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

Abstract

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...

Global Urine Metabolomics in Patients Treated with First-Line Tuberculosis Drugs and Identification of a Novel Metabolite of Ethambutol

“…AABA could be an N-dealkylation product of EDBA. The N-dealkylation reaction catalyzed by cytochrome P450 superfamily members is one of the common metabolic steps for drugs that have secondary and tertiary amines (32). The correlation value between EDBA and AABA of 0.71 also support our hypothesis.…”

Latest Advances Towards Ras Inhibition: A Medicinal Chemistry Perspective

“…Thec omputational assessment (Figure 3) of ARS-853 revealed drug-like physicochemical properties,that is,agood balance between polarity and lipophilicity of the compound (total polar surface area (TPSA), logD,corrected molecular weight), which result in good solubility and medium membrane permeability in intestinal Caco cells. [21] 2) Thep henol moiety could undergo phase II metabolism (e.g., the formation of conjugates with glucuronic acid) or in the case of ortho-amino phenols,t he system could be oxidized to the corresponding quinone imines,w hich are known to be reactive metabolites [22] which can cause toxicity. However,A RS-853 shows low metabolic stability,p articularly in rat and human liver microsomes,a s well as asignificant efflux ratio in the Caco assay,which is an indication that it can be recognized as asubstrate by acellular transporter.T hree obvious potential metabolic hot spots can be identified:1 )the oxidative dealkylation of the various amines and amides in the molecule.…”

“…However,A RS-853 shows low metabolic stability,p articularly in rat and human liver microsomes,a s well as asignificant efflux ratio in the Caco assay,which is an indication that it can be recognized as asubstrate by acellular transporter.T hree obvious potential metabolic hot spots can be identified:1 )the oxidative dealkylation of the various amines and amides in the molecule. [21] 2) Thep henol moiety could undergo phase II metabolism (e.g., the formation of conjugates with glucuronic acid) or in the case of ortho-amino phenols,t he system could be oxidized to the corresponding quinone imines,w hich are known to be reactive metabolites [22] which can cause toxicity. [23] 3) Ther eactive electrophilic "warhead" might react unspecifically with other electrophiles.D espite the positive results obtained against 1584 other proteins (2740 surface-exposed cysteineresidues), which showed excellent selectivity for K-Ras G12C ,the reactive nature of ARS-853 would therefore necessitate additional caution with respects to off-target interactions in vivo.T his hurdle can be overcome though, [24] as exemplified recently by the successful developments of osimertinib [25a] and afatinib [25b] (EGFR inhibitors), and ibrutinib [25c,d] (a BTK inhibitor).…”

Fortschritte bei der Ras‐Inhibition aus medizinisch‐chemischer Perspektive

“…[18] Das Profil von ARS-853 nähert sich auch den strengen Kriterien des Structural Genomics Consortium (SGC) füre ine Verwendung als In-vitro-Sonde ("probe", z. Eine computergestützte Evaluierung von ARS-853 unter Verwendung einer Bayer-Software [20] [21] 2) Die Phenoleinheit kçnnte einen Phase-II-Metabolismus eingehen (z. Eine computergestützte Evaluierung von ARS-853 unter Verwendung einer Bayer-Software [20] [21] 2) Die Phenoleinheit kçnnte einen Phase-II-Metabolismus eingehen (z.…”

“…B. On-Target-Potenz in vitro < 100 nm, > 30-fache Selektivitätr elativ zur Zielproteinfamilie,O n-Target-Effekt in Zellen < 1 mm)a n. [19] Sein Profil bleibt jedoch vermutlich ungeeignet fürd ie Verwendung in vivo,u nd eine weitere Optimierung kçnnte sich als schwierig erweisen, da da der Optimierungsraum, der sich durch die Struktur-Wirkungs-Korrelation (SAR) ergibt, eng zu sein scheint. Eine computergestützte Evaluierung von ARS-853 unter Verwendung einer Bayer-Software [20] [21] 2) Die Phenoleinheit kçnnte einen Phase-II-Metabolismus eingehen (z. B. Bildung von Konjugaten mit Glucuronsäure), oder das System kçnnte,i mF all von ortho-Aminophenolen, zu den entsprechenden Chinoniminen oxidiert werden, die bekanntermaßen reaktive Metaboliten sind [22] und toxische Wirkung haben kçnnen.…”