Crystal of a cytochrome-ligand complex and methods of use
The teachings relates to the three-dimensional structure of a crystal of a cytochrome protein complexed with a ligand. The three-dimensional structure of four cytochrome P450 2A6-ligand complexes are disclosed. Cytochrome P450 2A6-ligand crystal structures, wherein the ligand is an inhibitor molecule, are useful for providing structural information that may be integrated into drug screening and drug design processes. Thus, the teachings also relate to methods for utilizing a crystal structure of a cytochrome P450 2A6-ligand complex for identifying, designing, selecting, or testing inhibitors of the cytochrome protein. Such inhibitors are useful as therapeutics for the treatment or modulation of i) diseases; ii) disease symptoms; or iii) the effect of other physiological events mediated by the cytochrome.
1. A crystalline complex comprising human cytochrome P450 2A6 in complex with a ligand: wherein the ligand is selected from the group consisting of 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, and 4,4′-dipyridyldisulfide; wherein the human cytochrome P450 2A6 comprises a protein having the amino acid sequence set forth in SEQ ID NO: 2; and wherein the crystalline complex has space group P2 1 , unit cell dimensions a=70.61±1.8 Å, b=157.59±1.8 Å, c=103.54±1.8 Å, β=92.25±0.50°.
2. A method of identifying a compound which interferes with an activity of human cytochrome P450 2A6, the method comprising:
performing structure based drug design to identify a candidate inhibitor using a three-dimensional structure of human cytochrome P450 2A6 in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide which is defined by the atomic coordinates of Table 1, 2, 4 or 5, respectively, determined from an X-ray diffraction quality co-crystal of human cytochrome P450 2A6 protein in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide, wherein said protein comprises the amino acid sequence as set forth in SEQ ID NO: 2, and wherein said co-crystal has space group P2 1 , unit cell dimensions a=70.61±1.8 Å, b=157.59±1.8 Å, c=103.54±1.8 Å, β=92.25±0.50°; and
contacting the candidate inhibitor with the human cytochrome P450 2A6, wherein the inhibition of monooxygenase activity of the human cytochrome P450 2A6 by the candidate inhibitor identifies the candidate inhibitor as a compound which interferes with an activity of human cytochrome P450 2A6.
3. A method of screening for inhibiting activation of a procarcinogen in vitro, the method comprising:
designing a candidate inhibitor of human cytochrome P450 2A6 by performing structure based drug design to identify a candidate inhibitor using a three-dimensional structure of human cytochrome P450 2A6 in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide which is defined by the atomic coordinates of Table 1, 2, 4 or 5, respectively, determined from an X-ray diffraction quality co-crystal of human cytochrome P450 2A6 protein in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide, wherein said protein comprises the amino acid sequence as set forth in SEQ ID NO: 2, and wherein said co-crystal has space group P2 1 , unit cell dimensions a=70.61±1.8 Å, b=157.59±1.8 Å, c=103.54±1.8 Å, β=92.25±0.50°;
contacting a sample comprising human cytochrome P450 2A6 with the candidate inhibitor; and
selecting the candidates that inhibit activation of a procarcinogen in vitro.
4. The method of claim 3 , wherein the procarcinogen is selected from the group consisting of N′-nitrosonornicotine (NNN), 4-(methylnitrosamino)-1-(3pyridyl)-1-butanone (NNK), and a combination thereof.
5. The method of claim 3 , wherein the inhibitor is an antibody directed against the cytochrome P450 2A6.
6. A method of designing a compound which interferes with an activity of human cytochrome P450 2A6, the method comprising:
providing on a digital computer a three-dimensional structure of human cytochrome P450 2A6 in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide which is defined by the atomic coordinates of Table 1, 2, 4 or 5, respectively, determined from an X-ray diffraction quality co-crystal of human cytochrome P450 2A6 protein in complex with 8-methoxypsoralen, coumarin, (5-(pyridin-3-yl)furan-2-yl)methanamine, or 4,4′-dipyridyldisulfide, wherein said protein comprises the amino acid sequence as set forth in SEQ ID NO: 2, and wherein said co-crystal has space group P2 1 , unit cell dimensions a=70.61±1.8 Å, b=157.59±1.8 Å, c=103.54±1.8 Å, β=92.25±0.50°; and
employing software comprised by the digital computer to design the compound which is predicted to bind to the human cytochrome P450 2A6.
7. The method of claim 6 , further comprising:
synthesizing the compound; and
evaluating the compound for an ability to interfere with a monooxygenase activity of the human cytochrome P450 2A6.
8. The method of claim 6 , wherein the compound is designed by computational interaction with reference to a three dimensional site of the structure of cytochrome P450 2A6 in complex with the ligand, wherein the three dimensional site comprises a plurality of cytochrome P450 2A6 amino acids, numbered with reference to the sequence of SEQ ID NO: 1, selected from the group consisting of Phe107, Phe111, Phe118, Phe209, Phe480, Va1117, Asn297, Ile 300, Gly301, Thr305, Ile366, Leu370, and combinations thereof.
9. The method of claim 6 , further comprising employing software comprised by the digital computer to design a compound which is predicted not to bind to a cytochrome P450 other than human cytochrome P450 2A6.
10. The method of claim 9 , wherein the cytochrome P450 other than human cytochrome P450 2A6 is a cytochrome P450 selected from the group consisting of cytochrome P450 2C8, cytochrome P450 2C9, cytochrome P450 3A4, and combinations thereof.