Predicting Drug Metabolism:  A Site of Metabolism Prediction Tool Applied to the Cytochrome P450 2C9

Zamora, Ismael; Afzelius, Lovisa; Cruciani, Gabriele

doi:10.1021/jm021104i

Cited by 145 publications

(150 citation statements)

References 42 publications

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“…The identification of SOM with the FLAP methodology was compared with the results from the previously known SOM prediction software MetaSite (Zamora et al, 2003). This methodology considers structural complementarity between the active site of the enzyme and the ligand as well as reactivity of the ligand.…”

Section: Methodsmentioning

confidence: 99%

“…The preferred site of metabolism for these compounds was then identified by aligning the compounds to CYP2D6 probe substrates, using the program FLAP (Baroni et al, 2007). The site of metabolism (SOM) prediction program MetaSite (Zamora et al, 2003) was also used and compared with the results from FLAP. In addition, some compounds were selected for experimental determinations of the major metabolites formed, the rate of formation of N-dealkylated product, as well as the inhibition potential in recombinant CYP2D6.…”

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confidence: 99%

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The Molecular Basis of CYP2D6-Mediated N-Dealkylation: Balance between Metabolic Clearance Routes and Enzyme Inhibition

Bonn¹,

Masimirembwa²,

Aristei³

et al. 2008

Drug Metab Dispos

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ABSTRACT:N-Dealkylation is a commonly observed metabolic reaction for drugs containing secondary and tertiary amines. On searching the literature, it is obvious that this reaction is far less common among cytochrome P450 2D6 catalyzed reactions compared with other cytochromes P450. The CYP2D6 pharmacophore and characteristic features in the active site cavity suggest a favored substrate orientation that prevents N-dealkylation from occurring. In this study, the literature was searched for N-dealkylated and non-Ndealkylated CYP2D6 substrates. The hypothesis that was suggested and confirmed demonstrated that N-dealkylation occurs by this enzyme when the preferred site of metabolism is blocked toward other oxidative metabolic pathways. An interesting observation was also that addition of stable groups at preferred sites of metabolism generally improved the metabolic stability but also resulted in retained or increased inhibition of the enzyme. In addition, the effect of pH on N-and O-dealkylation of dextromethorphan was shown to be consistent with the hypothesis that an ionized amino function favored substrate dockings resulting in O-dealkylation.Cytochrome P450 2D6 (CYP2D6) is a polymorphic member of the cytochrome P450 superfamily important for the metabolism of a variety of xenobiotics (Guengerich, 2003). In drug discovery research it is of great interest to identify whether a compound is a substrate or not, and considerable effort has been put into the development of models to identify substrates and/or inhibitors of CYP2D6. Several pharmacophore models have been published identifying common features in CYP2D6 substrates and inhibitors (Koymans et al., 1992;de Groot et al., 1997de Groot et al., , 1999Lewis et al., 1997). The pharmacophore comprises basic nitrogen atom 5-7 or 10 Å from the site of oxidation, a flat hydrophobic region near the site of oxidation and a negative molecular electrostatic potential coplanar with this hydrophobic region (see examples in Fig. 1). The intramolecular distances of 5 and 7 Å were combined by Koymans et al. (1992) in a model assuming a carboxylate group as an anchor point in the protein with one of the oxygen atoms interacting with the "5-Å substrates" and the other with the "7-Å substrates." Since several substrates with approximately 10 Å between the nitrogen atom and the site of oxidation were also known, refined models were constructed including this intramolecular distance (Lewis et al., 1997). Even though the early pharmacophore models are rather crude, they have been successful in predicting the influence of CYP2D6 in the metabolism of xenobiotics as well as predicting possible sites of metabolism [e.g., 75% predictability (de Groot et al., 1999)].Structural information of CYP2D6 from homology models (de Groot et al., 1996;De Rienzo et al., 2000) and a crystal structure of ligand-free CYP2D6 (Rowland et al., 2006) revealed two acidic amino acids, Glu216 and Asp301, and two phenylalanine residues, Phe120 and Phe483, in the active site cavity. This was compatible with t...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

The Molecular Basis of CYP2D6-Mediated N-Dealkylation: Balance between Metabolic Clearance Routes and Enzyme Inhibition

Bonn¹,

Masimirembwa²,

Aristei³

et al. 2008

Drug Metab Dispos

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“…In MetaSite, the active site of the protein is characterized using MIF interactions with different probes, and a set of distance-based descriptors is calculated by taking the oxygen atom in the heme as reference. The different atoms of the substrate are ranked in agreement with the similarity to the protein, and the top ranked positions are selected as the possible metabolic sites (Zamora et al, 2003;Cruciani et al, 2005). A well defined active site is also essential for this methodology.…”

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confidence: 99%

Comparison of Methods for the Prediction of the Metabolic Sites for Cyp3a4-Mediated Metabolic Reactions

Zhou

Afzelius²,

Grimm³

et al. 2006

Drug Metab Dispos

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ABSTRACT:Predictions of the metabolic sites for new chemical entities, synthesized or only virtual, are important in the early phase of drug discovery to guide chemistry efforts in the synthesis of new compounds with reduced metabolic liability. This information can now be obtained from in silico predictions, and therefore, a thorough and unbiased evaluation of the computational techniques available is needed. Several computational methods to predict the metabolic hot spots are emerging. In this study, metabolite identification using MetaSite and a docking methodology, GLUE, were compared. Moreover, the published CYP3A4 crystal structure and computed CYP3A4 homology models were compared for their usefulness in predicting metabolic sites. A total of 227 known CYP3A4 substrates reported to have one or more metabolites adding up to 325 metabolic pathways were analyzed. Distancebased fingerprints and four-point pharmacophore derived from GRID molecular interaction fields were used to characterize the substrate and protein in MetaSite and the docking methodology, respectively. The CYP3A4 crystal structure and homology model with the reactivity factor enabled achieved a similar prediction success (78%) using the MetaSite method. The docking method had a relatively lower prediction success (ϳ57% for the homology model), although it still may provide useful insights for interactions between ligand and protein, especially for uncommon reactions. The MetaSite methodology is automated, rapid, and has relatively accurate predictions compared with the docking methodology used in this study.The cytochromes P450 (P450s) belong to a superfamily of hemecontaining enzymes that metabolize a wide range of therapeutic agents. CYP3A4 is the most abundant human hepatic P450 isoform and is responsible for the metabolism of about 50% of known drugs with wide structural diversity (Guengerich, 1999). From a drug development perspective, a new drug candidate that is susceptible to CYP3A4 metabolism may not be able to reach the target at an effective concentration or may be involved in drug-drug interactions when coadministered with other CYP3A4 substrates or inhibitors. In silico prediction of the primary metabolic site from the molecular structure may assist in the identification of the metabolite formed through the metabolic reaction, or could be used to guide the synthesis of metabolically stable compounds or direct the metabolism to certain P450 enzymes. Experimental studies at early drug discovery stage on metabolic reactions of new chemical entities can usually allocate the metabolic site(s) to a certain fragment of the molecule. To guide chemists to synthesize new compounds with improved metabolic properties, information on the exact metabolic site is preferred. This information may be obtained from in silico predictions, and therefore, we need a thorough and unbiased evaluation of the computational techniques available.Mainly four approaches are considered in the literature to address the prediction of the metabolic sites.1. Molecu...

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“…139,140 The model is an automated docking system with reactivity correction (i.e., reactivity of the different atomic parts toward the heme are used to determine the preferred sites of attack). The software predicts the preferred sites of attack of the query compound by the enzyme, and provides the user sets of modifications of the query compound to reduce the CYP mediated metabolism.…”

Section: In Silico Modelsmentioning

confidence: 99%

Review of the Availability ofIn VitroandIn SilicoMethods for Assessing Dermal Bioavailability

DumontCoralie

PrietoPilar

AsturiolDavid

et al. 2015

Applied In Vitro Toxicology

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The exposure of the skin to consumer products, drugs, and environmental chemicals can result in their penetrating the skin barrier and entering systemic circulation, potentially resulting in adverse effects in the skin and other organs. The assessment of dermal penetration and bioavailability (including penetration, metabolism, and entry into the systemic circulation) is therefore an important consideration in the risk assessment of chemicals. The skin is a heterogeneous organ with a multilayer structure. Based on its architecture and physiology, substances can penetrate through three major ways but can also be blocked in the different skin layers and in the skin appendages, which act as reservoir. In addition to that, as the skin is a metabolically competent organ, substances can undergo metabolism. After a brief description of the skin architecture, this review will focus on the skin penetration mechanisms and skin metabolic capacities. The skin absorption has traditionally been tested in vivo on animals. However, with the new legislation (i.e., Registration, Evaluation, Authorisation, and Restriction of Chemicals Regulation or Cosmetics Regulation), alternatives to animal testing have to be implemented. In a second part, this review will provide a description of the main in vitro and in silico or computational models available to study skin absorption and skin metabolism (i.e., ex vivo skin models, artificial membrane barriers, primary cells and cell lines, Quantitative Structure-Activity Relationship [QSAR], simulators for the prediction of skin metabolism).

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Predicting Drug Metabolism: A Site of Metabolism Prediction Tool Applied to the Cytochrome P450 2C9

Cited by 145 publications

References 42 publications

The Molecular Basis of CYP2D6-Mediated N-Dealkylation: Balance between Metabolic Clearance Routes and Enzyme Inhibition

The Molecular Basis of CYP2D6-Mediated N-Dealkylation: Balance between Metabolic Clearance Routes and Enzyme Inhibition

Comparison of Methods for the Prediction of the Metabolic Sites for Cyp3a4-Mediated Metabolic Reactions

Review of the Availability ofIn VitroandIn SilicoMethods for Assessing Dermal Bioavailability

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