Predicting Oxidation Sites with Order of Occurrence among Multiple Sites for CYP4A-mediated Reactions

Construction of a fused grid-based CYP2C8-Template system and the application

A ligand-accessible space in the CYP2C8 active site was reconstituted as a fused grid-based Template∗ with the use of structural data of the ligands. An evaluation system of CYP2C8-mediated metabolism has been developed on Template with the introduction of the idea of Trigger-residue initiated ligand-movement and fastening. Reciprocal comparison of the data of simulation on Template with experimental results suggested a unified way of the interaction of CYP2C8 and its ligands through the simultaneous plural-contact with Rear-wall of Template. CYP2C8 was expected to have a room for ligands between vertically standing parallel walls termed Facial-wall and Rear-wall. Both the walls were separated by a distance corresponding to 1.5-Ring (grid) diameter size, which was termed Width-gauge. The ligand sittings were stabilized through contacts with Facial-wall and the left-side borders of Template including specific Position 29, left-side border of Rings I/J, or Left-end, after Trigger-residue initiated ligand-movement. Trigger-residue movement is suggested to force ligands to stay firmly in the active site and then to initiate CYP2C8 reactions. Simulation experiments for over 350 reactions of CYP2C8 ligands supported the system established.

Construction of a fused grid-based CYP2C18-Template system and its application to drug metabolism

Detailed estimation of cytochrome P450 (CYP)-mediated metabolisms of medicine and other chemicals is necessary for the efficacy and safety assessments. Data on the metabolisms mediated by minor CYP enzymes like CYP2C18 are often not available in metabolisms and safety assessments of chemicals except for medical drugs developed recently. A ligand-accessible space in the active site of human CYP2C18 was thus reconstituted as a fused grid-based Template with the use of structural data of its ligands. An evaluation system of CYP2C18-mediated metabolism was then developed on Template with the introduction of the idea of movement and fastening of ligands after Trigger-residue contact. Reciprocal comparison of the data of simulations on Template with experimental results suggested a unified way of the interaction of CYP2C18, in similar to the CYP2C8 interaction (Drug Metab Pharmacokinet 2023, in press). These experiments also displayed the roles of initial Trigger-residue-localizations on their distinct catalyses among human CYP2C enzymes. Simulation experiments for over 130 reactions of CYP2C18 ligands supported the system established.

Effects of acidic non-steroidal anti-inflammatory drugs on human cytochrome P450 4A11 activity: Roles of carboxylic acid and a sulfur atom in potent inhibition by sulindac sulfide

Cytochrome P450 4A11 (CYP4A11) has many endogenous and exogenous compounds containing a carboxyl group in their structure as substrates. If drugs with this characteristic potently attenuate the catalytic function of CYP4A11, drug-drug interactions may occur. Acidic non-steroidal anti-inflammatory drugs (NSAIDs) possess a carboxylic acid in their structure. However, it remains unclear whether these drugs inhibit CYP4A11 activity. The present study examined the inhibitory effects of acidic NSAIDs on CYP4A11 activity using human liver microsomes (HLMs) and recombinant CYP4A11. Sulindac sulfide, ibuprofen, and flurbiprofen effectively decreased the luciferin-4A O-demethylase activity of HLMs and recombinant CYP4A11 (inhibition rates of 30-96% at an inhibitor concentration of 100 μM), while salicylic acid, aspirin, diclofenac, mefenamic acid, indomethacin, etodolac, ketoprofen, loxoprofen, S-naproxen, pranoprofen, zaltoprofen, and oxaprozin exhibited weaker inhibitory activity (inhibition rates up to 23%). Among the drugs tested, sulindac sulfide was the most potent inhibitor of CYP4A11 activity. A kinetic analysis of the inhibition of CYP4A11 by sulindac sulfide revealed mixed-type inhibition for HLMs (Ki = 3.38 μM) and recombinant CYP4A11 (Ki = 4.19 μM). Sulindac sulfide is a pharmacologically active metabolite of sulindac (sulfoxide form), which is also oxidized to sulindac sulfone. To elucidate the role of a sulfur atom of sulindac sulfide in the inhibition of CYP4A11, the inhibitory effects of sulindac sulfide and its oxidized forms on CYP4A11 activity were examined. The potency of inhibition against HLMs was greater in the order of sulindac sulfide, sulindac, and sulindac sulfone; IC50 values were 6.16, 52.7, and 71.6 μM, respectively. The present results indicate that sulindac sulfide is a potent inhibitor of CYP4A11. These results and the molecular modeling of CYP4A11 with sulindac sulfide and its oxidized forms suggest that a sulfur atom of sulindac sulfide as well as its carboxylic acid play important roles in the inhibition of CYP4A11.

Application of fused-grid-based CYP-Template systems for genotoxic substances to understand the metabolisms

Understanding of metabolic processes is a key factor to evaluate biological effects of carcinogen and mutagens. Applicability of fused-grid Template* systems of CYP enzymes (Drug Metab Pharmacokinet 2019, 2020, 2021, and 2022) was tested for three phenomena. (1) Possible causal relationships between CYP-mediated metabolisms of β-naphthoflavone and 3-methylcholanthrene and the high inducibility of CYP enzymes were examined. Selective involvement of non-constitutive CYP1A1, but not constitutive CYP1A2, was suggested on the oxidative metabolisms of efficient inducers, β-naphthoflavone and 3-methylcholanthrene. These results supported the view of the causal link of their high inducibility with their inefficient metabolisms due to the lack of CYP1A1 in livers at early periods after the administration of both inducers. (2) Clear differences exist between human and rodent CYP1A1 enzymes on their catalyses with heterocyclic amines, dioxins and polyaromatic hydrocarbons (PAHs). Reciprocal comparison of simulation results with experimental data suggested the rodent specific site and distinct sitting-preferences of ligands on Template for human and rodent CYP1A1 enzymes. (3) Enhancement of metabolic activation and co-mutagenicity have been known as phenomena associated with Salmonella mutagenesis assay. Both the phenomena were examined on CYP-Templates in ways of simultaneous bi-molecule bindings of distinct ligands as trigger and pro-metabolized molecules. α-Naphthoflavone and norharman served consistently as trigger-molecules to support the oxidations of PAHs and arylamines sitting simultaneously as pro-metabolized molecules on Templates of CYP1A1, CYP1A2 and CYP3A4. These CYP-Template simulation systems with deciphering capabilities are promising tools to understand the mechanism basis of metabolic activations and to support confident judgements in safety assessments.

Construction of a fused grid-based CYP2C19-Template system and the application

A ligand-accessible space in the CYP2C19 active site was reconstituted as a fused grid-based Template with the use of structural data of the ligands. An evaluation system of CYP2C19-mediated metabolism has been developed on Template with the introduction of the idea of Trigger-residue initiated ligand-movement and fastening. Reciprocal comparison of the data of simulation on Template with experimental results suggested a unified way of the interaction of CYP2C19 and its ligands through the simultaneous plural-contact with Rear-wall of Template. CYP2C19 was expected to have a room for ligands between vertically standing parallel walls termed Facial-wall and Rear-wall, which were separated by a distance corresponding to 1.5-Ring (grid) diameter size. The ligand sittings were stabilized through contacts with Facial-wall and the left-side borders of Template including specific Position 29 or Left-end after Trigger-residue initiated ligand-movement. Trigger-residue movement is suggested to force ligands to stay firmly in the active site and then to initiate CYP2C19 reactions. Simulation experiments for over 450 reactions of CYP2C19 ligands supported the system established.

Deciphering Key Interactions of Ligands with CYP3A4-Template* system

Cytochrome P450 (CYP)-mediated metabolisms are often associated with biological and toxicological events of chemicals. A major hepatic enzyme, CYP3A4, showed clear distinctions on their catalyses even among ligands having resemble structures. To better understand mechanisms of their distinct catalyses, possible associations of ligand interactions at specific parts of CYP3A4 residues were investigated using CYP3A4-Template system developed (DMPK 2019 and 2020). A placement was available selectively for CYP3A4-mediated R-thalidomide 5-oxidation on Template, but not for the 5’-oxidation and the S-isomer oxidations. Similar placements were generated for pomalidomide (4-amino-thalidomide), but not for a poor ligand, lenalidomide (3-deoxy-pomalidomide). The latter ligand took placements lacking IJK-Interaction or sticking the 4-amino part beyond the facial-side wall on Template. A placement was available for the tert-butyl oxidation of terfenadine, but not for an analog, ebastine. Their interactions with upper-Cavity-2 residue were expected to differ at their sites of oxygen substituents. Some phenolic antioxidants behave distinctly toward biological oxidations in vitro and in vivo. Butylated hydroxytoluene is oxidized to the peroxy-derivative in vitro, but solely to the oxidized metabolites at the benzyl and tert-butyl methyl positions in vivo. Involvement of CYP3A4 were suggested for all the three reactions from the placements on Template. Tocopherols were also applied on Template for the oxidations for chroman and side-chain terminals. The primary placement was suggested to undergo the futile-recycling through formation of the peroxide intermediate subsequently to lead the substantial lack of the CYP3A4-mediated oxidation. These data suggest the effectiveness of CYP3A4-Template assessment to understand the causal basis of poor oxidations and also to verify the in vivo contribution of CYP3A4-mediated peroxidative reactions.

Development of template systems for ligand interactions of CYP3A5 and CYP3A7 and their distinctions from CYP3A4 template

Starting from established CYP3A4 Template (DMPK. 2019, and 2020), CYP3A5 and CYP3A7 Templates have been constructed to be reliable tools for verification of their distinct catalytic properties. A distinct occupancy was observed on CYP3A4-selective ligands, but not on the non-selective ligands, in simulation experiments. These ligands often invade into Bay-1 region during the migration from Entrance to Site of oxidation in simulation experiments. These results offered an idea of the distinct localization of Bay-1 residue on CYP3A5 Template, in which the Bay-1 residue stayed closely to Template border. The idea also accounted for the higher oxidation rates of CYP3A5, than of CYP3A4, of noscapine and schisantherin E through their enhanced sitting-stabilization. Typical CYP3A7 substrates such as zonisamide and retinoic acids took their placements without occupying a left side region of Template for their metabolisms. In turn, the occupancies of the left-side region were inevitably observed among poor ligands of CYP3A7. Altered extent of IJK-Interaction or localization of a specific residue at the left-side would thus explain distinct catalytic properties of CYP3A7 on Template. These data suggest the alteration of each one of Template region, from CYP3A4 Template, led to the distinct catalytic properties of CYP3A5 and CYP3A7 forms.

Applications of a grid-based CYP3A4 Template system to understand the interacting mechanisms of large-size ligands; part 4 of CYP3A4 Template study

Catalytic interactions of CYP3A4 with large-size ligands have been studied on the Template established in our previous studies using polyaromatic hydrocarbon and steroid ligands (DMPK 34: 113-125 and 351-364 2019 and in press 2020). Typical CYP3A4-substrates including erythromycin, cyclosporin A (ca.1200 Da), ivermectin B1a and taxanes were applied successfully and regioselective metabolisms of these ligands were reconstituted faithfully on Template. These results suggest the applicability of CYP3A4 Template throughout broadened sizes of CYP3A4 ligands. Macrolide antibiotics showed distinct degrees of tight sittings in Width-gauge, a tool for accommodation measure. The observed differences were associated with different inhibitory/inactivation potentials of troleandomycin, erythromycin, clarithromycin and azithromycin, suggesting CYP3A4 Template also as a tool for drug-interaction mechanisms. Slight expansion of Template area was made at near Site of oxidation from simulation results of antitumor agent, rilpivirine, in the present study. Ligand entry from left side of Template is also suggested from macrolide interactions. Broadened applicability of the refined CYP3A4 Template were assured with experiments with various large-size ligands.

Prediction and Characterization of CYP3A4-mediated Metabolisms of Azole Fungicides: an Application of the Fused-grid Template* system

Human CYP3A4 is involved in metabolisms of diverse hydrophobic chemicals. Using the data of therapeutic azole fungicides known to interact with CYP3A4, applicability of CYP3A4 Template system was first confirmed to reconstitute faithfully the interaction on Template. More than twenty numbers of pesticide azoles were then applied to the Template system. All the azole stereo-isomers applied, except for talarozole, interacted through nitrogen atoms of triazole or imidazole parts and sat stably for inhibitions through fulfilling three-essential interactions. For their CYP3A4-mediated oxidations, clear distinctions were suggested among the enantiomers and diastereomers of azole pesticides on Templates. Thus, the stereoisomers would have their-own regio- and stereo-selective profiles of the metabolisms. A combined metabolic profile of each azole obtained with CYP3A4 Template system, however, resembled with the reported profile of the in vivo metabolism in rats. These results suggest the major roles of CYP3A forms on the metabolisms of most of azole pesticides in both rats and humans. Free triazole is a metabolite of azole fungicides having a methylene-spacer between triazole and the rest of the main structures in experimental animals and humans. During the simulation experiments, a placement for the oxidation of a methylene spacer between the triazole and main carbon-skeleton was found to be available throughout the azole fungicides tested on Template. The occurrence of this reaction to lead to triazole-release is thus discussed in relation to the possible involvement of CYP3A forms.

Solving the interactions of steroidal ligands with CYP3A4 using a grid-base template system

Using over fifty steroidal ligands, CYP3A4 Template system established in our previous study (DMPK 34: 113-125, 2019) has been evaluated for the applicability for prediction of regioselective metabolisms of steroids in the present study. Plural regional interactions near Site of Oxidation of CYP3A4 (Slide-down and Adaptation) are newly defined for steroid ligands in addition to previously characterized Trigger- and IJL-interactions on Template. Interaction of steroids at ring-A with CYP3A4 residue (Front-residue), at the facial side of Ring B of Template, determined the availability of ligand sitting at Rings A and B of Template. Steroids having 3-one-4-ene structures, which are not stacked on Front-residue, thus slide down for their 6-oxidations. Some steroids with 3β-ol structures undergo the further right-side movement (Adaptation) for their 7-oxidations. Similar overpassing phenomena are also expected for steroid 15/16-oxidations and 2/1-oxidations. Allowable width on ligand accommodation was also defined as Width-gauge of Template. Reciprocal comparison of sittings of steroids on Template with experimental data offered idea of CYP3A4-mediated oxidations of steroids through seven distinct types of placements on Template and of the relationship with their usage abundance. The present system would offer practical way for structural identification and verification of CYP3A4-mediated metabolisms of various types of steroids.

Construction of a CYP2E1-template system for prediction of the metabolism on both site and preference order

We have constructed an in silico system for the prediction of CYP2E1-mediated reaction using a two-dimensional template derived from substrate structures. Although CYP2E1 prefers small-size molecules for the substrates, the enzyme mediates oxidations of large-size molecules, such as benzo[a]pyrene. Overlays of these substrates, to assemble their sites of oxidation into a specific area, suggested a range of regions frequently occupied. The region, having a benzo[a]pyrene-like shape, was thus used as a CYP2E1 template. In this system, atoms in substrates, except for hydrogen atoms, were placed on corners of honeycomb structures of the template after having expanded the structures. Using published data for the metabolism on more than 80 substrates of CYP2E1, the core template was further refined to verify the adjacent area and to define the relative contribution of template positions for the catalysis. The positions on the template were classified into four different point (0-3) groups, depending on relative usage. In addition, we set independent points (-5 to 3) for specific positions to incorporate three-dimensional or functional information. Total scores from both position-occupancy and -function points were calculated for all the orientations of possible conformers of test substrates, and the scores were found to predict the relative abundance (i.e., order) as well as the regioselectivity of human CYP2E1 reactions with high fidelities.