TY - JOUR
T1 - Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism
T2 - A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants
AU - Leth, Rasmus
AU - Ercig, Bogac
AU - Olsen, Lars
AU - Jørgensen, Flemming Steen
PY - 2019/2/25
Y1 - 2019/2/25
N2 - Cytochrome P450 102A1 from Bacillus megaterium (BM3) is a fatty acid hydroxylase that has one of the highest turnover rates of any mono-oxygenase. Recent studies have shown how mutants of BM3 can produce metabolites of known drug compounds similar to those observed in humans. Single-point mutations in the binding pocket change the regioselective metabolism of fenamic acids from aromatic hydroxylation to aliphatic hydroxylation. This study is concerned with the individual contribution from accessibility and reactivity for drug metabolism with a future goal to develop fast methods for prediction. For a BM3 M11 mutant as well as the M11 V87F and M11 V87I mutants, we studied the metabolism of the nonsteroidal anti-inflammatory drugs (NSAIDs) mefenamic acid, meclofenamic acid, tolfenamic acid, and diclofenac. Density functional theory (DFT; B3LYP and B3LYP-D3) calculations for all possible reactions were performed using a porphyrin model reacting with the four substrates. Molecular dynamics (MD) simulations were used to determine the potential sites of metabolism that are accessible. Finally, we combine reactivity and accessibility for each potential site to interpret the experimentally determined metabolism. Generally, the 3 and 5 positions (on the ring containing the acidic substituent) and the 2, 3, and 4 positions are most reactive, whereas 4, 5, 3, and 4 are most accessible. Combining reactivity and accessibility show that the 5, 3, and 4 positions are predicted to be most prone to be metabolized, in agreement with experimentally observed data. Reactivity seems to be the dominant factor in the CYP-mediated metabolism of these NSAIDs, which is consistent with previously published methods based solely on reactivity.
AB - Cytochrome P450 102A1 from Bacillus megaterium (BM3) is a fatty acid hydroxylase that has one of the highest turnover rates of any mono-oxygenase. Recent studies have shown how mutants of BM3 can produce metabolites of known drug compounds similar to those observed in humans. Single-point mutations in the binding pocket change the regioselective metabolism of fenamic acids from aromatic hydroxylation to aliphatic hydroxylation. This study is concerned with the individual contribution from accessibility and reactivity for drug metabolism with a future goal to develop fast methods for prediction. For a BM3 M11 mutant as well as the M11 V87F and M11 V87I mutants, we studied the metabolism of the nonsteroidal anti-inflammatory drugs (NSAIDs) mefenamic acid, meclofenamic acid, tolfenamic acid, and diclofenac. Density functional theory (DFT; B3LYP and B3LYP-D3) calculations for all possible reactions were performed using a porphyrin model reacting with the four substrates. Molecular dynamics (MD) simulations were used to determine the potential sites of metabolism that are accessible. Finally, we combine reactivity and accessibility for each potential site to interpret the experimentally determined metabolism. Generally, the 3 and 5 positions (on the ring containing the acidic substituent) and the 2, 3, and 4 positions are most reactive, whereas 4, 5, 3, and 4 are most accessible. Combining reactivity and accessibility show that the 5, 3, and 4 positions are predicted to be most prone to be metabolized, in agreement with experimentally observed data. Reactivity seems to be the dominant factor in the CYP-mediated metabolism of these NSAIDs, which is consistent with previously published methods based solely on reactivity.
UR - http://www.scopus.com/inward/record.url?scp=85062084069&partnerID=8YFLogxK
U2 - 10.1021/acs.jcim.8b00750
DO - 10.1021/acs.jcim.8b00750
M3 - Journal article
C2 - 30758202
AN - SCOPUS:85062084069
SN - 1549-9596
VL - 59
SP - 743
EP - 753
JO - Journal of Chemical Information and Modeling
JF - Journal of Chemical Information and Modeling
IS - 2
ER -