Prediction of Drug-Drug Interactions based on Time-Dependent Inhibition from High Throughput Screening of Cytochrome P450 3A4 Inhibition

Quantitative prediction of CYP3A induction-mediated drug-drug interactions in clinical practice

There have been no reports on the quantitative prediction of CYP3A induction-mediated decreases in AUC and Cmax for drug candidates identified as a "victims" of CYP3A induction. Our previous study separately evaluated the fold-induction of hepatic and intestinal CYP3A by known inducers using clinical induction data and revealed that we were able to quantitatively predict the AUC ratio (AUCR) of a few CYP3A substrates in the presence and absence of CYP3A inducers. In the present study, we investigate the predictability of AUCR and also Cmax ratio (CmaxR) in additional 54 clinical studies. The fraction metabolized by CYP3A (fm), the intestinal bioavailability (Fg), and the hepatic intrinsic clearance (CLint) of substrates were determined by the in vitro experiments as well as clinical data used for calculating AUCR and CmaxR. The result showed that 65-69% and 65-67% of predictions were within 2-fold of observed AUCR and CmaxR, respectively. A simulation using multiple parameter combinations suggested that the variability of fm and Fg within a certain range might have a minimal impact on the calculation output. These findings suggest that clinical AUCR and CmaxR of CYP3A substrates can be quantitatively predicted from the preclinical stage.

Fluorescence-Based High-Throughput Assays for Investigating Cytochrome P450 Enzyme-Mediated Drug-Drug Interactions

The cytochrome P450 enzymes (CYPs), a group of heme-containing enzymes, catalyze oxidative metabolism of a wide range of drugs and xenobiotics, as well as different endogenous molecules. Strong inhibition of human CYPs is the most common cause of clinically associated pharmacokinetic drug-drug/herb-drug interactions (DDIs/HDIs), which may result in serious adverse drug reactions, even toxicity. Accurate and rapid assessing of the inhibition potentials on CYP activities for therapeutic agents is crucial for the prediction of clinically relevant DDIs/HDIs. Over the past few decades, significant efforts have been invested into developing optical substrates for the human CYPs, generating a variety of powerful tools for high-throughput assays to detect CYP activities in biologic specimens and for screening of CYP inhibitors. This minireview focuses on recent advances in optical substrates developments for human CYPs, as well as their applications in screening CYP inhibitors and DDIs/HDIs studies. The examples for rational design and optimization of highly specific optical substrates for the target CYP enzyme, as well as applications in investigating CYP-mediated DDIs, are illustrated. Finally, the challenges and future perspectives in this field are proposed. Collectively, this review summarizes the reported optical-based biochemical assays for highly efficient CYP activities detection, which strongly facilitated the discovery of CYP inhibitors and the investigations on CYP-mediated DDIs. SIGNIFICANCE STATEMENT: Optical substrates for cytochrome P450 enzymes (CYPs) have emerged as powerful tools for the construction of high-throughput assays for screening of CYP inhibitors. This mini-review covers the advances and challenges in the development of highly specific optical substrates for sensing human CYP isoenzymes, as well as their applications in constructing fluorescence-based high-throughput assays for investigating CYP-mediated drug-drug interactions.

A dual-modal graph learning framework for identifying interaction events among chemical and biotech drugs

Drug-drug interaction (DDI) identification is essential to clinical medicine and drug discovery. The two categories of drugs (i.e. chemical drugs and biotech drugs) differ remarkably in molecular properties, action mechanisms, etc. Biotech drugs are up-to-comers but highly promising in modern medicine due to higher specificity and fewer side effects. However, existing DDI prediction methods only consider chemical drugs of small molecules, not biotech drugs of large molecules. Here, we build a large-scale dual-modal graph database named CB-DB and customize a graph-based framework named CB-TIP to reason event-aware DDIs for both chemical and biotech drugs. CB-DB comprehensively integrates various interaction events and two heterogeneous kinds of molecular structures. It imports endogenous proteins founded on the fact that most drugs take effects by interacting with endogenous proteins. In the modality of molecular structure, drugs and endogenous proteins are two heterogeneous kinds of graphs, while in the modality of interaction, they are nodes connected by events (i.e. edges of different relationships). CB-TIP employs graph representation learning methods to generate drug representations from either modality and then contrastively mixes them to predict how likely an event occurs when a drug meets another in an end-to-end manner. Experiments demonstrate CB-TIP's great superiority in DDI prediction and the promising potential of uncovering novel DDIs.

Assessment of the in vitro cytochrome P450 (CYP) inhibition potential of nafithromycin, a next generation lactone ketolide antibiotic

Nafithromycin is a next generation lactone ketolide antibiotic slated to enter phase III clinical development in India for the treatment of CABP as a shorter 800 mg-OD X3 day therapeutic regimen. Nafithromycin exhibits potent activity against MDR Streptococcus pneumoniae including erythromycin and telithromycin-resistant resistant strains. Older macrolides/ketolides are reported to be potent inhibitors of CYP3A4/5. To facilitate comparative assessment of drug-drug interaction potential, CYP inhibitory activities of nafithromycin was evaluated in comparison with clarithromycin, telithromycin, cethromycin and solithromycin. CYP inhibitory activities were assessed against key CYP isoforms (CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6 and CYP3A4/5) using human liver microsomes. Additionally, time-dependent inhibition (TDI), metabolism-based inhibition (MBI) and k _inact /K _I activities were also investigated for CYP3A4/5. Nafithromycin did not inhibit key CYP enzymes and was found to be a weak inhibitor of CYP3A4/5. Comparator antibiotics were found to be potent inhibitors with 2- to 50-fold leftward shifts in CYP3A4/5 IC50 values, while such shift was not noted for nafithromycin. k _inact /K _I ratio of nafithromycin was 3- to 153-fold lower than comparator drugs, further substantiating its lower affinity for CYP3A4/5. In sum, weaker inhibition and lower k _inact /K _I ratio for CYP3A4/5, points towards nafithromycin's lower propensities towards clinical drug-drug interactions as compared to other macrolides/ketolides antibiotics.

Impact of Intracellular Concentrations on Metabolic Drug-Drug Interaction Studies

Accurate prediction of drug-drug interactions (DDI) is a challenging task in drug discovery and development. It requires determination of enzyme inhibition in vitro which is highly system-dependent for many compounds. The aim of this study was to investigate whether the determination of intracellular unbound concentrations in primary human hepatocytes can be used to bridge discrepancies between results obtained using human liver microsomes and hepatocytes. Specifically, we investigated if Kp_uu could reconcile differences in CYP enzyme inhibition values (K_i or IC₅₀). Firstly, our methodology for determination of Kp_uu was optimized for human hepatocytes, using four well-studied reference compounds. Secondly, the methodology was applied to a series of structurally related CYP2C9 inhibitors from a Roche discovery project. Lastly, the Kp_uu values of three commonly used CYP3A4 inhibitors—ketoconazole, itraconazole, and posaconazole—were determined and compared to compound-specific hepatic enrichment factors obtained from physiologically based modeling of clinical DDI studies with these three compounds. Kp_uu obtained in suspended human hepatocytes gave good predictions of system-dependent differences in vitro. The Kp_uu was also in fair agreement with the compound-specific hepatic enrichment factors in DDI models and can therefore be used to improve estimations of enrichment factors in physiologically based pharmacokinetic modeling.

Time-dependent inhibition (TDI) of CYP1A2 by a CYP3A4-mediated reactive metabolite: proposal for a novel mechanism of irreversible TDI by a non-suicide substrate

1. The purpose of this study was to clarify the mechanism of DSP-1053 time-dependent inhibition (TDI) for CYP1A2. 2. DSP-1053 inhibited time- and concentration-dependently CYP1A2 activity in human liver microsomes even in a dilution assay. However, DSP-1053 was not metabolized by recombinant human CYP1A2. These findings indicate that the inhibitory effect of DSP-1053 on CYP1A2 does not follow a general mechanism-based inhibition (MBI) because it did not seem to be a suicide substrate. 3. In fact, CYP1A2 was not inhibited with DSP-1053 pre-incubation in recombinant human CYP1A2. On the other hand, CYP1A2 was potently inhibited after pre-incubation with DSP-1053 in a mixture of human recombinant CYP1A2 and CYP3A4. In addition, DSP-1053 TDI of CYP1A2 in human liver microsomes was drastically reduced not only by addition of a CYP3A4 inhibitor, but also by addition of potassium cyanide (KCN), which is a trapping agent for iminium ions. We also confirmed in this study that CYP1A2 suicide inhibition by DSP-1053 metabolites generated by CYP3A4 had only minimal role in DSP-1053 TDI of CYP1A2. 4. In conclusion, a possible mechanism for DSP-1053 TDI of CYP1A2 is that DSP-1053 iminium ion, which is generated by CYP3A4, departs from CYP3A4 without inhibiting it and covalently binds to CYP1A2.

Structure-Based Inhibitor Design for Evaluation of a CYP3A4 Pharmacophore Model

Human cytochrome P450 3A4 (CYP3A4) is a key xenobiotic-metabolizing enzyme that oxidizes and clears the majority of drugs. CYP3A4 inhibition may lead to drug-drug interactions, toxicity, and other adverse effects but, in some cases, could be beneficial and enhance therapeutic efficiency of coadministered pharmaceuticals that are metabolized by CYP3A4. On the basis of our investigations of analogs of ritonavir, a potent CYP3A4 inactivator and pharmacoenhancer, we have built a pharmacophore model for a CYP3A4-specific inhibitor. This study is the first attempt to test this model using a set of rationally designed compounds. The functional and structural data presented here agree well with the proposed pharmacophore. In particular, we confirmed the importance of a flexible backbone, the H-bond donor/acceptor moiety, and aromaticity of the side group analogous to Phe-2 of ritonavir and demonstrated the leading role of hydrophobic interactions at the sites adjacent to the heme and phenylalanine cluster in the ligand binding process. The X-ray structures of CYP3A4 bound to the rationally designed inhibitors provide deeper insights into the mechanism of the CYP3A4-ligand interaction. Most importantly, two of our compounds (15a and 15b) that are less complex than ritonavir have comparable submicromolar affinity and inhibitory potency for CYP3A4 and, thus, could serve as templates for synthesis of second generation inhibitors for further evaluation and optimization of the pharmacophore model.

P450-Based Drug-Drug Interactions of Amiodarone and its Metabolites: Diversity of Inhibitory Mechanisms

In this study, IC50 shift and time-dependent inhibition (TDI) experiments were carried out to measure the ability of amiodarone (AMIO), and its circulating human metabolites, to reversibly and irreversibly inhibit CYP1A2, CYP2C9, CYP2D6, and CYP3A4 activities in human liver microsomes. The [I]u/Ki,u values were calculated and used to predict in vivo AMIO drug-drug interactions (DDIs) for pharmaceuticals metabolized by these four enzymes. Based on these values, the minor metabolite N,N-didesethylamiodarone (DDEA) is predicted to be the major cause of DDIs with xenobiotics primarily metabolized by CYP1A2, CYP2C9, or CYP3A4, while AMIO and its N-monodesethylamiodarone (MDEA) derivative are the most likely cause of interactions involving inhibition of CYP2D6 metabolism. AMIO drug interactions predicted from the reversible inhibition of the four P450 activities were found to be in good agreement with the magnitude of reported clinical DDIs with lidocaine, warfarin, metoprolol, and simvastatin. The TDI experiments showed DDEA to be a potent inactivator of CYP1A2 (KI = 0.46 μM, kinact = 0.030 minute(-1)), while MDEA was a moderate inactivator of both CYP2D6 (KI = 2.7 μM, kinact = 0.018 minute(-1)) and CYP3A4 (KI = 2.6 μM, kinact = 0.016 minute(-1)). For DDEA and MDEA, mechanism-based inactivation appears to occur through formation of a metabolic intermediate complex. Additional metabolic studies strongly suggest that CYP3A4 is the primary microsomal enzyme involved in the metabolism of AMIO to both MDEA and DDEA. In summary, these studies demonstrate both the diversity of inhibitory mechanisms with AMIO and the need to consider metabolites as the culprit in inhibitory P450-based DDIs.

Ritonavir analogues as a probe for deciphering the cytochrome P450 3A4 inhibitory mechanism

Inactivation of human drug-metabolizing cytochrome P450 3A4 (CYP3A4) could lead to serious adverse events such as drug-drug interactions and toxicity. However, when properly controlled, CYP3A4 inhibition may be beneficial as it can improve clinical efficacy of co-administered therapeutics that otherwise are quickly metabolized by CYP3A4. Currently, the CYP3A4 inhibitor ritonavir and its derivative cobicistat are prescribed to HIV patients as pharmacoenhancers. Both drugs were designed based on the chemical structure/activity relationships rather than the CYP3A4 crystal structure. To unravel the structural basis of CYP3A4 inhibition, we compared the binding modes of ritonavir and ten analogues using biochemical, mutagenesis and x-ray crystallography techniques. This review summarizes our findings on the relative contribution of the heme-ligating moiety, side chains and the terminal group of ritonavir-like molecules to the ligand binding process, and highlights strategies for a structure-guided design of CYP3A4 inactivators.

In Vitro Evaluation of Reversible and Time-Dependent Inhibitory Effects of Kalanchoe crenata on CYP2C19 and CYP3A4 Activities

Kalanchoe crenata popularly known as "dog's liver" is used in most African countries for the treatment of chronic diseases such as diabetes, asthma and HIV/AIDS related infections. The evaluation of K. crenata for herb-drug interactions has not been reported. This study therefore aims to evaluate the risk of K. crenata for herb-drug interaction in vitro. Crude methanol and fractions of K. crenata were incubated and preincubated with recombinant human CYP2C19 and CYP3A4. Comparative studies were conducted in both human liver microsomes and recombinant human CYP to ascertain the inhibition profile of the crude extract and the various fractions. The cocktail approach of recombinant human CYPs was conducted to confirm the inhibition potential of the fractions in the presence of other CYPs. The results showed significant time-dependent inhibition of tested samples on CYP3A4 with crude methanol (39KC), fractions 45A, 45B and 45D given IC50 fold decrease of 3.29, 2.26, 1.91 and 1.49, respective. Time dependent kinetic assessment of 39KC and 45D showed KI and kinact values for 39KC as 1.77 µg/mL and 0.091 min(-1) while that of 45D were 6.45 µg/mL and 0.024 min(-1), respectively. Determination of kinact based on IC50 calculations yielded 0.015 and 0.04 min(-1) for 39KC and 45D, respectively. Cocktail approach exhibited fold decreases in IC50 for all test fractions on CYP3A4 within the ranges of 2.10 - 4.10. At least one phytoconstituent in the crude methanol extract of Kalanchoe crenata is a reversible and time-dependent inhibitor of CYP3A4.

Evaluation of drug interaction potential of Labisia pumila (Kacip Fatimah) and its constituents

Labisia pumila (Kacip Fatimah) is a popular herb in Malaysia that has been traditionally used in a number of women's health applications such as to improve libido, relieve postmenopausal symptoms, and to facilitate or hasten delivery in childbirth. In addition, the constituents of this plant have been reported to possess anticancer, antioxidant, and anti-inflammatory properties. Clinical studies have indicated that cytochrome P450s (CYPs), P-glycoprotein (P-gp), and Pregnane X receptor (PXR) are the three main modulators of drug-drug interactions which alter the absorption, distribution, and metabolism of drugs. Given the widespread use of Kacip Fatimah in dietary supplements, the current study focuses on determining the potential of its constituents to affect the activities of CYPs, P-gp, or PXR using in vitro assays which may provide useful information toward the risk of herb-drug interaction with concomitantly used drugs. Six compounds isolated from the roots of L. pumila (2 saponins and 4 alkyl phenols) were tested, in addition to the methanolic extract. The extract of L. pumila showed a significant time dependent inhibition (TDI) of CYP3A4, reversible inhibition of CYP2C9 and 2C19 and a weak inhibition of 1A2 and 2D6 as well as an inhibition of P-gp and rifampicin-induced PXR activation. The alkyl phenols inhibited CYP3A4 (TDI), CYP2C9, and 2C19 (reversible) while saponins inhibited P-gp and PXR. In conclusion, L. pumila and its constituents showed significant modulation of all three regulatory proteins (CYPs, P-gp, and PXR) suggesting a potential to alter the pharmacokinetic and pharmacodynamic properties of conventional drugs if used concomitantly.

Pyridine-substituted desoxyritonavir is a more potent inhibitor of cytochrome P450 3A4 than ritonavir

Utilization of the cytochrome P450 3A4 (CYP3A4) inhibitor ritonavir as a pharmacoenhancer for anti-HIV drugs revolutionized the treatment of HIV infection. However, owing to ritonavir-related complications, there is a need for development of new CYP3A4 inhibitors with improved pharmacochemical properties, which requires a full understanding of the CYP3A4 inactivation mechanisms and the unraveling of possible inhibitor binding modes. We investigated the mechanism of CYP3A4 interaction with three desoxyritonavir analogues, containing the heme-ligating imidazole, oxazole, or pyridine group instead of the thiazole moiety (compounds 1, 2, and 3, respectively). Our data show that compound 3 is superior to ritonavir in terms of binding affinity and inhibitory potency owing to greater flexibility and the ability to adopt a conformation that minimizes steric clashing and optimizes protein-ligand interactions. Additionally, Ser119 was identified as a key residue assisting binding of ritonavir-like inhibitors, which emphasizes the importance of polar interactions in the CYP3A4-ligand association.

Mechanism-based inhibition profiles of erythromycin and clarithromycin with cytochrome P450 3A4 genetic variants

Inhibition of cytochrome P450 (CYP) 3A4 is the major cause of drug-drug interactions (DDI). We have previously reported that the genetic variation of CYP3A4 significantly affected the inhibitory profiles of typical competitive inhibitors. In addition to competitive inhibition, some clinically significant DDI are attributable to mechanism-based inhibition (MBI). However, the differences in the MBI kinetics among CYP3A4 genetic variants remain to be characterized. In this study, we quantitatively investigated the inhibition kinetics of MBI inhibitors, erythromycin and clarithromycin, on the CYP3A4 variants CYP3A4.1, 4.2, 4.7, 4.16, and 4.18. The activity of CYP3A4 was assessed using testosterone 6β-hydroxylation with recombinant CYP3A4. Both erythromycin and clarithromycin decreased the activity of CYP3A4 in a time-dependent manner. The maximum inactivation rate constants, k(inact,max), of erythromycin for CYP3A4.2 and CYP3A4.7 were 0.5-fold that for CYP3A4.1, while that for CYP3A4.16 and CYP3A4.18 were similar to that for CYP3A4.1. The K(I) values of erythromycin for CYP3A4.2, 4.7, 4.16, and 4.18 were 1.2-, 0.4-, 2.2- and 0.72-fold those of CYP3A4.1, respectively. Similar results were obtained for clarithromycin. In conclusion, the inhibitory profiles of MBI inhibitors, as well as competitive inhibitors, may possibly differ among CYP3A4 variants. This difference may contribute to interindividual differences in the extent of DDI based on MBI.

Mechanism-based inhibition of CYP1A1 and CYP3A4 by the furanocoumarin chalepensin

The cytochrome P450 (P450, CYP) 2A6 inhibitor chalepensin was found to inhibit human CYP1A1, CYP1A2, CYP2A13, CYP2C9, CYP2D6, CYP2E1, and CYP3A4 to different extents. CYP1A1 and CYP3A4 underwent pronounced mechanism-based inactivation by chalepensin and had the smallest IC50 ratios of inhibition with NADPH-fortified pre-incubation (IC50(+)) to that without pre-incubation (IC50(-)). CYP2E1 had the least susceptibility to mechanism-based inactivation. This inactivation of CYP1A1 and CYP3A4 exhibited time-dependence, led to a loss of spectrophotometrically detected P450, and could not be fully recovered by dialysis. Pre-incubation with chalepensin did not affect NADPH-P450 reductase activity. Cytosol-supported glutathione conjugation protected CYP3A4 but not CYP1A1 against the inactivation by chalepensin. Cytosolic decomposition of chalepensin may contribute partially to the protection. The high epoxidation activities of CYP1A1, CYP2A6, and CYP3A4 were in agreement with their pronounced susceptibilities to mechanism-based inactivation by chalepensin. Considering both the IC50 values and inactivation kinetic parameters, the threshold concentrations of chalepensin for potential drug interactions through inhibition of CYP2A6 and CYP3A4 were estimated to be consistently low. These results demonstrate that chalepensin inhibits multiple P450s and that epoxidation activity is crucial for the potential drug interaction through mechanism-based inhibition.

Discovery of tofogliflozin, a novel C-arylglucoside with an O-spiroketal ring system, as a highly selective sodium glucose cotransporter 2 (SGLT2) inhibitor for the treatment of type 2 diabetes

Inhibition of sodium glucose cotransporter 2 (SGLT2) has been proposed as a novel therapeutic approach to treat type 2 diabetes. In our efforts to discover novel inhibitors of SGLT2, we first generated a 3D pharmacophore model based on the superposition of known inhibitors. A search of the Cambridge Structural Database using a series of pharmacophore queries led to the discovery of an O-spiroketal C-arylglucoside scaffold. Subsequent chemical examination combined with computational modeling resulted in the identification of the clinical candidate 16d (CSG452, tofogliflozin), which is currently under phase III clinical trials.

Mechanism of cytochrome P450-3A inhibition by ketoconazole

OBJECTIVES

Ketoconazole is extensively used as an index inhibitor of cytochrome P450-3A (CYP3A) activity in vitro and in vivo, but the mechanism of ketoconazole inhibition of CYP3A still is not clearly established.

METHODS

Inhibition of metabolite formation by ketoconazole (seven concentrations from 0.01 to 1.0 µm) was studied in human liver microsomes (n = 4) at six to seven substrate concentrations for triazolam, midazolam, and testosterone, and at two substrate concentrations for nifedipine.

KEY FINDINGS

Analysis of multiple data points per liver sample based on a mixed competitive-noncompetitive model yielded mean inhibition constant K(i) values in the range of 0.011 to 0.045 µm. Ketoconazole IC50 increased at higher substrate concentrations, thereby excluding pure noncompetitive inhibition. For triazolam, testosterone, and midazolam α-hydroxylation, mean values of α (indicating the 'mix' of competitive and noncompetitive inhibition) ranged from 2.1 to 6.3. However, inhibition of midazolam 4-hydroxylation was consistent with a competitive process. Determination of K(i) and α based on the relation between 50% inhibitory concentration values and substrate concentration yielded similar values. Pre-incubation of ketoconazole with microsomes before addition of substrate did not enhance inhibition, whereas inhibition by troleandomycin was significantly enhanced by pre-incubation.

CONCLUSIONS

Ketoconazole inhibition of triazolam α- and 4-hydroxylation, midazolam α-hydroxylation, testosterone 6β-hydroxylation, and nifedipine oxidation appeared to be a mixed competitive-noncompetitive process, with the noncompetitive component being dominant but not exclusive. Quantitative estimates of K(i) were in the low nanomolar range for all four substrates.

Consideration of reliable concentrations for prediction of change in enzyme activity by mechanism-based inactivation using physiologically-based pharmacokinetic model simulations

Using physiologically-based pharmacokinetic model simulations with the assumption that elimination of inactivator is not altered by mechanism-based inactivation (MBI) of the target enzyme, we examined at what concentrations the influence of MBI could be accurately and simply predicted. The method utilizing maximum unbound systemic concentration as the inactivator concentration (method 1) tended to overestimate this influence, and accuracy expressed as the ratio of estimated and exact fold decrease in enzyme activity ranged from 0.80 to 8.41. In addition, when the volume of distribution was large or the absorption rate constant was small, method 1 provided relatively precise estimation, with the ratio of nearly 1. We propose use of two concentrations, the steady-state average unbound liver concentration and maximum limit of steady-state average unbound liver concentration, to predict the effects of MBI. The accuracy of prediction of MBI using these two concentrations ranged from 0.90 to 1.04 and 0.92 to 2.96, respectively, and was higher than that with method 1. These two concentrations can be obtained early in the drug development process, and estimated results can be expected to contribute to determination of the effects of MBI.

Binding kinetics and mechanism of action: toward the discovery and development of better and best in class drugs

Binding kinetics (BK), an often overlooked key aspect of the broader concept of drug mechanism of action (MOA), is increasingly recognized as a springboard from pharmacokinetics (PK) to pharmacodynamics, and as a critical differentiator and predictor for drug efficacy and safety. Just as greater attention to PK issues has helped reduce the attrition of drugs tested in clinical trials, the emerging paradigm shift from primarily affinity/potency-emphasized to a more holistic BK-perceptive and MOA-informed approach is expected to further enhance the success of drug discovery and development. This perspective attempts to envision what this new approach looks like when proper emphasis is placed on BK and MOA in designing better and best in class drugs.