Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450
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1 Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450 Julianna Oláh, 1 Adrian J. Mulholland* and Jeremy N. Harvey* School of Chemistry and Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS UK. Adrian.mulholland@bris.ac.uk, Jeremy.harvey@bris.ac.uk SUPPORTING INFORMATION I. Dextromethorphan topology file and most important parameters II. III. IV. Cartesian coordinates of the located stationary points in the QM only calculations Cartesian coordinates of the atoms in the QM region in the QM/MM transition states and starting structures Fig. S1. Dextromethorphan docked into the active site of P450 2D6. The two stereoisomers of the protonated Dextromethorphan can interact either with Glu216 or with Asp301. Fig.S2. Distances measured in the MD simulations of P450 2D6 with dextromethorphan docked into the active site. The OH distances were measured between the ferryl-oxygen atom and the alpha-hydrogen atoms (the three colors in the diagrams correspond to the three alphahydrogen atoms ) A: The protonated amino-group of dextromethorphan interacts with Glu216. B: protonated amino-group of dextromethorphan interacts with Asp301. Fig.S3. Distances measured in the MD simulations of P450 2D6 with dextromethorphan docked into the active site. The OC distances were measured between the ferryl-oxygen atom and the ortho carbon atoms. red: simulation in which hydrogen bond exists between Glu216 and dextromethorphan blue: simulation in which hydrogen bond exists between Asp301 and dextromethorphan Fig.S4. QM/MM adiabatic energy scan profiles for A. hydrogen-abstraction B. aromatic carbon oxidation. V. Table S1. Selected geometrical parameters of QM only transition states (at the B3LYP/LACVP** level) and QM/MM optimized starting structures and transition states. 1 Present address: Materials Structure and Modeling Research Group of the Hungarian Academy of Sciences, Budapest University of Technology and Economics,P.O. Box 91, 1521 Budapest, Hungary
2 I. Dextromethorphan topology file and most important parameters Non standard atom types: MASS 210 OCE O aromatic ether oxygen MASS 211 NT N tertiary protonated amine nitrogen MASS 212 CT C aliphatic sp3 C bonded to 4 carbon atoms, RESI DEX protonated dextromethorphan GROUP ATOM C1 CT ATOM C2 CT ATOM C3 CT ATOM C4 CT ATOM C5 CT ATOM C6 CT ATOM C7 CT ATOM C8 CT ATOM C9 CA ATOM C10 CA ATOM C11 CA ATOM C12 CA ATOM C13 CA ATOM C14 CA ATOM N15 NT ATOM C16 CT ATOM C17 CT ATOM O18 OCE ATOM C19 CT Ca from the paper ATOM C20 CT ATOM H21 HA ATOM H22 HA ATOM H23 HA ATOM H24 HP ATOM H25 HA ATOM H26 HA ATOM H27 HA ATOM H28 HA ATOM H29 HA ATOM H30 HA ATOM H31 HA ATOM H32 HA ATOM H33 HA ATOM H34 HA ATOM H35 HA ATOM H36 HP ATOM H37 HP ATOM H38 HA 0.090
3 ATOM H39 HA ATOM H40 HA ATOM H41 HA ATOM H42 HA ATOM H43 HA ATOM H44 HA ATOM H45 HA ATOM H46 HC BOND C1 C2 C1 C6 C1 H44 C1 H45 BOND C2 C3 C2 C10 C2 C17 C3 C4 BOND C3 C7 C3 H25 C4 C5 C4 H38 BOND C4 H39 C5 C6 C5 H40 C5 H41 BOND C6 H42 C6 H43 C7 C8 C7 N15 BOND C7 H26 C8 C9 C8 H34 C8 H35 BOND C9 C10 C9 C11 C10 C14 C11 C12 BOND C11 H36 C12 C13 C12 H37 C13 C14 BOND C13 O18 C14 H24 N15 C16 N15 C20 BOND N15 H46 C16 C17 C16 H30 C16 H31 BOND C17 H32 C17 H33 O18 C19 C19 H21 BOND C19 H22 C19 H23 C20 H27 C20 H28 BOND C20 H29 IMPR C9 C10 C11 C8 IMPR C10 C9 C14 C2 IMPR C14 C10 C13 H24 IMPR C13 O18 C12 C14 IMPR C12 C13 C11 H37 IMPR C11 C12 C9 H36 PATCHING FIRS NONE LAST NONE BONDS V(bond) = Kb(b - b0)**2 Kb: kcal/mole/a**2 b0: A atom type Kb b0 CT1 NT CA OCE NT CT NT CT NT HC CT3 OCE CT0 CT CT0 CT CT0 CA ANGLES V(angle) = Ktheta(Theta - Theta0)**2
4 V(Urey-Bradley) = Kub(S - S0)**2 Ktheta: kcal/mole/rad**2 Theta0: degrees Kub: kcal/mole/a**2 (Urey-Bradley) S0: A atom types Ktheta Theta0 Kub S0 NT CT1 CT ALLOW ALI POL NT CT1 CT ALLOW ALI POL NT CT2 CT ALLOW ALI POL CA CA OCE from OH1 CA CA CT1 NT CT force const. from CT2 NH1 C CT1 NT CT force const. from CT2 NH1 C CT2 NT CT force const. from CT2 NH1 C NT CT3 HA ALLOW ALI POL NT CT2 HA ALLOW ALI POL NT CT1 HA ALLOW ALI POL HC NT CT ALLOW POL ALI HC NT CT ALLOW POL ALI HC NT CT ALLOW POL ALI CA OCE CT from ether article cit. see above, but equilibrium value from QM OCE CT3 HA from ether article cit. see above CT2 CT2 CT ALLOW ALI CT2 CT1 CT ALLOW ALI CT1 CT1 CT ALLOW ALI HA CT2 CT ALLOW ALI CT2 CT0 CT ALLOW ALI CT2 CT0 CT ALLOW ALI CT2 CT0 CA ALLOW ALI CT1 CT0 CA ALLOW ALI CT0 CA CA ALLOW ALI ARO CT0 CT1 HA ALLOW ALI NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 adm jr., 5/08/91, suggested cutoff scheme V(Lennard-Jones) = Eps(i,j)*[(Rmin(i,j)/r(i,j))**12-2(Rmin(i,j)/r(i,j))**6] epsilon [kcal/mole]: Eps(i,j) = sqrt(eps(i) * eps(j)) Rmin/2 [A]: Rmin(i,j) = Rmin/2(i) + Rmin/2(j) atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 NT OCE CT from CT, from CT1x: needs work END
5 II. Cartesian coordinates of the located stationary points in the QM only calculations anisole B3LYP/lacvp** Total energy C C C C C C O C H H H H H H H H Compound I (doublet) B3LYP/lacvp** Total energy N C C C H C H N C C C H C H N C C C H C H N C C C H C H C C C C H H H H Fe O S H Compound I (quartet) B3LYP/lacvp** Total energy N C C C H C H N C C C H C H N C C C H C H N C C C H C H C C C C H H H H Fe O S H H-abstraction TS state (quartet) B3LYP/lacvp** Total energy H S
6 O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H-abstraction TS state (doublet) B3LYP/lacvp** Total energy H S O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H Aromatic carbon oxidation TS state (quartet) B3LYP/lacvp** Total energy H S O Fe
7 N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H Aromatic carbon oxidation TS state (doublet) B3LYP/lacvp** Total energy H S O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H Dextromethorphan stereoisomer A B3LYP/6-31G* Total energy C C C C C C
8 C C C C C C C C N C C O C C H H H H H H H H H H H H H H H H H H H H H H H H H H O C C H H H H H H H H H H H H H H H H H H H H H H H H H H Dextromethorphan stereoisomer B B3LYP/6-31G* Total energy C C C C C C C C C C C C C C N C C
9 III. Cartesian coordinates of the atoms in the QM region in the QM/MM transition states and starting structures Snapshot 1 TS zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 1 minimum zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H
10 H H H H H H Snapshot 2 TS zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 2 minimum zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H
11 H H H H H H H H Snapshot 3 TS zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 3 minimum zmat Aromatic carbon oxidation C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H
12 H H H H H H H H H H Snapshot 1 TS zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 1 minimum zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H
13 H H H H H H H H H H H H Snapshot 2 TS zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 2 minimum zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H
14 H H H H H H H H H H H H H H Snapshot 3 TS zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 3 minimum zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H
15 H H H H H H H H H H H H H H H H Snapshot 1 TS (doublet state) zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O C H H H H H H H H H H H H H H H H H Snapshot 1 minimum (doublet state) zmat Hydrogen abstraction C S H H O Fe N N N N C C C C C C C C C C C C C C C C C H C H C H C H C C C C C C O
16 C H H H H H H H H H H H H H H H H H
17 IV. Figures Fig. S1. Dextromethorphan docked into the active site of P450 2D6. The two stereoisomers of the protonated Dextromethorphan can interact either with Glu216 or with Asp301.
18 OH distance (A) OH distance (A) A 7 6,5 6 5,5 5 4,5 4 3,5 3 2, time (ps) B 7,5 7 6,5 6 5,5 5 4,5 4 3,5 3 2, time (ps) Fig.S2. Distances measured in the MD simulations of P450 2D6 with dextromethorphan docked into the active site. The OH distances were measured between the ferryl-oxygen atom and the alpha-hydrogen atoms (the three colors in the diagrams correspond to the three alphahydrogen atoms ) A: The protonated amino-group of dextromethorphan interacts with Glu216. B: protonated amino-group of dextromethorphan interacts with Asp301.
19 OC distance (A) 5 4,8 4,6 4,4 4,2 4 3,8 3,6 3,4 3,2 3 2,8 2, time (ps) Glu216 Asp301 Fig.S3. Distances measured in the MD simulations of P450 2D6 with dextromethorphan docked into the active site. The OC distances were measured between the ferryl-oxygen atom and the ortho carbon atoms. red: simulation in which hydrogen bond exists between Glu216 and dextromethorphan blue: simulation in which hydrogen bond exists between Asp301 and dextromethorphan
20 DE(kcal/mol) DE (kcal/mol) A Hydrogen abstraction 30,0 25,0 20,0 15,0 10,0 Snapshot 1 Snapshot 2 Snapshot 3 Snapshot 1 (doublet) 5,0 0,0 1 1,2 1,4 1,6 1,8 2 2,2 2,4 H-O distance (A) B 40,0 Aromatic carbon oxidation 35,0 30,0 25,0 20,0 Snapshot 3 Snapshot 1 Snapshot 2 15,0 10,0 5,0 0,0 1,5 1,7 1,9 2,1 2,3 2,5 2,7 2,9 3,1 C-O distance (A) Fig.S4. QM/MM adiabatic energy scan profiles for A. hydrogen-abstraction B. aromatic carbon oxidation.
21 V. Table S1. Selected geometrical parameters of QM only transition states (at the B3LYP/LACVP** level) and QM/MM optimized starting structures and transition states. C 2 -O (oxyl) CH OH TS (doublet) QM TS Aromatic carbon oxidation Hydrogen abstraction (quartet) Snapshot 1 TS minimum Snapshot 2 TS minimum Snapshot 3 TS minimum QM TS (doublet) TS (quartet) Snapshot 1 TS minimum Snapshot 2 TS minimum Snapshot 3 TS minimum Snapshot 1 TS doublet + minimum this profile was started from the same geometry as Snapshot 1, and the profile was followed in the doublet state. (It is not the reoptimization of the structures obtained in the quartet energy profile).
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