In silico prediction of acyl glucuronide reactivity

Transacylation and hydrolysis of the acyl glucuronides of ibuprofen and its α-methyl-substituted analogues investigated by 1H NMR spectroscopy and computational chemistry: Implications for drug design

Drugs and drug metabolites containing a carboxylic-acid moiety can undergo in vivo conjugation to form 1-β-O-acyl-glucuronides (1-β-O-AGs). In addition to hydrolysis, these conjugates can undergo spontaneous acyl migration, and anomerisation reactions, resulting in a range of positional isomers. Facile transacylation has been suggested as a mechanism contributing to the toxicity of acyl glucuronides, with the kinetics of these processes thought to be a factor. Previous 1H NMR spectroscopic and HPLC-MS studies have been conducted to measure the degradation rates of the 1-β-O-AGs of three nonsteroidal anti-inflammatory drugs (ibufenac, R-ibuprofen, S-ibuprofen) and a dimethyl-analogue (termed here as "bibuprofen"). These studies have also determined the relative contributions of hydrolysis and acyl migration in both buffered aqueous solution, and human plasma. Here, a detailed kinetic analysis is reported, providing the individual rate constants for the acyl migration and hydrolysis reactions observed in buffer for each of the 4 AGs, together with the overall degradation rate constants of the parent 1-β-O-AGs. Computational modelling of the reactants and transition states of the transacylation reaction using density functional theory indicated differences in the activation energies that reflected the influence of both substitution and stereochemistry on the rate of transacylation/hydrolysis.

Acyl glucuronide reactivity in perspective

Acyl glucuronidation is a common metabolic fate for acidic drugs and their metabolites and, because these metabolites are reactive, they have been linked to adverse drug reactions (ADRs) and drug withdrawals. However, alternative routes of metabolism leading to reactive metabolites (e.g., oxidations and acyl-CoA thioesters) mean that unambiguous proof that acyl glucuronides are toxic is lacking. Here, we review the synthesis and reactivity of these metabolites, and describe the use of molecular modelling and in vitro and in vivo reactivity assessment of acyl glucuronide reactivity. Based on the emerging structure-dependent differences in reactivity and protein adduction methods for risk assessment for acyl glucuronide-forming acid drugs or drug candidates in drug discovery/development are suggested.

Structural investigations of stereoselective profen binding by equine and leporine serum albumins

Serum albumin, the most abundant transport protein of mammalian blood, interacts with various nonsteroidal anti-inflammatory drugs (NSAIDs) affecting their disposition, metabolism, and excretion. A big group of chiral NSAIDs transported by albumin, profens, is created by derivatives of 2-arylpropionic acid. The chiral center in the structures of profens is adjacent to the carboxylate moiety and often determines different pharmacological properties of profen enantiomers. This study describes crystal structures of two albumins, isolated from equine and leporine serum, in complexes with three profens: ibuprofen, ketoprofen, and suprofen. Based on three-dimensional structures, the stereoselectivity of albumin is discussed and referred to the previously published albumin complexes with drugs. Drug Site 2 (DS2) of albumin, the bulky hydrophobic pocket of subdomain IIIA with a patch of polar residues, preferentially binds (S)-enantiomers of all investigated profens. Almost identical binding mode of all these drugs clearly indicates the stereoselectivity of DS2 towards (S)-profens in different albumin species. Also, the affinity studies show that DS2 is the major site that presents high affinity towards investigated drugs. Additionally, crystallographic data reveal the secondary binding sites of ketoprofen in leporine serum albumin and ibuprofen in equine serum albumin, both overlapping with previously identified naproxen binding sites: the cleft formed between subdomains IIIA and IIIB close to the fatty acid binding site 5 and the niche created between subdomains IIA and IIIA, called fatty acid site 6.

Kinetic modelling of acyl glucuronide and glucoside reactivity and development of structure–property relationships

Detailed kinetic and transition structure modelling to rationalise the differences in reactivity observed between the acyl glucuronide and glucoside metabolites of a series of phenylacetic acid analogues.

New Perspectives on Acyl Glucuronide Risk Assessment in Drug Discovery: Investigation of In vitro Stability, In situ Reactivity, and Bioactivation

Background:

Acyl glucuronides of xenobiotics have been a subject of wide interest from the pharmaceutical industry with respect to biochemical reactivity, hepatic disposition, and enterohepatic cir-culation. The reactivity and lack of stability of an acyl glucuronide for a clinical candidate could pose ma-jor developability concerns. To date, multiple in vitro assays have been published to assess the risk asso-ciated with acyl glucuronides. Despite this fact, the translation of these findings to predicting clinical safe-ty remains poor.

Methods:

In the present investigation, we aimed to provide simplified in vitro strategy to understand the bioactivation potential of acyl glucuronides of 10 commercial, carboxylic acid containing drugs that have been categorized as “safe,” “warning,” or “withdrawn” with respect to their marketed use. Acyl migration was measured as a function of the number of peaks observed in LC-MSn analysis. In addition, we carried out reactive intermediate trapping studies with glutathione and methoxylamine to identify the key interme-diates in the transacylation bioactivation and glycation pathways, respectively. We also conducted reaction phenotyping with recombinant UDP-glucuronosyltransferase (UGT) Supersomes® to investigate if the formation of acyl glucuronides could be linked to specific UGT isoform(s).

Results:

Our results were in line with reported values in the literature. Our assay could be used in discov-ery research where half-life calculation completely eliminated the need to chemically synthesize the acyl glucuronide standard for risk assessment. We captured our results for risk assessment in a flow chart to simplify the various complex in vitro techniques historically presented.

Conclusion:

While the compounds tested from “withdrawn” and “warning category” all formed the glu-tathione adduct in buffer, none from “safe” category formed the glutathione adduct. In contrast, none of the compounds tested from any category formed methoxylamine conjugate, a reaction with putative alde-hyde moiety formed via acyl migration. These results, highly favor the nucleophilic displacement as a cause of the reactivity rather than the acyl migration via aldehyde formation. The workflow presented could also be applied in the discovery setting to triage new chemical entities of interest.

Chemo-Enzymatic Synthesis, Structural and Stereochemical Characterization, and Intrinsic Degradation Kinetics of Diastereomers of 1-β-O-Acyl Glucuronides Derived from Racemic 2-{4-[(2-Methylprop-2-en-1-yl)amino]phenyl}propanoic Acid

Alminoprofen, (RS)-2-{4-[(2-methylprop-2-en-1-yl)amino]phenyl}propanoic acid (ALP) 1, is a racemic drug categorized as a 2-arylpropanoic acid-class nonsteroidal anti-inflammatory drug. Pharmacokinetic studies of 1 in patients have revealed that the corresponding acyl glucuronide 5 is a major urinary metabolite, but little is known about the structure and stereochemistry of 5. The present work describes the synthesis of a diastereomeric mixture of 1-β-O-acyl glucuronides (2RS)-5 from 1 and methyl 2,3,4-tri-O-acetyl-1-bromo-1-deoxy-α-d-glucopyranuronate 2 using our chemo-enzymatic method that has complete specificity for the β-configuration. The structure of (2RS)-5 was characterized by ¹H and ¹³C NMR spectroscopy and high-resolution mass spectrometry as well as by complete hydrolysis by β-glucuronidase. The absolute stereochemistry of (2RS)-5 was determined by comparison with (2R)-5 synthesized alternatively from (2R)-1 and 2. Compound (2R)-1 was prepared in two steps starting from chiral (R)-2-(4-nitrophenyl)propanoic acid (2R)-6. Chiral resolution of (2RS)-1 was achieved using a chiral high-performance liquid chromatography column, and its stereochemistry was determined by comparison with (2R)-1. The intrinsic degradation rate constant of (2R)-5 was 0.405 ± 0.002 h^-1, which is approximately twice that of (2S)-5 (the k value was 0.226 ± 0.002 h^-1) under physiological conditions (pH 7.40, 37 °C).

Impact of Physicochemical Properties on Dose and Hepatotoxicity of Oral Drugs

A database containing maximum daily doses of 1841 marketed oral drugs was used to examine the influence of physicochemical properties on dose and hepatotoxicity (drug induced liver injury, DILI). Drugs in the highest ∼20% dose range had significantly reduced mean lipophilicity and molecular weight, increased fractional surface area, increased % of acids, and decreased % of bases versus drugs in the lower ∼60% dose range. Drugs in the ∼20-40% dose range had intermediate mean properties, similar to the mean values for the full drug set. Drugs that are both large and highly lipophilic almost invariably do not have doses in the upper ∼20% range. The results show that oral druglike physicochemical properties are different according to these dose ranges, and this is consistent with maintenance of acceptable safety profiles as efficacious exposure increases. Verified DILI annotations from a compilation of >1000 approved drugs (Chen, M.; et al. Drug Discov. Today, 2016, 21, 648 ) were used. The drugs classified as "No DILI" ( n = 163) had significantly lower dose and lipophilicity, and higher Fsp3 (fraction of carbon atoms that are sp³ hybridized) versus the "Most DILI" ( n = 163) drugs. The percentages of acids were reduced and bases increased in the "No DILI" versus the "Most DILI" groups. Drugs classified as "Less DILI" or "Ambiguous DILI" had intermediate mean values of dose, lipophilicity, Fsp3, and % acids and bases. The impact of lipophilicity and Fsp3 on DILI increases in the upper 20% versus the lower 80% dose range, and a simple decision tree model predicted "No DILI" versus "Most DILI" outcomes with 82% accuracy. The model correctly classified 19 of 22 drugs (86%) that failed in development due to human hepatotoxicity. Because many oral drugs lacking DILI annotations are predicted to be "Most DILI", the model is best used preclinically in conjunction with experimental DILI mitigation.

Glycine conjugation: importance in metabolism, the role of glycine N-acyltransferase, and factors that influence interindividual variation

INTRODUCTION

Glycine conjugation of mitochondrial acyl-CoAs, catalyzed by glycine N-acyltransferase (GLYAT, E.C. 2.3.1.13), is an important metabolic pathway responsible for maintaining adequate levels of free coenzyme A (CoASH). However, because of the small number of pharmaceutical drugs that are conjugated to glycine, the pathway has not yet been characterized in detail. Here, we review the causes and possible consequences of interindividual variation in the glycine conjugation pathway.

AREAS COVERED

The authors review the importance of CoASH in metabolism, formation and toxicity of xenobiotic acyl-CoAs, and mechanisms for restoring levels of CoASH. They focus on GLYAT, glycine conjugation, how genetic variation in the GLYAT gene could influence glycine conjugation, and the emerging roles of glycine metabolism in cancer and musculoskeletal development.

EXPERT OPINION

The substrate selectivity of GLYAT and its variants needs to be further characterized, as organic acids can be toxic if the corresponding acyl-CoA is not a substrate for glycine conjugation. GLYAT activity affects mitochondrial ATP production, glycine availability, CoASH availability, and the toxicity of various organic acids. Therefore, variation in the glycine conjugation pathway could influence liver cancer, musculoskeletal development, and mitochondrial energy metabolism.