Applications of high-throughput ADME in drug discovery

Assessment of physicochemical and pharmacological properties is now conducted at very early stages of drug discovery for the purpose of accelerating the conversion of hits and leads into qualified development candidates. In particular, in vitro absorption, distribution, metabolism and elimination (ADME) assays and in vivo drug metabolism pharmacokinetic (DMPK) studies are being conducted throughout the discovery process, from hit generation through to lead optimization, with the goal of reducing the attrition rate of these potential drug candidates as they progress through development. Because the continuing trend in drug discovery has been to access ADME information earlier and earlier in the discovery process, the need has arisen within the analytical community to introduce faster and better analytical methods to enhance the 'developability' of drug leads. Strategies for streamlined ADME assessment of drug candidates in discovery and pre-clinical development are presented within.     

ADME-AP: a database of ADME associated proteins

Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.     

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, blood-brain barrier and water solubility). AVAILABILITY: http://www.pkdb.ifsc.usp.br     

QSAR and ADME

The prediction from structure of ADME (absorption, distribution, metabolism, elimination) of drug candidates is an important goal to achieve since it can considerably reduce the cost of drug development. Using our database of 10,700 QSAR, we are now reaching the point where we can make many useful comparisons that illustrate how ADME is a practical way to describe the way organic compounds react with living systems. We also show that Caco-2 cells are useful to model absorption, but the most generally useful parameter is the octanol/water partition coefficient. It should be noted, however, that in our opinion, an in silico prediction of ADME is still a long way in the future.     

In vitro ADME profiling using high-throughput rapidfire mass spectrometry: cytochrome p450 inhibition and metabolic stability assays

Early assessment of absorption, distribution, metabolism, and excretion (ADME) properties of drug candidates has become an essential component of modern drug discovery. ADME characterization is important in identifying compounds early that are likely to fail in later clinical development because of suboptimal pharmacokinetic properties or undesirable drug-drug interactions. Proper utilization of ADME results, meanwhile, can prioritize candidates that are more likely to have good pharmacokinetic properties and also minimize potential drug-drug interactions. By integrating a RapidFire system with an API4000 mass spectrometer (RF-MS), we have established a high-throughput capability to profile compounds (>100 compounds/wk) in a panel of ADME assays in parallel with biochemical and cellular characterizations. Cytochrome P450 inhibition and time-dependent inhibition assays and microsomal stability assays were developed and fully optimized on the system. Compared with the classic liquid chromatography-mass spectrometry method, the RF-MS system generates consistent data with approximately 20-fold increase in throughput. The lack of chromatographic separation of compounds, substrates, and metabolites can complicate data interpretation, but this occurs in a small number of cases that are readily identifiable. Overall, this system has enabled a real-time and quantitative measurement of a large number of ADME samples, providing a rapid evaluation of clinically important drug-drug interaction potential and drug metabolic stability.     

In silico pKa Prediction and ADME Profiling

Improving the ADME profile of drug candidates is a critical step in lead optimization, and because pK_a affects most ADME properties such as lipophilicity, solubility, and metabolism, it is extremely advantageous to predict pK_a in order to guide the design of new compounds. However, accurately (<0.5 log units) predicting pK_a by empirical methods can be challenging especially for novel series, because of lack of knowledge on determinants of pK_a (steric effects, ring effects, H‐bonding, etc.), and because of limited experimental data on the effects of specific chemical groups on the ionization of an atom. To address these issues, we recently developed the computational package MoKa, which integrates graphical and command line tools designed for computational and medicinal chemists to predict the pK_a values of organic compounds. Here, we present the major issues considered when we developed MoKa, such as the accurate selection of training data, the fundamentals of the methodology (which has also been extended to predict protein pK_a), the treatment of multiprotic compounds, and the selection of the dominant tautomer for the calculation. Last, we illustrate some specific applications of MoKa to predict solubility, lipophilicity, and metabolism.     

A quantitative model for metabolic intervention using gut microbes

As medicine shifts toward precision-based and personalized therapeutics, utilizing more complex biomolecules to treat increasingly difficult and rare conditions, microorganisms provide an avenue for realizing the production and processing necessary for novel drug pipelines. More so, probiotic microbes can be co-opted to deliver therapeutics by oral administration as living drugs, able to survive and safely transit the digestive tract. As living therapeutics are in their nascency, traditional pharmacokinetic–pharmacodynamic (PK–PD) models for evaluating drug candidates are not appropriate for this novel platform. Using a living therapeutic in late-stage clinical development for phenylketonuria (PKU) as a case study, we adapt traditional oral drug delivery models to properly evaluate and inform the engineering of living therapeutics. We develop the adapted for living therapeutics compartmental absorption and transit (ALT-CAT) model to provide metrics for drug efficacy across nine age groups of PKU patients and evaluate model parameters that are influenced by patient physiology, microbe selection and therapeutic production, and dosing formulations. In particular, the ALT-CAT model describes the mathematical framework to model the behavior of orally delivered engineered bacteria that act as living therapeutics by adapting similar methods that have been developed and widely-used for small molecular drug delivery and absorption.     

Application of a rapid and integrated analysis system (RIAS) as a high-throughput processing tool for in vitro ADME samples by liquid chromatography/tandem mass spectrometry

Over the past decade, drug discovery programs have started to address the optimization of key ADME properties already at an early stage of the process. Hence, analytical chemists have been confronted with tremendously rising sample numbers and have had to develop methodologies accelerating quantitative liquid chromatography/tandem mass spectrometry (LC/MS/MS). This article focuses on the application of a generic and fully automated LC/MS/MS, named Rapid and Integrated Analysis System (RIAS), as a high-throughput platform for the rapid quantification of drug-like compounds in various in vitro ADME assays. Previous efforts were dedicated to the setup and feasibility study of a workflow-integrated platform combining a modified high-throughput liquid handling LC/MS/MS system controlled by a customized software interface and a customized data-processing and reporting tool. Herein the authors present an extension of this previously developed basic application to a broad set of ADME screening campaigns, covering CYP inhibition, Caco-2, and PAMPA assays. The platform is capable of switching automatically between various ADME assays, performs MS compound optimization if required, and provides a speed of 8 s from sample to sample, independently of the type of ADME assay. Quantification and peak review are adopted to the high-throughput environment and tested against a standard HPLC-ESI technology.     

Fc-fusion proteins and FcRn: structural insights for longer-lasting and more effective therapeutics

Nearly 350 IgG-based therapeutics are approved for clinical use or are under development for many diseases lacking adequate treatment options. These include molecularly engineered biologicals comprising the IgG Fc-domain fused to various effector molecules (so-called Fc-fusion proteins) that confer the advantages of IgG, including binding to the neonatal Fc receptor (FcRn) to facilitate in vivo stability, and the therapeutic benefit of the specific effector functions. Advances in IgG structure-function relationships and an understanding of FcRn biology have provided therapeutic opportunities for previously unapproachable diseases. This article discusses approved Fc-fusion therapeutics, novel Fc-fusion proteins and FcRn-dependent delivery approaches in development, and how engineering of the FcRn–Fc interaction can generate longer-lasting and more effective therapeutics.     

Potential agents for cancer and obesity treatment with herbal medicines from the green garden

Many classes of bioactive drug-like molecules derived from traditional herbal plants are becoming attractive as alternative medicines for the treatment of severe chronic diseases such as cancer and obesity. A set of chemically synthesized drugs that is capable of both inhibiting cancer growth and reducing body weight for treatment of obesity have severe side effects including nausea, vomiting, diarrhea as well as producing increased blood pressure and headache, respectively. For decades, drug candidates from herbal plants have been considered as potential therapeutic agents because they are generally safer, less toxic, and have fewer lethal side effects than chemically synthesized or semi-synthetic drugs. Understanding the key factors affecting pharmacological effects and clinical outcomes has been a critical theme of natural product research. However, standardized sample preparation methods, well-controlled scientific studies, and validation studies are needed before herbal therapeutics can be introduced into the global market. This review will address the current advances in using traditional herbal plants, including the pharmacological effects and the challenges faced during the development of new drugs. The safety issues associated with toxicity and the effectiveness of the herbs in specific diseases such as cancer and obesity are also discussed.     

microRNA治疗在癌症及其他疾病中的研究进展*

microRNAs(miRNAs)是一类内源性、非编码小分子RNAs(约22 nt),在基因表达调控中发挥关键作用。已有研究表明,miRNAs失调是造成多种人类疾病的原因,如癌症、病毒感染及自身免疫性疾病等。补充或抑制miRNAs功能与活性已成为多种疾病治疗的新策略,抗肿瘤miR-34 mimics、治疗HCV感染的anti-miR-122等基于miRNAs的治疗方案已进入临床试验。重点就miRNAs治疗在癌症及其他疾病中的最新研究进展进行综述,并对目前开发安全有效miRNAs治疗策略所面临的挑战进行分析。     

MDR1基因多态性及其临床相关性研究进展

体内外研究证明,人体中P—gP在药物的吸收、分布、代谢和排泄（ADME）过程中发挥了非常重要的作用。多药耐药基因MDR1（ABCB1）是P-gP的编码基因。药物基因组学和遗传药理学研究发现在不同个体中MDR1基因多态性与P—gP表达和功能的改变密切相关,而且这些多态位点存在基因型分布和等位基因频率的种族差异性。近几年,已陆续发现在MDR1基因中有50处单核苷酸多态性（SNPs）和3处插入与缺失多态性。随后,大量文献报道某些位点的SNPs如C3435T会使个体患病的易感性增加。因此人们相信,深入研究MDR1基因多态性与P—gP的生理和生化方面的相关性将对个体医疗有着非常深远的意义。文章总结了国外最新的研究进展并结合本实验室的工作着重讨论了4个方面：1）P—gP对药代动力学性质的影响：2）MDR1基因多态性及其对遗传药理学性质的影响;3）MDR1^C3435T的单核苷酸多态性与P-gP表达和功能之间的相关性：4）MDR1基因多态性与人类某些疾病之间的相关性。     

Therapeutic peptides: technological advances driving peptides into development

As potential therapeutics, peptides offer several advantages over small molecules (increased specificity) and antibodies (small size). Nevertheless, a number of key issues have hampered their use as drug candidates. A series of new technologies have recently been developed that allow peptides to be viable drug candidates in areas usually restricted to protein therapeutics, such as monoclonal antibodies. These include the development of various types of peptide-conjugates that have lower rates of clearance and hence the potential to increase the exposure of peptide drug candidates in chronic diseases. Structural additions have also been made to peptides, including the use of unnatural amino acids, mainchain modifications and other novel substitutions, which have helped to improve peptide stability and further their therapeutic potential.     

Acridine-based (thio)semicarbazones and hydrazones: Synthesis,in vitro urease inhibition,molecular docking and in-silico ADME evaluation

Urease is a bacterial enzyme that is responsible for virulence of various pathogenic bacteria such as Staphylococcus aureus, Proteus mirabilis, Klebsiella pneumoniae, Ureaplasma urealyticum, Helicobacter pylori and Mycobacterium tuberculosis. Increased urease activity aids in survival and colonization of pathogenic bacteria causing several disorders especially gastric ulceration. Hence, urease inhibitors are used for treatment of such diseases. In search of new molecules with better urease inhibitory activity, herein we report a series of acridine derived (thio)semicarbazones (4a-4e, 6a-6l) that were found to be active against urease enzyme. Molecular docking studies were carried out to better comprehend the preferential mode of binding of these compounds against urease enzyme. Docking against urease from pathogenic bacterium S. pasteurii was also carried out with favorable results. In silico ADME evaluation was done to determine drug likeness of synthesized compounds.     

Exploring critical determinants of protein amyloidogenesis: a review

The transformation of polypeptide chains from their globular native structure to fibrillar aggregates has been a matter of great concern because of the involvement of these aggregates in the onset of several degenerative diseases. These aggregates exhibit highly ordered cross β sheet structures and are known as ‘amyloids’. Formation of amyloids in the body is associated with cytotoxicity due to direct interaction of the aggregated species with the cell membrane leading to cellular permeability or due to loss of functionality of the proteins involved in the amyloid formation. The preference of polypeptide chains to remain in their native conformation or to aggregate into amyloids is guided by several factors such as its conformation at specific condition, concentration, physicochemical properties of the amino acid sequence and so on. In the current review, we have reviewed the different factors that guide the transition of proteins from their natively folded state to the amyloidogenic state. Understanding the critical determinants of amyloidogenesis is vital towards deciphering the molecular mechanism of amyloidogenesis and for the development of effective therapeutics against amyloidosis. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Alcohol ADME in Primates Studied with Positron Emission Tomography

Background and Purpose

The sensitivity to the intoxicating effects of alcohol as well as its adverse medical consequences differ markedly among individuals, which reflects in part differences in alcohol''s absorption, distribution, metabolism, and elimination (ADME) properties. The ADME of alcohol in the body and its relationship with alcohol''s brain bioavailability, however, is not well understood.

Experimental Approach

The ADME of C-11 labeled alcohol, CH₃ ¹¹CH₂OH, 1 and C-11 and deuterium dual labeled alcohol, CH₃ ¹¹CD₂OH, 2 in baboons was compared based on the principle that C–D bond is stronger than C–H bond, thus the reaction is slower if C–D bond breaking occurs in a rate-determining metabolic step. The following ADME parameters in peripheral organs and brain were derived from time activity curve (TAC) of positron emission tomography (PET) scans: peak uptake (C_max); peak uptake time (T_max), half-life of peak uptake (T_1/2), the area under the curve (AUC_60min), and the residue uptake (C_60min).

Key Results

For 1 the highest uptake occurred in the kidney whereas for 2 it occurred in the liver. A deuterium isotope effect was observed in the kidneys in both animals studied and in the liver of one animal but not the other. The highest uptake for 1 and 2 in the brain was in striatum and cerebellum but 2 had higher uptake than 1 in all brain regions most evidently in thalamus and cingulate. Alcohol''s brain uptake was significantly higher when given intravenously than when given orally and also when the animal was pretreated with a pharmacological dose of alcohol.

Conclusion and Implications

The study shows that alcohol metabolism in peripheral organs had a large effect on alcohol''s brain bioavailability. This study sets the stage for clinical investigation on how genetics, gender and alcohol abuse affect alcohol''s ADME and its relationship to intoxication and medical consequences.     

Human umbilical cord mesenchymal stem cell-derived extracellular vesicles: A novel therapeutic paradigm

Mesenchymal stem cells (MSCs) have been revealed to hold great potential for the development of new treatment approaches for various diseases. However, the clinical use of these cells is limited due to their tumorigenic effects. The therapeutic benefits of MSCs are largely dependent on paracrine factors including extracellular vesicles (EVs). EVs are nano-sized bilayer membrane structures containing lipids, microRNAs and proteins which play key roles in cell-to-cell communications. Because of their lower immunogenicity, tumorigenicity, and easier management, EVs have emerged as a new promising alternative to whole-cell therapy. Therefore, this paper reviews current preclinical studies on the use of EVs derived from human umbilical cord MSCs (hucMSCs) as a therapeutic approach in treatment of several diseases including neurological, cardiovascular, liver, kidney, and bone diseases as well as the cutaneous wound, inflammatory bowel disease, cancers, infertility, and other disorders.     

酶类药物现状、问题及展望

随着生物制药的迅速发展,许多酶类药物应运而生,在治疗代谢疾病、心血管疾病、癌症等诸多疾病上发挥着越来越重要的作用。但是酶类药物也存在一些不足,如潜在的免疫原性、较短的体内半衰期,以及较差的组织靶向性,影响了酶类药物的疗效和应用。为克服这些缺点,人们已开发出多种技术,如通过糖基化、聚乙二醇修饰等分子工程技术提升酶蛋白药效,另一方面酶基因疗法也已成功用于多种酶缺陷疾病的治疗。基于酶类药物的迅速发展和广泛的应用前景,本文对酶类药物的现状进行较详细的阐述,并对酶类药物的优势、所存在的问题及未来发展趋势进行分析和评述。