Long-noncoding RNAs (lncRNAs) in drug metabolism and disposition,implications in cancer chemo-resistance

Drug metabolism is an orchestrated process in which drugs are metabolized and disposed through a series of specialized enzymes and transporters. Alterations in the expression and/or activity of these enzymes and transporters can affect the bioavailability (pharmacokinetics, or PK) and therapeutic efficacy (pharmacodynamics, or PD) of drugs. Recent studies have suggested that the long non-coding RNAs (lncRNAs) are highly relevant to drug metabolism and drug resistance, including chemo-resistance in cancers, through the regulation of drug metabolism and disposition related genes. This review summarizes the regulation of enzymes, transporters, or regulatory proteins involved in drug metabolism by lncRNAs, with a particular emphasis on drug metabolism and chemo-resistance in cancer patients. The perspective strategies to integrate multi-dimensional pharmacogenomics data for future in-depth analysis of drug metabolism related lncRNAs are also proposed. Understanding the role of lncRNAs in drug metabolism will not only facilitate the identification of novel regulatory mechanisms, but also enable the discovery of lncRNA-based biomarkers and drug targets to personalize and improve the therapeutic outcome of patients, including cancer patients.     

Quantitative clinical pharmacology is transforming drug regulation

Prior to 1970s, development and regulation of new drugs was devoid of a fully quantitative, pathophysiological conceptual foundation. Malcolm Rowland pioneered, in collaboration with colleagues and friends, our modern understanding of drug clearance concepts, and equipped drug development and regulatory scientists with key investigative tools such as physiologically-based pharmacokinetic (PBPK) modeling, standardized approaches to characterizing drug metabolism, and microdosing. From the 1970s to the present, Malcolm Rowland has contributed to key advances in pharmacokinetics that have had transformational impacts on drug regulatory science. These advances include concepts that have led to the fundamental understanding that mechanistically derived, quantitative variations in drug concentrations, rather than assigned dosage alone, drive pharmacodynamic effects (PKPD)—including disease biomarkers and clinical outcomes. This body of knowledge has transformed drug development and regulatory science theory and practice from naïve empiricism to a mechanism/model-based, quantitative scientific discipline. As a result, it is now possible to incorporate pre-clinical in vitro data on drug physico-chemical properties, metabolizing enzymes, transporters and permeability properties into PBPK-based simulations of expected PK distributions and drug–drug interactions in human populations. The most comprehensive application of PK-PD is in the modeling and simulation of clinical trials in the context of model-based drug development and regulation, imbedded in the “learn-confirm paradigm”. Regulatory agencies have embraced these advances and incorporated them into regulatory requirements, approval acceleration pathways and regulatory decisions. These developments are reviewed here, with emphasis on key contributions of Malcolm Rowland that facilitated this transformation.     

慢性肾功能不全对药动学影响研究进展

慢性肾功能不全是临床常见疾病之一,主要经肾消除及主要经非肾途径消除的药物,药代动力学及药效学均受慢性肾功能不全疾病的影响。肾功能不全尤其是终末期肾病不仅直接减少药物的排泄,还能影响药物吸收、药物转运及药物代谢,从而影响药物的非肾消除。肾功能不全可直接抑制药物代谢酶及转运体的活性并减少酶及转运体在胃肠道、肝脏等多个器官的mRNA及蛋白的表达。引起这种抑制作用的原因尚不明确,血液透析可以部分抵消或逆转这种抑制作用并存在透析消除。     

Translational PK–PD modeling in pain

The current gap between animal research and clinical development of analgesic drugs presents a challenge for the application of translational PK–PD modeling and simulation. First, animal pain models lack predictive and construct validity to accurately reflect human pain etiologies and, secondly, clinical pain is a multidimensional sensory experience that can’t always be captured by objective and robust measures. These challenges complicate the use of translational PK–PD modeling to project PK–PD data generated in preclinical species to a plausible range of clinical doses. To date only a few drug targets identified in animal studies have shown to be successful in the clinic. PK–PD modeling of biomarkers collected during the early phase of clinical development can bridge animal and clinical pain research. For drugs with novel mechanism of actions understanding of the target pharmacology is essential in order to increase the success of clinical development. There is a specific interest in the application of human pain models that can mimic different aspects of acute/chronic pain symptoms and serves as link between animal and clinical pain research. In early clinical development the main objective of PK–PD modeling is to characterize the relationship between target site binding and downstream biomarkers that have a potential link to the clinical endpoint (e.g. readouts from the human pain models) so as to facilitate the selection of doses for proof of concept studies. In patient studies, the role of PK–PD modeling and simulation is to characterize and confirm patient populations in terms of responder profiles with the aim to find the right dose for the right patient.     

非酒精性脂肪肝对药动学影响研究进展

非酒精性脂肪肝（NAFLD）是一种最常见的慢性肝病,严重威胁人类健康。在影响药物代谢的各种因素中,慢性肝病所起的作用最重要,可导致肝脏基因表达、mRNA及蛋白表达改变。非酒精性脂肪肝动物模型和非酒精性脂肪肝炎患者的研究结果显示,非酒精性脂肪肝时药物代谢酶及药物转运体发生显著改变。药物代谢酶和药物转运体在药物代谢过程中发挥重要作用,其改变可能影响药物在体内的清除,导致诸多临床药物的疗效、毒副作用甚至药物相互作用的发生。随着非酒精性脂肪肝的流行,越来越多的药物用于非酒精性脂肪肝患者。因此本文就非酒精性脂肪肝对药动学影响的研究进展作一综述。     

Development of a Korean‐specific virtual population for physiologically based pharmacokinetic modelling and simulation

Physiologically based pharmacokinetic (PBPK) modelling and simulation is a useful tool in predicting the PK profiles of a drug, assessing the effects of covariates such as demographics, ethnicity, genetic polymorphisms and disease status on the PK, and evaluating the potential of drug–drug interactions. We developed a Korean‐specific virtual population for the SimCYP® Simulator (version 15 used) and evaluated the population's predictive performance using six substrate drugs (midazolam, S‐warfarin, metoprolol, omeprazole, lorazepam and rosuvastatin) of five major drug metabolizing enzymes (DMEs) and two transporters. Forty‐three parameters including the proportion of phenotypes in DMEs and transporters were incorporated into the Korean‐specific virtual population. The simulated concentration–time profiles in Koreans were overlapped with most of the observed concentrations for the selected substrate drugs with a < 2‐fold difference in clearance. Furthermore, we found some drug models within the SimCYP® library can be improved, e.g., the minor allele frequency of ABCG2 and the fraction metabolized by UGT2B15 should be incorporated for rosuvastatin and lorazepam, respectively. The Korean‐specific population can be used to evaluate the impact of ethnicity on the PKs of a drug, particularly in various stages of drug development.     

The potential of flavonoids to influence drug metabolism and pharmacokinetics by local gastrointestinal mechanisms

In recent years, public and scientific interest in plant flavonoids has tremendously increased due to postulated health benefits. Whereas the amount of flavonoids ingested with the regular diet is rather low, the use of supplements enriched with these polyphenolics is becoming increasingly popular. This raises concerns about possible interactions of flavonoids with therapeutic drugs, because both are xenobiotics and, thus, share at least partially the same metabolic pathways. A number of in vitro studies have shown effects of flavonoids on enzymes involved in xenobiotic metabolism, like cytochrome P450 monooxygenases and phase II conjugation enzymes, or on membrane transporters involved in drug excretion. Several investigations have also reported changes of drug bioavailability by certain flavonoids. This article attempts to present an overview of flavonoid effects on pathways involved in drug metabolism. It focuses on phase I and phase II enzymes as well as on transporters involved in drug metabolism which are expressed in the gastrointestinal tract.     

Metabolic and redox barriers in the skin exposed to drugs and xenobiotics

Introduction: Growing exposure of human skin to environmental and occupational hazards, to numerous skin care/beauty products, and to topical drugs led to a biomedical concern regarding sustainability of cutaneous chemical defence that is essential for protection against intoxication. Since skin is the largest extra-hepatic drug/xenobiotic metabolising organ where redox-dependent metabolic pathways prevail, in this review, publications on metabolic processes leading to redox imbalance (oxidative stress) and its autocrine/endocrine impact to cutaneous drug/xenobiotic metabolism were scrutinised.

Areas covered: Chemical and photo-chemical skin barriers contain metabolic and redox compartments: their protective and homeostatic functions. The review will examine the striking similarity of adaptive responses to exogenous chemical/photo-chemical stressors and endogenous toxins in cutaneous metabolic and redox system; the role(s) of xenobiotics/drugs and phase II enzymes in the endogenous antioxidant defence and maintenance of redox balance; redox regulation of interactions between metabolic and inflammatory responses in skin cells; skin diseases sharing metabolic and redox problems (contact dermatitis, lupus erythematosus, and vitiligo)

Expert opinion: Due to exceptional the redox dependence of cutaneous metabolic pathways and interaction of redox active metabolites/exogenous antioxidants with drug/xenobiotic metabolism, metabolic tests of topical xenobiotics/drugs should be combined with appropriate redox analyses and performed on 3D human skin models.     

In silico methods for predicting drug–drug interactions with cytochrome P-450s,transporters and beyond

Drug–drug interactions (DDIs) are associated with severe adverse effects that may lead to the patient requiring alternative therapeutics and could ultimately lead to drug withdrawal from the market if they are severe. To prevent the occurrence of DDI in the clinic, experimental systems to evaluate drug interaction have been integrated into the various stages of the drug discovery and development process. A large body of knowledge about DDI has also accumulated through these studies and pharmacovigillence systems. Much of this work to date has focused on the drug metabolizing enzymes such as cytochrome P-450s as well as drug transporters, ion channels and occasionally other proteins. This combined knowledge provides a foundation for a hypothesis-driven in silico approach, using either cheminformatics or physiologically based pharmacokinetics (PK) modeling methods to assess DDI potential. Here we review recent advances in these approaches with emphasis on hypothesis-driven mechanistic models for important protein targets involved in PK-based DDI. Recent efforts with other informatics approaches to detect DDI are highlighted. Besides DDI, we also briefly introduce drug interactions with other substances, such as Traditional Chinese Medicines to illustrate how in silico modeling can be useful in this domain. We also summarize valuable data sources and web-based tools that are available for DDI prediction. We finally explore the challenges we see faced by in silico approaches for predicting DDI and propose future directions to make these computational models more reliable, accurate, and publically accessible.     

Preclinical pharmacokinetics: an approach towards safer and efficacious drugs

Lack of efficacy and toxicity are considered to be major reasons for drug failures and pharmacokinetics governs them to a large extent. Compound with favorable pharmacokinetics is more likely to be efficacious and safe. Therefore, the preclinical pharmacokinetic evaluation should be comprehensive enough to ensure that compounds do not fail in the clinic. Preclinical ADME screening facilitates early elimination of weak candidates and directs the entire focus of the drug development program towards fewer potential lead candidates. Hence, it is mandatory that the pre-clinical candidates are subjected to as many possible reality checks. Reliance on in-vitro tests should be minimized because they do not represent the real physiological environment but rather slow down the pace of a drug discovery program. Compounds can be straight away subjected to in-vivo high throughput screens such as cassette dosing, cassette analysis or rapid rat screen etc. Candidates with the desired in-vivo pharmacokinetic profile may be further profiled in-vitro, using assays such as metabolic stability, reaction phenotyping, CYP-450 inhibition and induction, plasma protein binding etc. in human microsomes, human recombinant CYP-450 enzymes and human plasma. This also provides an early indication of whether the compound which worked in animals would work in human as well. In-vitro metabolic stability profile is a qualitative as well as quantitative comparison of metabolism of a compound in human and animal models. It helps in identifying the right model for toxicity studies. Extensive metabolism is generally considered a liability as it limits the systemic exposure and shortens the half-life of a compound. Several strategies such as reduction of lipophilicity, modification and / or blocking of metabolically soft spots and use of enzyme inhibitors; have been developed to combat metabolism. In spite of several concerns, the fact that active metabolites of several marketed drugs have been developed as drugs with better efficacy, safety and pharmacokinetics profile; cannot be denied. Therefore, instead of considering metabolic instability a liability it can be exploited as a tool for discovering better drugs. It is equally important to identify the metabolic pathways of the drug candidates by conducting in-vitro CYP450 reaction phenotyping assays. The identification of drug metabolizing enzymes involved in the major metabolic pathways of a compound helps in predicting the probable drug-drug interactions in human. Compounds with more than one metabolic pathway have less likelihood of clinically significant drug interactions. In-vitro CYP450 inhibition and induction screens are used to evaluate the potential of compound towards drug - drug interactions and the most prone candidates may either be discarded or taken ahead with a caution. It is known that only unbound drug is pharmacologically active and therefore the assessment of bound fraction by the estimation of plasma protein binding of a compound is another important parameter to be explored in-vitro. In addition to the process of 'weeding out' weak candidates early in the drug discovery process, it is equally important to identify the probable causes of poor ADME exhibited by some compounds as this information is useful to medicinal chemists for improving upon backbones that exhibit un favorable pharmacokinetic profile. Toxicity study is the foundation of an INDA (Investigational new drug application) and therefore, the final selection of a compound can be performed only after proper toxicological evaluation in animal models. Toxicokinetics forms an integral part of toxicity study and is used to assess the exposure of candidates in toxicity models and correlate the drug levels in blood and various tissues with the toxicological findings. Although in-vivo screening of compounds in animal models and in-vitro assays in human recombinant CYP-450 enzymes help in drug candidate selection, both approaches have their own limitations. There is no certainty that the selected candidates will exhibit the desired target PK profile in human and real human PK remains suspense until the compound enters Phase-1 clinical trial. The recognition of human micro dosing, (HMD) by medicines and healthcare products regulatory agency (MHRA) and European agency for evaluation of medicinal products [EMEA] is a stepping stone in the direction of obtaining human PK data early in the preclinical stage. This would gradually shift the focus of early drug development away from animal studies directly towards safe and ethical studies in human yielding more relevant and reliable pharmacokinetic data. HMD would provide an answer to the growing public demand for a reduction in the use of animals for pharmaceutical development.     

Functional significance of genetic polymorphisms in P-glycoprotein (MDR1, ABCB1) and breast cancer resistance protein (BCRP, ABCG2)

Recent pharmacogenomic/pharmacogenetic (PGx) studies have disclosed important roles for drug transporters in the human body. Changes in the functions of drug transporters due to drug/food interactions or genetic polymorphisms, for example, are associated with large changes in pharmacokinetic (PK) profiles of substrate drugs, leading to changes in drug response and side effects. This information is extremely useful not only for drug development but also for individualized treatment. Among drug transporters, the ATP-binding cassette (ABC) transporters are expressed in most tissues in humans, and play protective roles; reducing drug absorption from the gastrointestinal tract, enhancing drug elimination into bile and urine, and impeding the entry of drugs into the central nervous system and placenta. In addition to PK/pharmacodynamic (PD) issues, ABC transporters are reported as etiologic and prognostic factors (or biomarkers) for genetic disorders. Although a consensus has not yet been reached, clinical studies have demonstrated that the PGx of ABC transporters influences the overall outcome of pharmacotherapy and contributes to the pathogenesis and progression of certain disorders. This review explains the impact of PGx in ABC transporters in terms of PK/PD, focusing on P-glycoprotein and breast cancer resistance protein (BCRP).     

Assays to predict drug permeation across the blood-brain barrier, and distribution to brain

Drug discovery programmes to target or avoid the brain need to take into account the properties of the blood-brain barrier (BBB). The importance to CNS PK of the free drug concentration in brain is increasingly recognised, and assays for drug discovery programmes are being adjusted accordingly. In vitro models of the BBB continue to play an important role in this process. Good cell-based models using brain endothelium have been developed and validated for mechanistic studies, and some are suitable for medium to high throughput permeability screening and toxicology. Brain homogenate and brain slice methods allow estimation of drug partition into brain. In combination with in silico and in vivo models, the portfolio of methods establishing and predicting CNS drug PK is now very powerful, allowing much more accurate iterative feedback to chemists to optimise compound profiles through the drug discovery and development programme. The advantage of using models based on real BBB cellular anatomy and physiology is that they have the power to reveal and incorporate previously undiscovered properties, such as new transporters, metabolic enzymes and modulation, to form the basis for models mimicking neurological disorders as well as normal function, and to allow physiologically-based pharmacokinetic (PBPK) extrapolation from animal models to humans.     

Physiologically Based Oral Absorption Modelling to Study Gut-Level Drug Interactions

Physiologically based oral absorption models are in silico tools primarily used to guide formulation development and project the clinical performance of formulation variants. This commentary briefly discusses additional oral absorption model applications, focusing on gut-level drug interactions. Gut-level drug interactions can involve drug degradation, metabolic enzymes, transporters, gastrointestinal motility modulators, acid-reducing agents, and food. The growth in publications reporting physiologically based oral absorption model utilization and successful pharmacokinetic prediction (e.g., after acid-reducing agents or food coadministration) indicate that oral absorption models have achieved a level of maturity within the industry particularly over the past 15 years. Provided appropriate data and model validation, oral absorption modeling/simulation may serve as a surrogate for clinical studies by providing both mechanistic and quantitative understanding of oral delivery considerations on pharmacokinetics.     

Pharmacokinetic herb-drug interactions (part 1): origins, mechanisms, and the impact of botanical dietary supplements

Phytochemicals have been components of man's diet for millennia and are believed to have played a significant role in steering the functional development of xenobiotic metabolizing enzymes and transporters within the human gastrointestinal tract. Only recently, however, have plant secondary metabolites been recognized as modulators of human drug disposition. Despite exposure to thousands of structurally diverse dietary phytochemicals, only a few appear to significantly modulate human drug metabolizing enzymes and transporters. In some instances, these interactions may have beneficial effects like cancer prevention, whereas others may dramatically affect the pharmacokinetics of concomitantly administered drugs. In today's global economy, the opportunity for exposure to more exotic phytochemicals is significantly enhanced. Formulated as concentrated phytochemical extracts, botanical dietary supplements are vehicles for a host of plant secondary metabolites rarely encountered in the normal diet. When taken with conventional medications, botanical dietary supplements may give rise to clinically significant herb-drug interactions. These interactions stem from phytochemical-mediated induction and/or inhibition of human drug metabolizing enzymes and transporters.     

Genetically humanized mouse models of drug metabolizing enzymes and transporters and their applications

Abstract

1. Drug metabolizing enzymes and transporters play important roles in the absorption, metabolism, tissue distribution and excretion of various compounds and their metabolites and thus can significantly affect their efficacy and safety. Furthermore, they can be involved in drug–drug interactions which can result in adverse responses, life-threatening toxicity or impaired efficacy. Significant species differences in the interaction of compounds with drug metabolizing enzymes and transporters have been described.

2. In order to overcome the limitation of animal models in accurately predicting human responses, a large variety of mouse models humanized for drug metabolizing enzymes and to a lesser extent drug transporters have been created.

3. This review summarizes the literature describing these mouse models and their key applications in studying the role of drug metabolizing enzymes and transporters in drug bioavailability, tissue distribution, clearance and drug–drug interactions as well as in human metabolite testing and risk assessment.

4. Though such humanized mouse models have certain limitations, there is great potential for their use in basic research and for testing and development of new medicines. These limitations and future potentials will be discussed.     

Functional crosstalk of CAR-LXR and ROR-LXR in drug metabolism and lipid metabolism

Nuclear receptor crosstalk represents an important mechanism to expand the functions of individual receptors. The liver X receptors (LXR, NR1H2/3), both the α and β isoforms, are nuclear receptors that can be activated by the endogenous oxysterols and other synthetic agonists. LXRs function as cholesterol sensors, which protect mammals from cholesterol overload. LXRs have been shown to regulate the expression of a battery of metabolic genes, especially those involved in lipid metabolism. LXRs have recently been suggested to play a novel role in the regulation of drug metabolism. The constitutive androstane receptor (CAR, NR1I3) is a xenobiotic receptor that regulates the expression of drug-metabolizing enzymes and transporters. Disruption of CAR alters sensitivity to toxins, increasing or decreasing it depending on the compounds. More recently, additional roles for CAR have been discovered. These include the involvement of CAR in lipid metabolism. Mechanistically, CAR forms an intricate regulatory network with other members of the nuclear receptor superfamily, foremost the LXRs, in exerting its effect on lipid metabolism. Retinoid-related orphan receptors (RORs, NR1F1/2/3) have three isoforms, α, β and γ. Recent reports have shown that loss of RORα and/or RORγ can positively or negatively influence the expression of multiple drug-metabolizing enzymes and transporters in the liver. The effects of RORs on expression of drug-metabolizing enzymes were reasoned to be, at least in part, due to the crosstalk with LXR. This review focuses on the CAR-LXR and ROR-LXR crosstalk, and the implications of this crosstalk in drug metabolism and lipid metabolism.