Cytochrome_P450_2D6_CYP2D6_

Structure of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex (5TFT) from Homo sapiens

Created by: Samuel Wachamo

Structure of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex (PDB ID: 5TFT) from Homo sapiens is an inhibitor complex that inhibits a cleaving enzyme, BACE1.  BACE1 plays a significant role in the progression to Alzheimer’s disease (AD). Alzheimer’s disease is a neurological disorder that imparts a slow progression of cognitive decline, dementia, and ultimately death. Research on AD has yet to yield a successful treatment. Disease progression is marked by the deposition of amyloid β (Aβ) derived plaques in the hippocampal and cortical regions of the brain. The amyloid hypothesis proposes that increased Aβ production or decreased Aβ clearance is responsible for the molecular cascade that eventually leads to neurodegeneration and AD. Aβ production is initiated by the proteolytic cleavage of amyloid precursor protein (APP) by β-site APP cleaving enzyme (BACE1) within the endosome to afford a soluble N-terminal ectodomain of APP (sAPPβ) and the C-terminal fragment C99. The membrane-bound C99 is then cleaved by γ-secretase to release Aβ, including Aβx-40 and Aβx-42 isoforms. Accordingly, structure of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex plays a crucial role in the treatment of Alzheimer’s disease (1, 2).  

 The macromolecular entity of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex is cytochrome P450 2D6 (2). Cytochrome P450 2D6 from Homo sapiens is a heme-containing enzyme that is responsible for the metabolism of 25% of the known drugs. 2D6 generally only recognizes substrates containing a basic nitrogen and a planar aromatic ring. These features are found especially in a larger number of central nervous system and cardiovascular drugs that act on the G protein-coupled receptor superfamily of proteins. For this reason, 2D6 is the most widely studied isoform. The prominence of P450 2D6 in the metabolism of cationic drugs is thought to reflect the interactions of cationic substrates with active site amino acid side chains of Glu-216 and Asp-301, which are likely to orient substrates for metabolism (3).  

The activity of cytochrome P450 2D6 is dependent on its structure. Cytochrome P450 2D6 contains four subunits: A, B, C and D. The interactions of these subunits contribute to the function of cytochrome P450 2D6. Some of the roles of the subunits include binding site for residue P6U A 604, binding site for residue HEM B 601, binding site for residue Zn C 602, and binding site for residue P6U D 603 respectively. Each subunit also contains a different composition of secondary structures. For instance, chain A contains 49% helical (20 helices; 239 residues) and 9% beta sheet (18 strands; 46 residues) structure. Cytochrome P450 2D6 is responsible for the metabolism and elimination of approximately 25% of clinically used drugs, through addition or removal of certain functional groups, specifically, hydroxylation, demethylation, and dealkylation. The heme is anchored in the binding site by hydrogen bonds with side chains of Arg-101, Trp-128, His-376, Arg-132, Ser-437, and Arg-44. The 2D6 structure has a well-defined active site cavity above the heme group, containing many important residues that have been implicated in substrate recognition and binding, including Asp-301, Glu-216, Phe-483, and Phe-120. The crystal structure helps to explain how Asp-301, Glu-216, and Phe-483 can act as substrate binding residues and suggests that the role of Phe-120 is to control the orientation of the aromatic ring found in most substrates with respect to the heme.  Some of the functionally important residues in Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex can be classified based on their roles. Phe-120, Glu-244, and Phe-247 have rotational roles. Glu-216, Arg-101, Trp-128, and Ser-437 have anchoring roles. Other roles of residues include, formation of gate, and formation of hydrophobic cleft (2,3,5). 

Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex has three associated ligands. The first one is a heme or protoprophyrin IX containing FE. Hemes are prosthetic groups in some important proteins. The second one is (4S)-4-[2,4-difluoro-5-({[1-(trifluoromethyl)cyclopropyl]amino}methyl)phenyl]-4-methyl-5,6-dihydro-4H-1,3-thiazin-2-amine (P6U). This ligand plays an active role in the inhibition of BACE1. The third one is zinc ion (Zn). Zinc is involved in complex formation.  Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex has an isoelectric point of 7.58, and a molecular weight of 214588.97 Da. Both the pI and the molecular weight of Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex suit its function (2, 6). Since Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex is responsible for the metabolism of at least 25% of the known drugs, it has many structure-drug complexes including human cytochrome P450 2D6 BACE1 inhibitor 5 complex (PDB ID: 4XRY) (2).

According to PSI-BLAST, a program used to find proteins with similar primary structure with protein query, and Dali server, a method for finding proteins with tertiary structure similarity to a query, cytochrome P450 2B4 F429H in complex with 4-CPI (PDB ID: 4MGJ) resembles cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex (7, 8). The PSI-BLAST program assigns E value while the Dali server assigns Z score. As the total sequence homology increases, the E value decreases, and gaps between the query proteins increase the E value. A protein with an E value below 0.05 is considered significantly similar to the query. A Z-score above 2 indicates the proteins have significantly similar tertiary structures. Cytochrome P450 2B4 F429H in complex with 4-CPI is from Oryctolagus cuniculus (European rabbit). These two proteins have a Z score and E value of 47.1 and 4 x 10-168 respectively. These values imply that the two proteins have similar primary and tertiary structures. Unlike Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex, Cytochrome P450 2B4 F429H in complex with 4-CPI only has two ligands one of which is protoprophyrin IX containing FE (heme) like in cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex, and the other one is 4-(4 chlorophenyl) imidazole (CPZ). Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex has a secondary structure composition of 49% helices and 9% bet sheets in chain A while cytochrome P450 2B4 F429H in complex with 4-CPI has only one chain which contains 50% helices and 9% beta sheets (1, 6, 7).  

 Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex has many alternate conformations. The alternate conformation includes cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex (PDB ID: 5TFU), human cytochrome P450 2D6 BACE1 inhibitor 6 complex (4XRZ), and human cytochrome P450 2D6 BACE1 inhibitor 5 complex (4XRY). These alternate conformations as well as cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex act as an alternative aminomethyl linker that delivers similar potency and improved brain penetration relative to amide moiety.

Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex is biologically significant because this protein is involved in indirectly inhibiting deposition of amyloid β (Aβ) derived plaques in the hippocampal and cortical regions of the brain by inhibiting BACE1. Increased Aβ production is responsible for the molecular cascade that eventually leads to neurodegeneration and AD. As a result, Cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex plays a crucial role in stopping the cascade of AD causing reaction earlier in the process (1). To accomplish the inhibition of BACE1, the non-covalent interactions including hydrogen bonding, ionic interaction, hydrophobic interaction, and van deer Waals interactions that are seen with the heme and other groups determine the specificity of interactions and affinity of ligands. As more information is uncovered about cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex, treatments for deadly diseases such as Alzheimer’s disease are improving.