, exons, introns, 3'-UTRs, and intergenic regions, but not in CpG islands. Among 6mers with dinucleotides flanking CpG, those containing CGCG showed no effect from smoking, while those flanked with TT and AA displayed the strongest effects. At the gene level, smoking-related differences in methylation level were observed in CDKL1, ARTN, EDC3, CYP1B1, FAM131A, and MAGI2. Among candidate cancer genes, smoking reduced the methylation level in KRAS, ROS1, CDKN1A, CHRNB4, and CADM1. We conclude that smoking reduces long-term epigenome-wide methylation in bronchial stem cells, is impacted by the flanking sequence, and persists indefinitely beyond smoking cessation.

Combination with isopentenyl diphosphate isomerase gene affects expression of two linalool/nerolidol synthases isoforms from Lingzhi

GlSTS21 and GsSTS41, derived from Ganoderma lucidum (Leyss. ex Fr.) Karst. and G. sinense Zhao, Xu et Zhang, respectively, have been identified as linalool/nerolidol synthases. Although both enzymes catalyze the synthesis of linalool and nerolidol, they exhibit distinct sequences and conserved structural domains, as well as variations in their secondary and tertiary structures, and differences in the location and number of substrate binding sites. When subjected to identical modification methods, GlSTS21 and GsSTS41 demonstrated divergent production trends. Specifically, GlSTS21 achieved the highest production of nerolidol when constructed in the sequence of pET28a-T7-GlSTS21-T7-E. coli isopentenyl diphosphate isomerase (IDI). Conversely, the highest production of linalool by GlSTS21 occurred when it was arranged in the sequence of pET28a-T7-GlSTS21-T7-E. coli IDI. For GsSTS41, the optimal production of both linalool and nerolidol was attained when it was ligated in the sequence of pET28a-T7-E. coli IDI-T7 -GsSTS41. These findings provide valuable insights for future efforts aimed at optimizing product-focused selection in industrial production processes.

Exploration of functional cytochrome P450 4F enzymes in liver, intestine, and kidney from dogs, cats, pigs, and tree shrews and comparison of their metabolic capacities with human P450 4F2 and 4F12

Pigs are often used in drug metabolism studies because of their evolutionary proximity to humans, including similarities in their cytochromes P450 (P450s or CYPs). In the current study, the following cDNAs of novel CYP4Fs were isolated and characterized: dog CYP4F22 and CYP4F140; cat CYP4F22 and CYP4F140; pig CYP4F22, CYP4F52, CYP4F53, CYP4F54, CYP4F56, and CYP4F176; and tree shrew CYP4F22. Previously identified pig CYP4F55 cDNA was also isolated. These CYP4F cDNAs contained open reading frames of 522-531 amino acids and shared high sequence identities (60-92 %) with human CYP4Fs. Dog CYP4F3a and CYP4F3b cDNAs were also identified but lacked the 3' end of the coding region. Phylogenetic analysis of amino acid sequences showed that these CYP4Fs were clustered in a species-dependent manner, except for CYP4F3, CYP4F22, and CYP4F140, which were clustered in an isoform-dependent manner. All CYP4F genes, containing 12 coding exons, formed a gene cluster at the corresponding location of the genome in each species. Among the tissue samples analyzed, dog and cat CYP4F140 mRNAs were more abundantly expressed in liver/testis and kidney, respectively. Preferential expression of pig CYP4F mRNAs were found in liver, small intestine, and/or kidney, where the most abundant were CYP4F56, CYP4F52, and CYP4F176 mRNAs, respectively. Enzyme assays using recombinant proteins revealed that all these CYP4Fs oxidized the human CYP4F substrate arachidonic acid at the ω-position, indicating that they are functional enzymes. These findings suggest that dog, cat, pig, and tree shrew CYP4Fs have similar functional characteristics to human CYP4Fs.

Nomograms based on clinical factors to predict abnormal metabolism of psychotropic drugs

Interindividual variability in drug metabolism serves a critical role in the occurrence of adverse drug reactions. Factors such as age, sex, body mass index (BMI) and liver and renal function can influence the metabolism of antipsychotic medications. To the best of our knowledge, however, clinical prediction models based on these factors for estimating drug-metabolizing capacity have not yet been developed. Between January 2022 and September 2023, 185 adult patients (aged ≥18 years) who did not have cancer and were not critically ill, with or without comorbidities such diabetes, hypertension and liver and kidney diseases, who underwent pharmacogenetic testing at The First Hospital of Jilin University (Changchun, China) were enrolled. Clinical data were collected, and the participants were divided into training and validation cohorts. Logistic regression was performed to identify significant risk factors, which were incorporated into multivariable models to construct nomograms predicting psychotropic drug metabolism. A total of eight clinical indicators (BMI, hypertension, alkaline phosphatase, aspartate aminotransferase, cholinesterase, albumin to globulin ratio, urea, and uric acid) were significantly associated with psychotropic drug metabolism (all P<0.05). Based on these indicators, along with age and sex, prediction models for psychotropic drug metabolism were developed. The areas under the receiver operating characteristic curves for haloperidol, olanzapine, paroxetine, mirtazapine/venlafaxine and oxazepam/lorazepam in the validation dataset were 0.767, 0.767, 0.705, 0.740 and 0.789, respectively, indicating the models had moderate diagnostic efficiency. Nomograms were constructed to demonstrate the contribution of each indicator to drug metabolism capacity. To the best of our knowledge, the present study is the first to develop predictive models for psychotropic drug metabolism. These models offer clinicians practical tools to identify patients with impaired drug-metabolizing capacity, thereby enabling more precise and personalized medication management.

Cytochrome P450 3A gene family in gastric cancer: Unveiling diagnostic biomarkers and therapeutic targets for personalized treatment

The cytochrome P450 3A (CYP3A) gene family’s role in early progression of gastric cancer was comprehensively investigated. Its potential as a therapeutic target was evaluated. Upon literature review, aberrant expression of the CYP3A gene family has a strong correlation with gastric cancer onset, although the precise underlying mechanisms remain unclear. To assess its potential as a biomarker for early diagnosis and a therapeutic target, we have provided a comprehensive review of the regulatory mechanisms governing CYP3A gene family expression in gastric cancer, as well as its relation with early tumor progression and the tumor microenvironment. The CYP3A gene family is crucial in the proliferation, migration, and invasion of gastric cancer cells and promotes cancer progression by modulating inflammatory responses and oxidative stress within the tumor microenvironment. Furthermore, genetic polymorphisms in CYP3Aenzymes highlight its potential value in personalized medicine. Based on these findings, this paper explores the feasibility of developing inhibitors and activators targeting CYP3A enzymes and discusses potential applications in gene therapy. This research provides crucial theoretical support for the CYP3A gene family as an early diagnostic marker and therapeutic target for gastric cancer. In the future, multi-omics studies and large-scale clinical trials will be essential to advance clinical translation of these findings.

Improved Prediction of CYP2D6 Catalyzed Drug Metabolism by Taking Variant Substrate Specificities and Novel Polymorphic Haplotypes into Account

The polymorphic CYP2D6 enzyme plays a pivotal role in the metabolism of approximately 25% of clinically prescribed drugs. However, the impact of specific genetic variants on the interindividual variability in CYP2D6-mediated drug metabolism remains insufficiently quantified. This translational study sought to address this gap by analyzing the genotypes and phenotypes of patients in two large clinical cohorts, focusing on the metabolism of the CYP2D6 substrates risperidone and desmethyltamoxifen. The analysis incorporated novel polymorphic haplotypes and substrate-specific differences among the CYP2D6.1, CYP2D6.2, and CYP2D6.35 enzyme variants. The study revealed that CYP2D6.2 and CYP2D6.35 exhibit reduced metabolic capacity for these substrates, both in vivo and in an in vitro expression model. This was evidenced by decreased catalytic turnover (Kcat), decreased substrate affinity, and altered substrate docking. Furthermore, novel polymorphic haplotypes on the CYP2D6*1, CYP2D6*2, and CYP2D6*35 backgrounds were identified, each associated with a 30-40% increase in CYP2D6 activity. Incorporating these findings into prediction equations significantly improved the genetic prediction accuracy (R2) for CYP2D6-mediated metabolism of desmethyltamoxifen from 59% to 71% and risperidone, also metabolized by CYP3A4, from 42% to 46%. These results highlight the importance of accounting for drug-specific interactions with enzyme variants and integrating distinct polymorphic haplotypes into CYP pharmacogenomic models and guidelines for better translation into clinical practice.

Systematic Investigation of CYP3A4 Using Side-by-Side Comparisons of Apo, Active Site, and Allosteric-Bound States

Cytochrome P450 (CYP) 3A4 (CYP3A4) is a complex enzyme that metabolizes diverse substrates. It contains a large binding site accommodating diverse ligands, binding to active or allosteric sites. CYP3A4 does not always follow Michaelis-Menten kinetics. While Km reflects substrate affinity, it does not necessarily determine the enzyme's activity, though it is often considered indicative of substrate binding characteristics. The mechanism may be highly sophisticated and driven by multiple factors. This suggests that the ligand binding affinity alone may not explain the differential behavior of the enzyme conformational stability. Here, we analyzed sequence conserveness of 57 CYPs, followed by a detailed molecular dynamics simulation study (9 μs) on CYP3A4. We studied three CYP3A4 enzyme states (apo-state, active-site, and allosteric-site ligand-bound states) collected from the same experimental setup to reduce the systematic error. We found that the enzyme conformational stability followed a consistent trend of allosteric > active > apo states, which was inconsistent with the enzyme-ligand (active/allosteric) binding affinity and the ligand conformational stability. However, the heme group showed a significant protein affinity and stability pattern directly related to the enzyme stability, suggesting that the active/allosteric binding may work by influencing the heme-CYP3A4 binding affinity, and the allosteric ligand appeared to form the most stable enzyme state of the three studied states.

Edaravone ameliorates inflammation in ischemic stroke mouse by regulating the CYP1A1 pathway through gut microbiota

Inflammation is one of the main contributors to post-stroke injuries, and the disorders of the gut-brain axis post-stroke can further induce inflammation. Edaravone (3-methyl-1-phenyl-2-pyrazolin-5-one, EDA) is widely utilized neuroprotective medication for ischemic stroke in Japan, China, India, and other countries. However, the effects of EDA on peripheral inflammation and gut-brain axis repair post-stroke have not been revealed yet. In this study, we employed network pharmacology to identify the potential anti-inflammatory targets and signaling pathways that EDA may influence in the treatment of ischemic stroke. Then, we used 16S rDNA sequencing and molecular docking techniques to determine whether the anti-inflammatory effects of EDA are dependent on the gut-brain axis. Using morphological and molecular biology methods, we investigate how EDA reduces inflammatory response after ischemic stroke through gut microbiota and its metabolites. We demonstrated that EDA alleviated central and peripheral inflammation and rescued gut microbiota dysbiosis post-stroke. Meanwhile, EDA also improved intestinal histological features and decreased intestinal inflammation of post-stroke. The network pharmacology, 16S rDNA sequencing, and molecular docking results revealed that EDA could bind with the ESR1 and thereby regulate the expression of CYP1A1. Furthermore, EDA regulated CYP1A1-related metabolism and decreased the level of 20-HETE post-stroke through gut microbiota. Our study confirmed that EDA alleviated central and peripheral inflammation post-stroke by inhibiting CYP1A1 and CYP1A1-related metabolic through gut microbiota. CYP1A1 was a candidate target for treating ischemic stroke.

QM/MM Study of the Metabolic Oxidation of 6',7'-Dihydroxybergamottin Catalyzed by Human CYP3A4: Preferential Formation of the γ-Ketoenal Product in Mechanism-Based Inactivation

6',7'-Dihydroxybergamottin (DHB), a natural furanocoumarin found in grapefruit, is known to cause mechanism-based inactivation (MBI) of several cytochrome P450 enzymes (P450s) in humans, including CYP3A4. Despite its pharmacological significance, the precise microscopic mechanisms underlying the P450 MBI induced by DHB remain unclear. To address this, we employed molecular docking and molecular dynamics simulations to identify a plausible catalytic binding pose of DHB within CYP3A4. Subsequent quantum mechanics/molecular mechanics (QM/MM) calculations explored two possible reaction pathways (A and B). Path A involves the attack by compound I (Cpd I) at the C5 position of the furan moiety, leading to γ-ketoenal formation, while Path B targets the C4 position, yielding an epoxide. Path A exhibits a much lower activation energy barrier, indicating a strong kinetic preference. Additionally, the γ-ketoenal is thermodynamically more stable than the epoxide. Thus, even if the epoxide forms initially, it is likely to rearrange into the γ-ketoenal, either within the enzyme or in aqueous solution. Collectively, these findings suggest that the γ-ketoenal is the sole ultimate product of DHB oxidation by CYP3A4. This study provides valuable insights into CYP3A4 inactivation by grapefruit constituents and advances our understanding of food-drug interactions.

TIPE2 deficiency amplifies inflammation and immune dysregulation in MASH through modulating hepatic lipid metabolism and immune cell function

BACKGROUND

Metabolic Dysfunction-Associated Steatohepatitis (MASH) affects nearly 25% of the global population, yet there are no effective pharmacological treatments. Tumor necrosis factor α-induced protein 8-like 2 (TIPE2) is expressed in various immune cells and is crucial for regulating both innate and adaptive immune responses. However, its role in MASH development and the underlying mechanisms remain unclear.

METHOD

In this study, the role of TIPE2 in MASH was investigated using TIPE2 knockout (KO) mice and human hepatic LO2 cells. Immune cell infiltration, cytokine levels, and gene expression were analyzed. Techniques included flow cytometry for immune cell profiling, cytokine analysis, RNA sequencing, and quantitative PCR (qPCR) for validating gene expression changes.

RESULTS

TIPE2 was identified as a key regulator in MASH, influencing immune modulation and metabolic processes. TIPE2 KO mice exhibited increased infiltration and activation of natural killer (NK) cells, M1 macrophages, and myeloid-derived suppressor cells (MDSCs), along with elevated pro-inflammatory cytokines such as IFN-gamma, TNF-alpha, IL- 1 beta, and IL- 6. MDSCs from TIPE2 KO mice demonstrated enhanced PD-L1 expression, contributing to chronic liver inflammation through T cell suppression. RNA sequencing revealed that TIPE2 overexpression in human hepatic LO2 cells upregulated genes associated with amino acid biosynthesis, carbon metabolism, lipid regulation, glycolysis, and gluconeogenesis. These findings were supported by qPCR analyses of liver samples from mice, confirming TIPE2's role in maintaining lipid homeostasis and modulating immune responses.

CONCLUSION

The study highlights the pivotal role of TIPE2 in immune regulation and its influence on immune cell activation and inflammatory responses, which are critical in MASH progression. By exploring TIPE2-mediated immune regulation and its impact on the interplay between immune cell dynamics and liver metabolism, this research underscores TIPE2's central role in linking immune dysfunction to metabolic disturbances in MASH.

Comparison of the impact of chlordecone and its metabolite chlordecol on genes involved in pesticide metabolism in HepG2 cell line

Chlordecone (CLD) is an organochlorine pesticide that is highly resistant in the environment. This compound and its metabolite chlordecol (CLD-OH) still can be found in the French West Indies, after being banned 30 years ago. The novelty of this work lies in evaluating the toxicity of CLD-OH compared to CLD and examining the effects of these compounds on nuclear receptor (PXR, PPARα, and CAR) and metabolism-related genes (CYP2B6, CYP3A4) in vitro using HepG2 cell line as a model. Our study demonstrates that both compounds displayed an almost similar pattern of decrease in cell viability. Moreover, it was shown that CLD-OH can increase the expression of PXR, CYP3A4, and PPARα genes in comparison to CLD. The AKR1C4 gene showed a slight decrease in expression after CLD treatment. Collectively, this study provided a new finding into the impact of CLD-OH and compares the mode of action of CLD and its metabolite.

Decoding Allosteric Effects of Missense Variations in Drug Metabolism: Afrocentric CYP3A4 Alleles Explored

There is growing research on the allosteric behaviour of proteins, including studies on allosteric mutations that contribute to human diseases and the development of allosteric drugs. Allostery also plays a key role in drug metabolism, an essential factor in drug development. However, population specific variations, particularly in 3D protein structures, remain understudied. This study focuses on CYP3A4, a key enzyme responsible for metabolizing over 50% of FDA-approved drugs and often linked to adverse drug reactions. Given the vast genetic diversity of Africa, we investigated 13 CYP3A4 alleles from African populations using post-molecular dynamics analyses, with 12 being single variations and one containing a double variation. Except for one, all allele variations were located away from the active site, suggesting allosteric effects. Our comparative analyses of reference and variant structures, through hydrogen bond interactions, dynamic residue network analysis and substrate channel dynamics, revealed notable differences at both global and residue levels. The *32-I335T variant showed the largest changes compared to the reference structure, while *3-M445T (near normal metabolizer) exhibited the least change, with other variants falling in between. The *32-I335T variant showed a distorted conformation in the radius of gyration, a distinct kink in the I helix with specific hydrogen bonds and altered channel patterns. The *12-L373F variant, associated with reduced metabolism of midazolam and quinine, showed increased rigidity in its vicinity, potentially interfering with catalytic activity. Our findings align with clinical and wet lab data, suggesting that our approaches could be applied to analyse variants without clinical evidence.

Tale of Three N-Nitrosamines and the Variables Needed to Assess Their Carcinogenicity In Silico Incorporated into a Single Workflow

N-Nitrosamine impurities in pharmaceuticals present a considerable challenge for regulators and industry alike, where the absence of carcinogenic-potency studies has left a gap that must be adequately filled to protect public health. In the interim, this means balancing risk assessment with the necessity to continue research, development, and supply of pharmaceuticals. In the long term, we need a cost-effective solution that optimizes both. As if beholden to Newton's Third Law, every crisis breeds an opportunity of equal magnitude. Consequently, cross-industry consortia have been racing to find a solution by advancing our current science. Recent spotlight has been on in silico tools, as a fast and increasingly reliable alternative to in vivo and in vitro testing. Because N-nitrosamine bioactivation lends itself uniquely to quantum mechanics (QM) approaches, the integration of electronic-structure considerations has emerged as the dominant in silico approach. This signifies a considerable leap in predictive toxicology, which has, for much of its existence, relied on atomistic (quantitative) structure-activity relationships, i.e., (Q)SARs. Here we present a validation of an integrated docking-QM approach within the CADRE program and demonstrate its utility on three different impurities, N-nitroso-7-monomethylamino-6-deoxytetracycline, N-nitroso-dabigatran etexilate, and 1-methyl-4-nitrosopiperazine. We show that a combined in silico strategy, which considers bioavailability, transport, cytochrome P450 binding, and reactivity, can be leveraged to supplement the overly conservative Carcinogenic Potency Categorization Approach (CPCA) in setting the daily acceptable intake (AI) using defensible, highly mechanistic, and quantitative drivers of N-nitrosamine metabolism. To that end, we argue that while N-nitroso-7-monomethylamino-6-deoxytetracycline and 1-methyl-4-nitrosopiperazine are cohort-of-concern impurities, N-nitroso-dabigatran etexilate is not a potent carcinogen (TD50 > 1.5 mg/kg/day), contrasting the CPCA-derived AI. Lastly, we discuss how the CADRE tool can be integrated with the broader landscape of QM methods and the CPCA into a single harmonized in silico strategy for carcinogenicity assessment of N-nitrosamine impurities.

Using Genomics to Develop Personalized Cardiovascular Treatments

Advances in genomic technologies have significantly enhanced our understanding of both monogenic and polygenic etiologies of cardiovascular disease. In this review, we explore how the utilization of genomic information is bringing personalized medicine approaches to the forefront of cardiovascular disease management. We discuss how genomic data can resolve diagnostic uncertainty, support cascade screening, and inform treatment strategies. The role that genome-wide association studies have had in identifying thousands of risk variants for polygenic cardiovascular diseases, and how these insights, harnessed through the development of polygenic risk scores, could advance personalized risk prediction beyond traditional clinical algorithms. We detail how pharmacogenomics approaches leverage genotype information to guide drug selection and mitigate adverse events. Finally, we present the paradigm-shifting approach of gene therapy, which holds the promise of being a curative intervention for cardiovascular conditions.

Decoding the selective chemical modulation of CYP3A4

Drug-drug interactions associate with concurrent uses of multiple medications. Cytochrome P450 (CYP) 3A4 metabolizes a large portion of marketed drugs. To maintain the efficacy of drugs metabolized by CYP3A4, pan-CYP3A inhibitors such as ritonavir are often co-administered. Although selective CYP3A4 inhibitors have greater therapeutic benefits as they avoid inhibiting unintended CYPs and undesirable clinical consequences, the high homology between CYP3A4 and CYP3A5 has hampered the development of such selective inhibitors. Here, we report a series of selective CYP3A4 inhibitors with scaffolds identified by high-throughput screening. Structural, functional, and computational analyses reveal that the differential C-terminal loop conformations and two distinct ligand binding surfaces disfavor the binding of selective CYP3A4 inhibitors to CYP3A5. Structure-guided design of compounds validates the model and yields analogs that are selective for CYP3A4 versus other major CYPs. These findings demonstrate the feasibility to selectively inhibit CYP3A4 and provide guidance for designing better CYP3A4 selective inhibitors.

Chinese Guideline for the Diagnosis and Management of Drug-Induced Liver Injury in Primary Care (2024)

Drug-induced liver injury (DILI) is a drug-induced disease that not only complicates the treatment of the primary disease but may also lead to acute liver failure or even death in severe cases. Drugs commonly used in primary care, such as anti-infective agents and nonsteroidal anti-inflammatory drugs, are major causes of DILI. In addition, a large elderly population, comorbidities, and combination therapy with multiple drugs increase the risk of DILI in primary care. Therefore, primary care providers should proactively screen and monitor high-risk patients to identify potential DILI timely. Currently, diagnosis of DILI relies on the exclusion of liver diseases of other etiologies. Collection of detailed medical history of the patients and careful exclusion of other potential liver injury of other etiologies are crucial for accurate diagnosis. This guideline, developed based on evidence-based medicine from the latest research, aimed to provide primary care providers with professional guidance on the timely identification of suspected DILI cases and standardized diagnosis and management in clinical practice.

Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism

Microbiota-mediated drug metabolism can affect pharmacological efficacy. Here we conducted a systematic comparative metabolomics investigation of drug metabolism modes by evaluating the impacts of human gut commensal bacteria on 127 G-protein-coupled receptor (GPCR)-targeted drugs. For the most extensively metabolized drugs in our screen, we elucidated both conventional and unconventional drug transformations and the corresponding activities of generated metabolites. Comparisons of drug metabolism by a gut microbial community versus individual species revealed both taxon intrinsic and collaborative processes that influenced the activity of the metabolized drugs against target GPCRs. We also observed iloperidone inactivation by generating unconventional metabolites. The human gut commensal bacteria mixture incorporated sulfur in the form of a thiophene motif, whereas Morganella morganii used a cascade reaction to incorporate amino-acid-derived tricyclic systems into the drug metabolites. Our results reveal a broad impact of human gut commensal bacteria on GPCR-targeted drug structures and activities through diverse microbiota-mediated biotransformations.

A population physiologically based kinetic and toxicodynamic model for acute diazinon exposure

Organophosphate (OP) pesticide residues are frequently found in the environment and food products, with their acute exposures to humans posing a risk of neurotoxicity through acetylcholinesterase (AChE) inhibition. The aim of the present study is to develop a New Approach Methodology (a population-based physiologically based kinetic and toxicodynamic (PBK-TD) model) to define a health-based guidance value (HBGV) for acute exposure to diazinon as the model OP, taking into account human interindividual variability in physiology, toxicokinetics and toxicodynamics. Physiological and chemical-specific inputs for the PBK-TD model were obtained from literature or by in silico-in vitro strategies. Using this population model and Monte Carlo simulations, the dose-dependent response for DZN-induced erythrocyte AChE inhibition was generated to provide a point of departure (POD) for defining an acute reference dose (ARfD). The model simulates the toxicokinetic and toxicity data observed in humans well, and results reveal that toxicokinetic and not toxicodynamic variations are the main driver of the overall interindividual variability in susceptibility towards acute DZN exposure. The POD predicted for the sensitive adults is in agreement with a previously reported human no-observed-adverse-effect level (NOAEL). It is concluded that the population PBK-TD modeling defines a novel way to derive a POD for human health risk assessment with the incorporation of interindividual differences. In the next step, the inclusion of correlations between certain model parameters as well as cholinesterase inhibition in tissues other than the blood is expected to be a further refinement.

Antiepileptic drugs carbamazepine and valproic acid mediate transcriptional activation of CYP1A1 via aryl hydrocarbon receptor and regulation of estrogen metabolism

Cytochrome P450 1A1 (CYP1A1) actively catalyzes estrogen hydroxylation reactions and maintains the levels of neuroactive steroid estradiol. The widely prescribed first-line anti-epileptic drugs (AEDs) are considered to be a potent inducer of CYP1A1 and have also been observed to affect serum estradiol and calcium levels in patients with epilepsy. However, the ability of AEDs to interfere with CYP enzyme function and estrogen disposition is a relatively unexplored area. Here we investigate the effect of widely prescribed AEDs (carbamazepine and valproic acid) on CYP1A1 regulation and the levels of estradiol and calcium in cell supernatants of hepatocellular, HepG2, and neuronal, SH-SY5Y cells. We observed that both the AEDs significantly increased CYP1A1 expression and enzyme activity, which was accompanied by a decrease in estradiol and calcium levels in HepG2 cells. This induction of CYP1A1 mRNA and protein was fully prevented by aryl hydrocarbon receptor (AHR) knockdown and StemRegenin 1 (SR1) antagonism. Notably, the AEDs did not affect the AHR expression but regulated its nuclear translocation, potentially driving the transcriptional upregulation of CYP1A1. Furthermore, the knockdown of CYP1A1 in HepG2 cells elucidated a marked increase in estradiol and calcium levels. Later, this increase subsided upon AED exposure. Lastly, we observed a similar trend in estradiol and calcium alterations in SH-SY5Y cells on AED exposure, speculating the involvement of CYP1A1 induction via AEDs at neuronal sites. This work demonstrates that AEDs mediate the upregulation of CYP1A1 via an AHR-dependent mechanism and influence estrogen and calcium homeostasis.

CYP3A4 activity variations can lead to stratified metabolism of abemaciclib

The interindividual variability of CYP3A4 activity complicates precision pharmacotherapy, particularly for drugs with narrow therapeutic windows. To explore the relationship between CYP3A4 polymorphisms and metabolic phenotypes, this study used abemaciclib as a probe substrate within a translational framework. The in vitro platform combined a reconstituted enzyme catalysis system for high-throughput inhibitor screening with UPLC-MS/MS metabolic profiling. In vivo pharmacokinetic studies were performed in female SD rats, with optimized sampling during the elimination phase. Human CYP3A4 baculosomes were engineered using baculovirus-mediated expression in Sf21 cells to investigate genetic influences on metabolic variability. Molecular docking and dynamics simulations were also performed to investigate structural differences in inhibitory activity. Results showed that letrozole significantly inhibited CYP3A4-mediated abemaciclib metabolism, reduced its clearance and increased its area under the blood concentration-time curve (AUC) and maximum blood concentration (Cmax) through mixed inhibition. Moreover, CYP3A4 polymorphisms substantially impacted abemaciclib pharmacokinetics. Kinetic simulations revealed that the CYP3A4.28 variant formed a stable complex with letrozole, enhancing inhibition, while the CYP3A4.30 variant lost catalytic activity. These findings underscored the critical role of CYP3A4 activity and genetic polymorphisms in drug metabolism and highlighted the necessity for personalized treatment approaches.

Epidemiology and Risk Determinants of Drug-Induced Liver Injury: Current Knowledge and Future Research Needs

AIMS

Drug-induced liver injury (DILI) is a major global health concern resulting from adverse reactions to medications, supplements or herbal medicines. The relevance of DILI has grown with an aging population, the rising prevalence of chronic diseases and the increased use of biologics, including checkpoint inhibitors. This article aims to summarise current knowledge on DILI epidemiology and risk factors.

METHODS

This review critically appraises available evidence on DILI frequency, outcomes and risk determinants, focusing on drug properties and non-genetic host factors that may influence susceptibility.

RESULTS

DILI incidence varies across populations, with hospitalised patients experiencing notably higher rates than outpatients or the general population. Increased medication use, particularly among older adults and women, may partly explain age- and sex-based disparities in DILI incidence and reporting. Physiological changes associated with aging likely increase susceptibility to DILI in older adults, though further exposure-based studies are needed for definitive conclusions. Current evidence does not strongly support that women are inherently more susceptible to DILI than men; rather, susceptibility appears to depend on specific drugs. However, once DILI occurs, older age and female sex are associated with greater severity and poorer outcomes. Other less-studied host-related risk factors are also discussed based on available evidence.

CONCLUSIONS

This article summarises existing data on DILI frequency, outcomes, drug properties affecting hepatotoxicity and non-genetic host risk factors while identifying critical knowledge gaps. Addressing these gaps through future research could enhance understanding and support preventive measures.

Chanoclavine synthase operates by an NADPH-independent superoxide mechanism

More than ten ergot alkaloids comprising both natural and semi-synthetic products are used to treat various diseases1,2. The central C ring forms the core pharmacophore for ergot alkaloids, giving them structural similarity to neurotransmitters, thus enabling their modulation of neurotransmitter receptors3. The haem catalase chanoclavine synthase (EasC) catalyses the construction of this ring through complex radical oxidative cyclization4. Unlike canonical catalases, which catalyse H2O2 disproportionation5,6, EasC and its homologues represent a broader class of catalases that catalyse O2-dependent radical reactions4,7. We have elucidated the structure of EasC by cryo-electron microscopy, revealing a nicotinamide adenine dinucleotide phosphate (reduced) (NADPH)-binding pocket and a haem pocket common to all haem catalases, with a unique homodimeric architecture that is, to our knowledge, previously unobserved. The substrate prechanoclavine unprecedentedly binds in the NADPH-binding pocket, instead of the previously suspected haem-binding pocket, and two pockets were connected by a slender tunnel. Contrary to the established mechanisms, EasC uses superoxide rather than the more generally used transient haem iron-oxygen complexes (such as compounds I, II and III)8,9, to mediate substrate transformation through superoxide-mediated cooperative catalysis of the two distant pockets. We propose that this reactive oxygen species mechanism could be widespread in metalloenzyme-catalysed reactions.

Protective effects of Lavandula stoechas and Thymus numidicus essential oils against deltamethrin-induced hematological and biochemical toxicity in female rabbits

Recent studies have shown that essential oils (EOs) extracted from medicinal and aromatic plants have herbicidal and/or insecticidal properties, helping to mitigate the toxicity experienced by living organisms exposed to pesticides. Moreover, the primary compounds isolated from these EOs also have the potential to reduce pesticide-induced damage. The present work aimed to evaluate the protective effects of Thymus numidicus (TNEO) and Lavandula stoechas (LSEO) against Deltamethrin-induced toxicity in female rabbits. The results obtained by GC/MS analysis showed that monoterpenes and oxygenated monoterpenes were the main components of the EOs extracted from the aerial parts of Thymus numidicus and Lavandula stoechas. The use of the pesticide Deltamethrin caused significant damage to the liver and kidneys (p < 0.05), together with blood disorders, signs of restlessness and tremors. However, females treated with TNEO showed better tolerance than the group treated with LSEO. The combination of both oils showed more pronounced protective effects. This suggests a potential synergistic effect in reducing deltamethrin-induced toxicity.

Effect of metoprolol exposure following myocardial infarction on future cardiovascular events: a Mendelian randomization study

PURPOSE

The clinical benefit of up-titration of metoprolol to a guideline-recommended target dose after myocardial infarction (MI) is unknown. Our aim was to investigate whether variation in metoprolol exposure determined by cytochrome p450 enzyme 2D6 (CYP2D6) influences the occurrence of major adverse cardiovascular events (MACE) and cardiovascular death (CV death) among patients treated with metoprolol after MI.

METHOD

This Mendelian randomization study was performed using individual-level data from 1554 patients treated with metoprolol after an acute MI. CYPD26 genotype was applied as a binary genetic instrument assigning patients into two metoprolol exposure groups: CYP2D6 normal metabolizers (NM) (low exposure) and CYP2D6 intermediate and poor metabolizers (IM + PM) (high exposure). The null hypothesis of no association between the CYP2D6 metabolizer subgroup and MACE or CV death was tested using the Cox proportional hazards model. All-cause mortality and individual components of MACE were included as secondary outcomes.

RESULTS

In total, 879 (56.6%) patients were classified as NM and 675 (43.4%) as IM + PM. During the 3-year follow-up, 56 patients (6.4%) in the NM group had an outcome of MACE, and 24 (2.7%) patients died from CV disease. Corresponding frequency in the IM + PM group was 47 (7.0%) and 22 (3.3%), respectively. There was no association between genotype and MACE [unadjusted HR 1.12 (CI 0.76, 1.65)] or CV death [unadjusted HR 1.20 (CI 0.67, 2.14)], or between the CYP2D6 group and any of the secondary outcomes.

CONCLUSION

In patients treated with metoprolol after MI, variation in metoprolol exposure determined by CYP2D6 did not impact the occurrence of cardiovascular events.

Sex and Common Germline Variants Affect the Toxicity Profile and Pharmacokinetics of Alectinib: A Nationwide Cohort Study in Patients With ALK-Positive NSCLC

INTRODUCTION

Alectinib, a small-molecule kinase inhibitor, is used as first-line treatment for ALK-positive (ALK+) NSCLC. Albeit generally well-tolerated, a considerable subset of patients requires dose adjustments due to drug-related toxicity. Single-nucleotide polymorphisms in genes related to the metabolism of alectinib may upfront identify patients at risk for toxicity.

METHODS

In this multicenter observational cohort study in patients with advanced ALK+ NSCLC receiving alectinib treatment, we investigated the association between toxicity, pharmacokinetics, and key genetic variants in ABCB1, CYP3A4, PPAR-α, POR, and CYP3A5. Data on demographics, adverse events, and alectinib trough levels were collected from five hospitals.

RESULTS

Among 215 patients, 47% experienced severe toxicity. Women experienced more severe toxicity (female versus male: 56% versus 34%; p = 0.001) and had +35% higher alectinib trough levels (p < 0.001). Homozygous carriers of the PPAR-α 209G>A variant exhibited a higher incidence of grade greater than or equal to 3 toxicity (38%) compared with patients who carried at least one wild-type allele (11%) (p = 0.004). This remained significant after Bonferroni correction. Patients who experienced severe toxicity had +18.5% (95% confidence interval: 2.9%-36.6%; p = 0.019) higher trough levels.

CONCLUSIONS

Female patients encounter more severe toxicity due to higher alectinib exposure, which warrants further exploration. PPAR-α 209G>A significantly increased relevant alectinib-induced toxicity, most likely due to an increase in alectinib exposure. Pretreatment testing for genetic variants with a subsequent dose reduction could provide a viable approach to reduce alectinib-related toxicity.

Role of Cytochromes P450 in Intestinal Barrier Function: Possible Involvement in the Pathogenesis of Leaky Gut Syndrome

The intestinal barrier constitutes the largest surface of the human body communicating with the external environment. Alterations affecting elements of intestinal wall may lead to increased intestinal permeability and resulting translocation of bacteria or its components to the bloodstream in the form of the "leaky gut syndrome" (LGS). One of the most common causes of LGS is the disruption of tight junctions (TJ) maintained by tight junction proteins (TJP). LGS and associated alterations in TJP are observed in numerous gastrointestinal (GI) diseases, including inflammatory bowel diseases (IBD) such as Crohn's disease (CD) and ulcerative colitis (UC). Current literature indicates the key role of LGS in many pathological processes, further emphasizing the need for effective pharmacological approaches to treat this syndrome. One of the potential pharmacological targets in LGS treatment are members of the cytochrome P450 (CYP450) superfamily. By affecting intestinal permeability, they may lead to LGS development. It was found that the expression of CYP8B1 synthesizing cholic acid and CYP26 degrading all-trans retinoic acid indirectly influence TJs. CYP2E1 responsible for the metabolism of a wide variety of chemicals, including ethanol, plays a crucial role in the impairment of the intestinal wall. Contrarily, the overexpression of CYP27B1 has a protective effect on the intestinal integrity. CYP1A1, CYP2A6, CYP2J2 and CYP3A were also suggested to influence the GI tract, through their capability to metabolize serotonin, nicotine, endocannabinoids and gemcitabine, respectively. This review summarizes the findings on the role of CYP450 isoforms in intestinal hyperpermeability and their potential involvement in the pathophysiology of LGS.

Functional Characterization of Cytochromes P450 Linked to Herbicide Detoxification and Selectivity in Winter Wheat and the Problem Competing Weed Blackgrass

The selective chemical control of wild grasses in wheat is primarily determined by the relative rates of herbicide metabolism, with the superfamily of cytochromes P450 (CYPs) playing a major role in catalyzing phase 1 detoxification reactions. This selectivity is enhanced by herbicide safeners, which induce CYP expression in cereals, or challenged by the evolution of nontarget site resistance (NTSR) in weeds such as blackgrass. Using transcriptomics, proteomics, and functional expression in recombinant yeast, CYPs linked to safener treatment and NTSR have been characterized in wheat and blackgrass. Safener treatment resulted in the induction of 13 families of CYPs in wheat and 5 in blackgrass, with CYP71, CYP72, CYP76, and CYP81 members active toward selective herbicides in the crop. Based on their expression and functional activities, three inducible TaCYP81s were shown to have major roles in safening in wheat. In contrast, a single AmCYP81 that was enhanced by NTSR, but not by safening, was found to dominate herbicide detoxification in blackgrass.

Effects of Crocus sativus and its active constituents on cytochrome P450: a review

Cytochrome P450 (CYP) enzymes play an important role in the biotransformation of drugs and endogenous substances. Clinical medications and herbal remedies can either enhance or inhibit the activity of CYP enzymes, leading to potential drug interactions between herbal supplements and prescribed medications. Such interactions can lead to serious consequences, especially for drugs with a narrow therapeutic index, such as digoxin, warfarin, and cyclosporine A. In this review article, we provide an updated review of the impact of saffron, and its active constituents, safranal and crocin, on the 12 major human CYP enzymes and possible drug interactions between saffron and prescription drugs. The available evidence indicates that saffron and its active constituents affect the expression or activity of some CYP isoforms, including the CYP1A1/2, CYP3A4, and CYP2E1 subfamily. Considering the important role of these CYPs in the biotransformation of frequently prescribed medications and the activation of procarcinogen into carcinogenic metabolites, it can be expected that the consumption of saffron and its active constituents may influence the pharmacokinetics and toxicity of several substances. In particular, given the critical role of CYP3A4 in drug metabolism, and saffron's inhibitory impact on this CYP enzyme, it appears that saffron's most significant interaction is linked to its inhibition of CYP3A4. In addition, the inhibitory effect of saffron on CYP1A1/2, and CYP2E1 expression can play a role in the chemopreventive effect of this herbal medicine. Additional research is crucial for evaluating the clinical significance of these interactions in patients who consume saffron along with prescription drugs and determining the dose that can lead to drug interactions.

The quest to define cancer-specific systems parameters for personalized dosing in oncology

INTRODUCTION

Clinical trials in oncology initially recruit heterogeneous populations, without catering for all types of variability. The target cohort is often not representative, leading to variability in pharmacokinetics (PK). To address enrollment challenges in clinical trials, physiologically based pharmacokinetic models (PBPK) models can be used as a guide in the absence of large clinical studies. These models require patient-specific systems data relevant to the handling of drugs in the body for each type of cancer, which are scarce.

AREAS COVERED

This review explores system parameters affecting PK in cancer and highlights important gaps in data. Changes in drug-metabolizing enzymes (DMEs) and transporters have not been fully investigated in cancer. Their impaired expression can significantly affect capacity for drug elimination. Finally, the use of PBPK modeling for precision dosing in oncology is highlighted. Google Scholar and PubMed were mainly used for literature search, without date restriction.

EXPERT OPINION

Model-informed precision dosing is useful for dosing in sub-groups of cancer patients, which might not have been included in clinical trials. Systems parameters are not fully characterized in cancer cohorts, which are required in PBPK models. Generation of such data and application of cancer models in clinical practice should be encouraged.

Spatial Profiling of Multiple Enzymatic Activities at Single Tissue Sections via Fenton-Promoted Electrochemiluminescence

Profiling multiple enzymatic activities in tissue is crucial for understanding complex metabolic and signaling networks, yet remains a challenge with existing optical microscopies. Here, we developed a Fenton-promoted luminol electrochemiluminescence (ECL) imaging method to achieve the spatial mapping of multiple enzymatic activities within a single tissue section. This method quantitatively visualizes individual enzymatic activity by combining the enzymatic conversion of substrates with the chemical confinement of the locally produced hydrogen peroxide. To achieve high-resolution spatial imaging by limiting the diffusion (∼500 μm) of hydrogen peroxide, iron oxide nanoparticles were coated on the tissue surface to initiate the Fenton process, locally converting hydrogen peroxide into short-lived hydroxyl radicals with a nanometer-scale diffusion range. The Fenton-promoted ECL emission is confined at the enzymatic conversion sites, offering unprecedented spatial visualization of four tumor-associated oxidases within a single tissue section. Colocalization revealed a synergistic effect between lysyl oxidase and quiescin sulfhydryl oxidase on post-translational modifications of tumor extracellular matrix proteins, along with a previously undiscovered interaction with amiloride-sensitive amine oxidase, which could not be distinguished based on expressions or single enzymatic activity alone. This approach offers a novel activity-based protein profiling tool at the tissue level, providing new data for future enzynomic research and multimodal imaging.

Genetic Variation and Sex-Based Differences: Current Considerations for Anesthetic Management

Biomedical sciences have made immense progress and numerous discoveries aimed at improving the quality of life and life expectancy in modern times. Anesthesiology is typically tailored to individual patients as its clinical effects depend on multiple factors, including a patient's physiological and pathological states, age, environmental exposures, and genetic variations. Sex differences are also paramount for a complete understanding of the effects of specific anesthetic medications on men and women. However, women-specific research and the inclusion of women in clinical trials, specifically during child-bearing years, remain disproportionately low compared to the general population at large. This review describes and summarizes genetic variations, including sex differences, that affect responses to common anesthetic medications such as volatile anesthetics, induction agents, neuromuscular blocking drugs, opioids, and local anesthetics. It also discusses the influence of genetic variations on anesthesia outcomes, such as postoperative nausea and vomiting, allergic reactions, pain, depth of anesthesia, awareness under anesthesia and recall, and postoperative delirium.

Engineered microtissues to model the effects of dynamic heterotypic cell signaling on iPSC-derived human hepatocyte maturation

In vitro human liver models are indispensable for compound metabolism/toxicity screening, disease modeling, and regenerative medicine. While induced pluripotent stem cell-derived human hepatocyte-like cells (iHeps) mitigate the sourcing limitations with primary human hepatocytes (PHHs), their functional maturity is rate-limiting for application use. During development, immature hepatoblasts interact with different non-parenchymal cell (NPC) types, such as mesenchyme and endothelia, in a spatiotemporal manner to progress through functional maturation. Modeling such interactions in vitro is critical to elucidate the key regulators of iHep maturation. Here, we utilized high-throughput droplet microfluidics to encapsulate iHeps within monodisperse collagen I microgels (Ø ∼ 250 µm), which were coated with NPCs to generate 'microtissues' placed within microwells in multiwell plates. Embryonic fibroblasts and liver sinusoidal endothelial cells (LSECs) induced the highest level of iHep maturation over 4+ weeks of culture compared to adult hepatic stellate cells (myofibroblastic), liver portal fibroblasts, dermal fibroblasts, and human umbilical vein endothelial cells. Combining iHep microtissues in plates with Transwell inserts containing different NPC types enabled the modeling of dynamic heterotypic signaling on iHep maturation; introducing embryonic fibroblast signaling first, followed by LSECs, led to the highest iHep maturation. Unique cytokine secretion profiles were detected across the top-performing microtissue configurations; stromal-derived factor-1 alpha was validated as one factor that enhanced iHep maturation. Lastly, gene expression patterns and regulatory networks showed adult PHH-like maturation in LSEC/iHep microtissues compared to iHep-only microtissues. Overall, microtissues are useful for elucidating the microenvironmental determinants of iHep maturation and for future use in downstream applications. STATEMENT OF SIGNIFICANCE: Induced pluripotent stem cell-derived hepatocyte-like cells (iHeps) hold great promise for drug screening, disease modeling, and regenerative medicine but often exhibit immature phenotypes. We utilized high-throughput droplet microfluidics to generate 3D microtissues containing iHeps and non-parenchymal cell (NPC) types to elucidate the effects of dynamic NPC signaling on iHep maturation. We observed that iHep maturation is significantly enhanced with embryonic fibroblasts and liver sinusoidal endothelial cells (LSEC) compared to adult liver fibroblasts and non-liver endothelia; the LSEC/iHep microtissues showed adult liver-like gene expression signatures. The highest iHep maturation in microtissues was achieved when mesenchymal stimulation was introduced first, followed by LSEC stimulation. Our platform provides a robust framework to elucidate cellular and molecular mediators of iHep maturation and biomedical applications.

Computation of domination degree-based topological indices using python and QSPR analysis of physicochemical and ADMET properties for heart disease drugs

Heart disease is a leading cause of death worldwide, highlighting the need for effective treatments for hypertension, arrhythmias, and high cholesterol. This study applies chemical graph theory to analyze the properties of seventeen heart disease drugs by evaluating minimal dominating sets and counting node appearances in these sets. Using Python, six domination degree-based topological indices from theϕ d -polynomial are computed. Regression analysis, including curvilinear and multilinear models, identified correlations between these indices and the physicochemical and ADMET properties of these drugs. QSPR models are developed to assess the ability of these indices to predict key properties, offering insights into their effectiveness for drug design.

CYP2A6 suppresses hepatocellular carcinoma via inhibiting SRC/Wnt/β-Catenin pathway

Patients with hepatocellular carcinoma (HCC) at advanced stages face limited treatment options, highlighting the urgent need for more effective early detection methods and advanced therapeutic modalities. Emerging evidence shows that multiple CYP450 proteins are involved in the pathogenesis of HCC. CYP1A2, CYP2E1 and CYP3A5 have been shown to modulate important signaling pathways, hereby inhibiting the proliferation and invasion of HCC cells. In this study we investigated the role of cytochrome P-450 2A6 (CYP2A6) in HCC progression, focusing on its potential as a diagnostic biomarker and therapeutic target. By analyzing TCGA and GEO databases, we found that the expression levels of CYP2A6 were significantly decreased in HCC compared to normal tissues. Overexpression of CYP2A6 resulted in reduced proliferation, migration, invasion, adhesion, tube-forming in PLC/PRF/5 and HepG2 cells in vitro, as well as tumorigenicity and metastasis in nude mice. Notably, the anti-HCC effects of CYP2A6 were independent of its metabolic functions. We demonstrated that CYP2A6 could bind to proto-oncogene tyrosine-protein kinase SRC (SRC) and inhibit the SRC/Wnt/β-Catenin pathway. Overexpression of SRC abrogated the inhibitory effects of upregulating CYP2A6 on the migration and invasion of PLC/PRF/5 cells. These results together suggest the potential of CYP2A6 as a biomarker and therapeutic target for HCC. Its modulation of the SRC/Wnt/β-Catenin pathway provides a new insight for HCC treatment.

Impact of variation in CYP3A and CYP2C8 on tucatinib metabolic clearance in human liver microsomes

Tucatinib is a small molecule tyrosine kinase inhibitor indicated for HER2-positive breast cancer. This recently approved drug is primarily metabolized by cytochrome P450 (P450) 2C8 and CYP3A. Given the interindividual variability in the pharmacokinetics of some kinase inhibitors, the present study explored how variability in CYP2C8 and CYP3A activities and concentrations can influence variability in overall tucatinib metabolic clearance in vitro. Tucatinib depletion, P450 activities, and P450 concentrations were measured in human liver microsomes from 21 donors (males n = 11, females n = 10). CYP2C8 and CYP3A activities were quantitated by liquid chromatography-tandem mass spectrometry analysis using the following marker reactions: amodiaquine N-deethylation and midazolam 1'-hydroxylation, respectively. CYP2C8, CYP3A4, and CYP3A5 protein concentrations were measured using quantitative targeted absolute proteomics. The minimum clearance rate was 2.01 μL/mg/min, and the maximum clearance rate was 28.9 μL/mg/min, indicating a 14.3-fold variation in the apparent tucatinib clearance between donors. Tucatinib clearance was significantly correlated with both CYP2C8 and CYP3A enzyme activities and protein concentrations in this donor cohort (r = 0.781, r = 0.904, r = 0.907, and r = 0.882, respectively). A multiple linear regression model was developed to determine the most significant parameters influencing tucatinib clearance. Overall, we found that CYP2C8 and CYP3A activities were significant predictors of tucatinib apparent clearance in human liver microsomes from individual donors. Proteomics data are available with identifier PXD057282 via ProteomeXchange. SIGNIFICANCE STATEMENT: The results from this study demonstrate a strong relationship between CYP2C8 and CYP3A phenotypes and interindividual variability in tucatinib metabolism. By elucidating how variability in CYP2C8 and CYP3A phenotypes influence tucatinib pharmacokinetics, this study has the potential to provide the framework for future studies that could inform dosing to minimize adverse events and improve therapeutic outcomes. Ultimately, understanding how individual cytochrome P450 phenotypes influence the clearance of cancer therapeutics will aid in the development of tailored regimens for diverse patient populations.

Evaluation of small interfering RNA-dependent knockdowns of drug-metabolizing enzymes in multiwell array culture of primary human hepatocyte spheroids for estimation of fraction metabolized

The determination of the relative contribution of different drug-metabolizing enzymes to the metabolism of slowly metabolized compounds is a challenging task. The quantification of low compound turnover in standard in vitro systems, such as liver microsomes or hepatocyte suspension cultures, can be difficult. Thus, the use of long-term liver models, such as HepatoPac (BioIVT) or liver spheroids, has been suggested. Inhibitors of cytochrome P450 (P450) enzymes, the most important group of drug-metabolizing enzymes, represent the current standard to evaluate the route of drug metabolism. However, a long-term inhibition in systems such as spheroid models may be technically challenging due to limited stability of some of the commonly used inhibitors. Small interfering RNA (siRNA)-dependent knockdown of P450 enzymes in spheroid cultures of primary human hepatocytes represents a novel alternative to the established methods. In the current study, we report the successful attenuation of the CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 isoforms via siRNA on gene expression, as well as on the functional level, for at least 7 days. The analysis revealed that the knockdowns had only minor effects on the overall transcriptome. They also showed acceptable selectivity towards drug-metabolizing enzymes, except for the knockdown of CYP2C19. Applicability of the system for the determination of the fraction metabolized of low clearance substances was examined using 6 compounds metabolized by different P450s. By introducing siRNA-dependent knockdowns in phenotypically relevant primary human hepatocyte spheroid cultures, we hope to provide a novel alternative to standard systems to elucidate clearance pathways in vitro. SIGNIFICANCE STATEMENT: Small interfering RNA-mediated gene knockdowns of different cytochrome P450 enzymes were shown to be effective in long-term primary human hepatocyte spheroid cultures, representing a novel alternative for reaction phenotyping. This method has the potential to improve the assessment of pharmacokinetic variability and victim drug-drug interaction risks due to enzyme polymorphism or inhibition/induction with more confidence, particularly for low clearance drug candidates. Furthermore, minor effects of the small interfering RNA-mediated gene knockdowns for different cytochrome P450 enzymes on cell viability and the transcriptome were observed which implies that this system may be useful in deconvoluting toxicity caused by metabolites.

Pharmacogenomics in Solid Tumors: A Comprehensive Review of Genetic Variability and Its Clinical Implications

Pharmacogenomics, the study of how genetic variations influence drug response, has become integral to cancer treatment as personalized medicine evolves. This review aims to explore key pharmacogenomic biomarkers relevant to cancer therapy and their clinical implications, providing an updated and comprehensive perspective on how genetic variations impact drug metabolism, efficacy, and toxicity in oncology. Genetic heterogeneity among oncology patients significantly impacts drug efficacy and toxicity, emphasizing the importance of incorporating pharmacogenomic testing into clinical practice. Genes such as CYP2D6, DPYD, UGT1A1, TPMT, EGFR, KRAS, and BRCA1/2 play pivotal roles in influencing the metabolism, efficacy, and adverse effects of various chemotherapeutic agents, targeted therapies, and immunotherapies. For example, CYP2D6 polymorphisms affect tamoxifen metabolism in breast cancer, while DPYD variants can result in severe toxicities in patients receiving fluoropyrimidines. Mutations in EGFR and KRAS have significant implications for the use of targeted therapies in lung and colorectal cancers, respectively. Additionally, BRCA1/2 mutations predict the efficacy of PARP inhibitors in breast and ovarian cancer. Ongoing research in polygenic risk scores, liquid biopsies, gene-drug interaction networks, and immunogenomics promises to further refine pharmacogenomic applications, improving patient outcomes and reducing treatment-related adverse events. This review also discusses the challenges and future directions in pharmacogenomics, including the integration of computational models and CRISPR-based gene editing to better understand gene-drug interactions and resistance mechanisms. The clinical implementation of pharmacogenomics has the potential to optimize cancer treatment by tailoring therapies to an individual's genetic profile, ultimately enhancing therapeutic efficacy and minimizing toxicity.

Design and evaluation of novel triazole derivatives as potential anti-gout inhibitors: a comprehensive molecular modeling study

Introduction

Gout is the most common inflammatory arthritis, characterized by hyperuricemia, tophus formation, joint disease, and kidney stones. Uric acid, the final byproduct of purine catabolism, is eliminated via the kidneys and digestive system. Xanthine oxidase (XO) catalyzes the conversion of hypoxanthine and xanthine into uric acid, making XO inhibitors crucial for treating hyperuricemia and gout. Currently, three XO inhibitors are clinically used, showing significant efficacy. A molecular modeling study on triazole derivatives aims to identify novel XO inhibitors using 3D-QSAR, molecular docking, MD simulations, ADMET analysis, and DFT calculations. These computational approaches facilitate drug discovery while reducing research costs.

Methods

Our work focuses on a series of synthesized anti-xanthine oxidase inhibitors, aiming to develop new inhibitors. A computational study was carried out to identify the xanthine oxidase inhibitory structural features of a series of triazole inhibitors using computational method.

Results

A model based on CoMFA and CoMSIA/SEA has been built to predict new triazole derivatives.

Discussion

The optimal model established from CoMFA and CoMSIA/SEA was successfully evaluated for its predictive capability. Visualization of the contour maps of both models showed that modifying the substituents plays a key role in enhancing the biological activity of anti-gout inhibitors. Molecular docking results for complexes N°8-3NVY and N°22-3NVY showed scores of -7.22 kcal/mol and -8.36 kcal/mol, respectively, indicating substantial affinity for the enzyme. Complex N°8-3NVY forms two hydrogen bonds with SER 69 and ASN 71, three alkyl bonds with ALA 70, LEU 74, and ALA 75, and one Pi-Pi T-shaped bond with PHE 68. Complex N°22-3NVY forms three hydrogen bonds with HIS 99, ARG 29, and ILE 91, and one halogen bond with LEU 128 at 3.60 Å. A MD study revealed that the N°22-3NVY complex remained highly stable throughout the simulation. Therefore, we proposed six new molecules, their anti-gout inhibitory activities were predicted using two models, and they were evaluated for Lipinski's rule, and ADMET properties. The results show that both Pred 4 and Pred 5 have better pharmacokinetic properties than the height potent molecule in the studied series, making these two compounds valuable candidates for new anti-gout drugs. Subsequently, using DFT study to evaluate the chemical reactivity properties of these two proposed compounds, the energy gap results revealed that both molecules exhibit moderate chemical stability and reactivity.

A digestive system microphysiological platform for assessment of internal-exposure risks and metabolic disease mechanisms induced by multi-size nano-plastics

Nano-plastics (NPs) are emerging hazardous environmental contaminants that pose health risks with size-dependent toxic effects and are potential risk factors for hepatocellular carcinoma (HCC) and lipid metabolism disorders including non-alcoholic fatty liver disease (NAFLD). However, their underlying molecular mechanisms remain unclear. To shed more light on the causes of these risks, we developed a digestive system microphysiological platform (DS-MPP) for simulating dynamic internal-exposure of multi-size NPs in the gastrointestinal tract and liver. Multi-omics analysis based on DS-MPP revealed hepatic cells are more sensitive to 72 μg/day NPs than gastrointestinal mucosa cells. Specifically, 50 nm NPs disrupt phospholipid metabolism, promote diacylglycerol (DG) accumulation, convert more DG to phosphatidic acid (PA) than triacylglycerol (TG), thus facilitating endocytic vesicles production. Meanwhile, it can active tumorigenesis related pathway mTOR, inducing HCC marked by CAB39. Moreover, 500 nm NPs promote NAFLD by inducing insulin resistance pathways and decreasing PLD1 expression. Our results demonstrate the mechanism of disease and metabolic disorders induced by NPs vary depending on particle size. DS-MPP is a reliable platform for evaluating risk of dynamic NPs exposure and elucidating mechanisms of related metabolic diseases. This platform provides a promising method for health risk assessment caused by environmental pollutants.

Proton Pump Inhibitor Use and Its Association with Lung Cancer Likelihood and Mortality: A Nationwide Nested Case-Control Study in Korea

BACKGROUND/OBJECTIVES

Proton pump inhibitors (PPIs) are widely used for acid-related gastrointestinal disorders, but their potential association with lung cancer risk and mortality remains underexplored and debated. This study sought to investigate the association between PPI use and lung cancer likelihood and mortality, focusing on the impact of PPI exposure history and duration.

METHODS

This study utilized data from 6795 lung cancer patients, 27,180 matched controls, and 4257 deceased and 2538 surviving lung cancer patients from the Korean National Health Insurance Service's Health Screening Cohort (2002-2019). Propensity score overlap weighting and logistic regression models were applied to assess the correlations between PPI usage history and duration with lung cancer risk and mortality, while standardized differences ensured balanced baseline characteristics.

RESULTS

Overall, PPI use was modestly associated, with a 19% increased likelihood of lung cancer occurrence (95% confidence intervals (CI): 1.12-1.26). Interestingly, prolonged PPI use (≥30 days) was linked to a 13% reduction in lung cancer incidence (95% CI: 0.80-0.94), particularly in subgroups such as older adults (≥70 years), individuals with gastroesophageal reflux disease (GERD) or hypertension, and those with low alcohol consumption. Conversely, overall PPI usage was linked with a 36% increased mortality likelihood among lung cancer patients (95% CI: 1.20-1.55), with prolonged use further correlating with a 27% higher mortality risk (95% CI: 1.05-1.53), especially in high-risk subgroups, including smokers, underweight individuals, and those with hypercholesterolemia or GERD.

CONCLUSIONS

These findings may suggest a complex and context-dependent relationship between PPI use and lung cancer outcomes, emphasizing the need for individualized risk assessments and careful prescribing practices.

The pharmacology of vitamin C

Ascorbic acid, the reduced form of vitamin C, is a ubiquitous small carbohydrate. Despite decades of focused research, new metabolic functions of this universal electron donor are still being discovered and add to the complexity of our view of vitamin C in human health. Although praised as an unsurpassed water-soluble antioxidant in plasma and cells, the most interesting functions of vitamin C seem to be its roles as specific electron donor in numerous biological reactions ranging from the well-known hydroxylation of proline to cofactor for the epigenetic master regulators ten-eleven translocation enzymes and Jumonji domain-containing histone-lysine demethylases. Some of these functions may have important implications for disease prevention and treatment and have spiked renewed interest in, eg, vitamin C's potential in cancer therapy. Moreover, some fundamental pharmacokinetic properties of vitamin C remain to be established including if other mechanisms than passive diffusion governs the efflux of ascorbate anions from the cell. Taken together, there still seems to be much to learn about the pharmacology of vitamin C and its role in health and disease. This review explores new avenues of vitamin C and integrates our present knowledge of its pharmacology. SIGNIFICANCE STATEMENT: Vitamin C is involved in multiple biological reactions of which most are essential to human health. Hundreds of millions of people are considered deficient in vitamin C according to accepted guidelines, but little is known about the long-term consequences. Although the complexity of vitamin C's physiology and pharmacology has been widely disregarded in clinical studies for decades, it seems clear that a deeper understanding of particularly its pharmacology holds the key to unravel and possibly exploit the potential of vitamin C in disease prevention and therapy.

Responses of nuclear receptor HR96 to the toxic dinoflagellate Prorocentrum lima in Crassostrea ariakensis

Diarrhetic shellfish toxins (DSTs) are widely distributed and the most common algal toxins and their metabolic detoxification mechanism in shellfish remains poorly understood. Nuclear receptors are pivotal in regulating the detoxification of xenobiotics across various species. In this study, we identified the homologous sequence HR96 of the PXR/VDR/CAR nuclear receptor gene in Crassostrea ariakensis, and found that it may play an important role in resistance to DSTs. Molecular docking results showed that DSTs could be used as ligands to activate the nuclear receptor HR96. After exposure to Prorocentrum lima (a DST-producing dinoflagellate), the DSTs content in the digestive gland tissue of C. ariakensis increased during the accumulation stage, followed by a decrease and then an increase with time during the depuration stage. With few exceptions, the expression levels and protein content of HR96 and related detoxification genes increased throughout the toxin accumulation and depuration stage, suggesting that HR96 may mediate the regulation of genes involved in metabolic detoxification, thereby protecting oysters from the toxic effects of DSTs. During the depuration stage, the toxin content in digestive gland tissues fluctuated but remained at a high level, and the tissue damage was not significantly reduced, which may be related to the migration of toxins among different tissues. Our findings may provide a new perspective on the response of oysters to DSTs and contribute to a deeper understanding of the role of nuclear receptors in environmental adaptation of bivalves.

Precision medication based on the evaluation of drug metabolizing enzyme and transporter functions

Pharmacogenomics, therapeutic drug monitoring, and the assessments of hepatic and renal function have made significant contributions to the advancement of individualized medicine. However, their lack of direct correlation with protein abundance/non-genetic factors, target drug concentration, and drug metabolism/excretion significantly limits their application in precision drug therapy. The primary task of precision medicine is to accurately determine drug dosage, which depends on a precise assessment of the ability to handle drugs in vivo, and drug metabolizing enzymes and transporters are critical determinants of drug disposition in the body. Therefore, accurately evaluating the functions of these enzymes and transporters is key to assessing the capacity to handle drugs and predicting drug concentrations in target organs. Recent advancements in the evaluation of enzyme and transporter functions using exogenous probes and endogenous biomarkers show promise in advancing personalized medicine. This article aims to provide a comprehensive overview of the latest research on markers used for the functional evaluation of drug-metabolizing enzymes and transporters. It also explores the application of marker omics in systematically assessing their functions, thereby laying a foundation for advancing precision pharmacotherapy.

Emerging biotechnologies for engineering liver organoids

The engineering construction of the liver has attracted enormous attention. Organoids, as emerging miniature three-dimensional cultivation units, hold significant potential in the biomimetic simulation of liver structure and function. Despite notable successes, organoids still face limitations such as high variability and low maturity. To overcome these challenges, engineering strategies have been established to maintain organoid stability and enhance their efficacy, laying the groundwork for the development of advanced liver organoids. The present review comprehensively summarizes the construction of engineered liver organoids and their prospective applications in biomedicine. Initially, we briefly present the latest research progress on matrix materials that maintain the three-dimensional morphology of organoids. Next, we discuss the manipulative role of engineering technologies in organoid assembly. Additionally, we outline the impact of gene-level regulation on organoid growth and development. Further, we introduce the applications of liver organoids in disease modeling, drug screening and regenerative medicine. Lastly, we overview the current obstacles and forward-looking perspectives on the future of engineered liver organoids. We anticipate that ongoing innovations in engineered liver organoids will lead to significant advancements in medical applications.

The resurgence of synthetic cannabinoid receptor agonists as adulterants in the Era of Cannabis legalization: Lessons from prior epidemics and clinical implications

Momentum towards legalization of medical and recreational cannabis drives a convergence between natural cannabinoids and their synthetic counterparts, creating new clinical challenges in a second wave of exposures. This review critically examines the emerging challenges posed by synthetic cannabinoid receptor agonists (SCRAs) and semi-synthetic cannabinoids, emphasizing their clinical implications. SCRAs are potent full agonist activity that have been identified as adulterants in several recreational substances, including cannabis and opioids. Adulteration often leads to unpredictable clinical outcomes and exacerbates the potential for drug interactions. Drawing parallels with other drug epidemics, this paper highlights the urgent need for clinical preparedness to address the nuanced presentations of cannabinoid toxicity, stressing the importance of patient history, physical examination, and judicious use of supportive laboratory tests. This review serves as a cautionary tale and call to action for researchers and policymakers. There is a clear need for robust quality control measures, enhanced public awareness campaigns, and development of evidence-based clinical guidelines to mitigate the health risks associated with intentional and unintentional use of synthetic cannabinoids.

Current hPSC-derived liver organoids for toxicity testing: Cytochrome P450 enzymes and drug metabolism

Drug-induced hepatotoxicity is the leading cause of attrition of drug candidates and withdrawal of marketed drugs owing to safety concerns. In most hepatotoxicity cases, the parent drugs are metabolized by cytochrome P450 (CYP) enzymes, generating reactive metabolites that bind to intracellular organelles and proteins, ultimately causing hepatocellular damage. A major limitation of animal models, which are widely used for toxicity assessment, is the discrepancy in CYP-mediated drug metabolism and toxicological outcomes owing to species differences between humans and animals. Two-dimensional (2D) hepatocytes were first developed as a promising alternative model using human pluripotent stem cells (hPSCs). However, their CYP expression was similar to that of the fetal liver, and they lacked CYP-mediated hepatic metabolism. CYP expression in hPSC-derived hepatic models is closely correlated with liver maturity. Therefore, liver organoids that are more mature than hPSC-derived hepatic models and mimic the structure and physiological functions of the human liver have emerged as new alternatives. In this review, we explored the role and essentiality of CYPs in human hepatotoxicity, their expression, and epigenetic regulation in hPSC-derived hepatocytes and liver organoids, as well as the current state of liver organoid technology in terms of CYP expression and activity, drug metabolism, and toxicity. We also discussed the current challenges and future directions for the practical use of liver organoids. In conclusion, we highlight the importance of methods and metrics for accurately assessing CYP expression and activity in liver organoids to enable the development of feasible models that reproduce hepatotoxicity in humans.

Alogliptin attenuates testicular damage induced by monosodium glutamate in both juvenile and adult male rats by activating autophagy: ROS dependent AMPK/mTOR

Monosodium glutamate (MSG) is one of the most commonly used food additives, known for its adverse health effects. Alogliptin (ALO) is a highly selective dipeptidyl peptidase-4 inhibitor, but its role in male reproductive function remains debated. The study was designed to evaluate and compare the potential of ALO in mitigating MSG-induced testicular toxicity in juvenile and adult male rats. Juvenile and adult male rats were treated with either MSG or pretreated with ALO before MSG administration. The rats then received ALO and MSG concurrently for 28 days. Testicular tissues were isolated and subjected to histo-biochemical and molecular assessments. Our results demonstrated that ALO reversed MSG-induced testicular injury, as evidenced by the restoration of reproductive hormone balance (increased serum luteinizing hormone and testosterone concentrations), suppression of oxidative stress injury (decreased testicular malondialdehyde, increased superoxide dismutase activity, and minimal 8-hydroxy-2'-deoxyguanosine immunoreactivity), inflammation (reduced testicular tumor necrosis factor-alpha levels), and fibrosis (decreased testicular collagen fiber deposition). Additionally, ALO impeded apoptosis and activated autophagy by decreasing caspase-3 activity, stimulating the AMPK/mTOR pathway, downregulating Bax and SQSTM-1/p62 expression, upregulating Bcl2 and Beclin 1, promoting testicular proliferation (increased number of proliferating cell nuclear antigen-positive cells in the testis), restoring glycogen content in the testis (mild to moderate periodic acid-Schiff reaction), and preserving testicular architecture. MSG induced more severe adverse testicular effects in juvenile rats, while ALO pretreatment was more protective in adult rats. ALO's anti-inflammatory, antioxidant, antiapoptotic, pro-autophagic, antifibrotic, and proliferative actions in the testis suggest its promising potential for combating male reproductive dysfunction.

The Nature of Nanodisc Lipids Influences Fragment-Based Drug Discovery Results

Membrane proteins (MPs) are important yet challenging targets for drug discovery. MPs can be reconstituted in protein-lipid Nanodiscs (NDs), which resemble the native membrane environment. Drug-membrane interactions can affect the apparent binding stoichiometry and affinity, as well as the kinetics of ligands for a particular target, which is important for the extrapolation to pharmacokinetic studies. To investigate the role of the membrane, we have applied fragment-based drug discovery (FBDD) methods to cytochrome P450 3A4 (CYP3A4), reconstituted in NDs composed of different phosphocholine lipids: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), dipalmitoylphosphatidylcholine (DPPC), or 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC). Surface plasmon resonance screening of fragments and marketed drugs revealed extensive binding to the empty ND, correlating with analyte hydrophobicity, and the binding was critically dependent on ND lipid composition. POPC NDs showed much higher binding of fragments than DMPC and DPhPC NDs, resulting in a lower hit rate for CYP3A4 in POPC NDs, which demonstrated that the choice of the ND lipid is crucial to the outcome of a screen. The number of binders that were rejected based on atypical binding kinetics was lower for monomeric CYP3A4 in NDs than for non-native oligomeric CYP3A4 without the ND. Several fragments were exclusively identified as hits for CYP3A4 in the presence of the ND membrane. It is concluded that the nature of the ND is a critical factor for fragment screening of membrane proteins.

Somatic Genomic Profiling of Pancreatic Ductal Adenocarcinomas From a Diverse Cohort of Patients

OBJECTIVES

Black/African American (B/AA) pancreatic ductal adenocarcinoma (PDAC) patients have worse clinical outcomes than White patients and are underrepresented in genomic databases. We aimed to expand our understanding of the PDAC somatic landscape from a diverse cohort.

MATERIALS AND METHODS

Formalin-fixed paraffin-embedded specimens from 24 surgically resected PDAC cases were collected, with self-reported race/ethnicity. Whole exome sequencing was performed on malignant and benign tissue. Bioinformatics analysis included deduction of genetic ancestry and somatic mutational analysis, with comparisons to public datasets.

RESULTS

Out of 24 cases, 17 identified as B/AA race; genetic ancestry analysis confirmed proportions of Sub-Saharan African ancestry greater than 47%. The most commonly mutated genes included KRAS, TP53, SMAD4, and CDKN2A. Comparison of mutations in our cohort versus publicly available, predominantly White datasets showed higher mutation frequencies of ATM, RREB1, BRCA1/2, KDM6A, ARID1A, BRAF, and MYC (P < 0.04). When cohorts were combined and analyzed by race, no mutation frequencies differences were observed, including KRAS.

CONCLUSIONS

Genomic analysis of PDAC tumors from B/AA and White patients demonstrate similarities in mutation frequencies. Larger studies are needed to further understand molecular characterizations across continental subpopulations. This study provides further rationale for equitable representation of diverse patients in genomic databases and clinical trials.

Probing into the plasma stability and microsomal stability of thiol-based prodrug derivatives: Using IYS-15, an HDAC inhibitor as the model thiol

Thiols have interesting bio-chemical properties and can be found in a number of approved drugs. However, some thiols exhibited poor plasma stability and microsomal stability, leading to poor in vivo activity and poor oral bio-availability, in spite of their potent activity in vitro. Prodrug is a classic strategy to improve drug pharmacokinetics. In this study, we designed and synthesized 25 prodrug derivatives of a potent thiol-based HDAC inhibitor, IYS-15, to explore the structure-plasma stability relationships and structure-microsomal stability relationships in these series. We also tried to identify the main metabolic enzymes participated in the metabolism of some representative thiol-based prodrug derivatives. This work thus presents a comparison between different prodrugs based on the same model thiol, giving insights into the stability profile of the synthesized prodrug derivatives in human plasma and human liver microsomes, and more importantly, might also provide structural guidance to medicinal chemists in the design of thiol-based prodrugs and other novel prodrugs with thiol-based linkers.