The mechanism of human aromatase (CYP 19A1) revisited: DFT and QM/MM calculations support a compound I-mediated pathway for the aromatization process

Abstract

Human aromatase is responsible for the last step of estrogen biosynthesis, for the aromatization of ring A of androstenedione or testosterone. In this work, the mechanism of aromatization was studied using gas phase and hybrid QM/MM calculations. It is shown that human aromatase can efficiently catalyze the aromatization process via a compound I (or compound II)-mediated pathway. The nature of the oxidant is very sensitive to the polarizing environment of the enzyme, as the oxidant has a compound I nature in the gas phase calculations, which is modulated by the enzyme environment to become a mixed compound I and compound II character. The electronic structure of the obtained QM-only and QM/MM stationary points is thoroughly discussed.

This is a preview of subscription content, log in to check access.

Scheme 1
Scheme 2
Scheme 3
Scheme 4
Fig. 1
Fig. 2
Fig. 3
Scheme 5
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

References

  1. 1.

    Groves JT (2005) Models and mechanisms of cytochrome P450 action. In: Ortiz de Montellano PR (ed) Cytochrome P450, 3rd edn. Kluwer Academic/Plenum Publishers, New York, pp 1–43

    Google Scholar 

  2. 2.

    Sligar SG (2010) Glimpsing the critical intermediate in cytochrome P450 oxidations. Science 330:924–925

    CAS  Article  Google Scholar 

  3. 3.

    Rittle J, Green MT (2010) Cytochrome P450 compound I: capture, characterization, and C-H bond activation kinetics. Science 330:933–937

    CAS  Article  Google Scholar 

  4. 4.

    Brodie AMH, Njar VCO (2000) Aromatase inhibitors and their application in breast cancer treatment. Steroids 65:171–179

    CAS  Article  Google Scholar 

  5. 5.

    Baum M, Budzar AU, Cuzik J, Forbes J, Houghton JH, Klijn JG, Sahmoud T (2002) Anastrozole alone or in combination with tamoxifen versus tamoxifen alone for adjuvant treatment of postmenopausal women with early breast cancer: first results of the ATAC Randomised Trial. Lancet 359:2131–2139

    CAS  Article  Google Scholar 

  6. 6.

    Bonneterre J, Buzdar A, Nabholtz JM, Robertson JF, Thurlimann B, von Euler M, Sahmoud T, Webster A, Steinberg M (2001) Anastrozole is superior to tamoxifen as first-line therapy in hormone receptor positive advanced breast carcinoma. Cancer 92:2247–2258

    CAS  Article  Google Scholar 

  7. 7.

    Brueggemeier RW (2002) Aromatase inhibitors in breast cancer therapy. Expert Rev Anticancer Ther 2:181–191

    CAS  Article  Google Scholar 

  8. 8.

    Ryan KJ (1958) Conversion of androstenedione to estrone by placental microsomes. Biochim Biophys Acta 27:658–659

    CAS  Article  Google Scholar 

  9. 9.

    Ortiz de Montellano PR, Devoss JJ (2005) Substrate oxidation by cytochrome P450 enzymes. In: Ortiz de Montellano PR (ed) Cytochrome P450, 3rd edn. Kluwer Academic/Plenum Publishers, New York, pp 183–245

    Google Scholar 

  10. 10.

    Groves JT, McClusky GA (1976) Aliphatic hydroxylation via oxygen rebound. oxygen transfer catalyzed by iron. J Am Chem Soc 98:859–861

    CAS  Article  Google Scholar 

  11. 11.

    Osawa Y, Shibata K, Rohrer D, Weeks C, Duax WL (1975) Reassignment of the Absolute Configuration of 19-Substituted 19-Hydroxysteroids and Stereomechanism of Estrogen Biosynthesis. J Am Chem Soc 97:4400–4402

    CAS  Article  Google Scholar 

  12. 12.

    Arigoni D, Battaglia R, Akhtar M, Smith T (1975) Stereospecificity of oxidation at C-19 in oestrogen biosynthesis. J Chem Soc, Chem Commun 6:185–186

    Article  Google Scholar 

  13. 13.

    Hosoda H, Fishman J (1974) Unusually facile aromatization of 2.beta.-hydroxy-19-oxo-4-androstene-3,17-dione to estrone: implications in estrogen biosynthesis. J Am Chem Soc 96:7325–7329

    CAS  Article  Google Scholar 

  14. 14.

    Goto J, Fishman J (1977) Participation of a nonenzymatic transformation in the biosynthesis of estrogens from androgens. Science 195:80–81

    CAS  Article  Google Scholar 

  15. 15.

    Hahn EF, Fishman J (1984) Immunological probe of estrogen biosynthesis: evidence for the 2 beta-hydroxylative pathway in aromatization of androgens. J Biol Chem 259:1689–1694

    CAS  Google Scholar 

  16. 16.

    Morand P, Williamson DG, Layne DS, Lompa-Krzymien L, Salvador J (1975) Conversion of an androgen epoxide into 17β-estradiol by human placental microsomes. Biochemistry 14:635–638

    CAS  Article  Google Scholar 

  17. 17.

    Mastalerz H, Morand P (1982) Acid- and base-catalysed reactions of 4β,5β- and 4α,5α-epoxyandrostane-3,17,19-trione. J Chem Soc, Perkin Trans 1:2611–2615

    Article  Google Scholar 

  18. 18.

    Brodie HJ, Kripalani KJ, Possanza G (1969) Mechanism of estrogen biosynthesis. VI. The stereochemistry of hydrogen elimination at C-2 during aromatization. J Am Chem Soc 91:1241–1242

    Article  Google Scholar 

  19. 19.

    Fishman J, Guzik H, Dixon D (1969) Stereochemistry of estrogen biosynthesis. Biochemistry 8:4304–4309

    CAS  Article  Google Scholar 

  20. 20.

    Akhtar M, Calder MR, Corina DL, Wright JN (1982) Mechanistic studies on C-19 demethylation in oestrogen biosynthesis. Biochem J 201:569–580

    CAS  Google Scholar 

  21. 21.

    Gantt SL, Denisov IG, Grinkova YV, Sligar SG (2009) The critical iron-oxygen intermediate in human aromatase. Biochem Biophys Res Commun 387:169–173

    CAS  Article  Google Scholar 

  22. 22.

    Davydov R, Makris TM, Kofman V, Werst DE, Sligar SG, Hoffman BM (2001) Hydroxylation of camphor by reduced oxy-cytochrome P450cam: mechanistic implications of EPR and ENDOR studies of catalytic intermediates in native and mutant enzymes. J Am Chem Soc 123:1403–1415

    CAS  Article  Google Scholar 

  23. 23.

    Graham-Lorence S, Amarneh B, White RE, Peterson JA, Simpson ER (1995) A three-dimensional model of aromatase cytochrome P450. Protein Sci 4:1065–1080

    CAS  Article  Google Scholar 

  24. 24.

    Tosha T, Kagawa N, Ohta T, Yoshioka S, Waterman MR, Kitagawa T (2006) Raman evidence for specific substrate-induced structural changes in the heme pocket of human cytochrome P450 aromatase during the three consecutive oxygen activation steps. Biochemistry 45:5631–5640

    CAS  Article  Google Scholar 

  25. 25.

    Hackett JC, Brueggemeier RW, Hadad CM (2005) The final catalytic step of cytochrome P450 aromatase: a density functional theory study. J Am Chem Soc 127:5224–5237

    CAS  Article  Google Scholar 

  26. 26.

    Sen K, Hackett JC (2012) Coupled electron transfer and proton hopping in the final step of CYP19-catalyzed androgen aromatization. Biochemistry 51:3039–3049

    CAS  Article  Google Scholar 

  27. 27.

    Mak PJ, Luthra A, Sligar SG, Kincaid JR (2014) Resonance Raman spectroscopy of the oxygenated intermediates of human CYP19A1 implicates a Compound I intermediate in the final lyase step. J Am Chem Soc 136:4825–4828

    CAS  Article  Google Scholar 

  28. 28.

    Khatri Y, Luthra A, Duggal R, Sligar SG (2014) Kinetic solvent isotope effect in steady-state turnover by CYP19A1 suggests involvement of Compound 1 for both hydroxylation and aromatization steps. FEBS Lett 588:3117–3122

    CAS  Article  Google Scholar 

  29. 29.

    Shaik S, Kumar D, de Visser SP, Altun A, Thiel W (2005) Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes. Chem Rev 105:2279–2328

    CAS  Article  Google Scholar 

  30. 30.

    Shaik S, Cohen S, Wang Y, Chen H, Kumar D, Thiel W (2010) P450 enzymes: their structure, reactivity, and selectivity—modeled by QM/MM calculations. Chem Rev 110:949–1017

    CAS  Article  Google Scholar 

  31. 31.

    Sivaramakrishnan S, Ouellet H, Matsumura H, Guan S, Moënne-Loccoz P, Burlingame AL, Ortiz de Montellano PR (2012) Proximal ligand electron donation and reactivity of the cytochrome P450 ferric-peroxo anion. J Am Chem Soc 134:6673–6684

    CAS  Article  Google Scholar 

  32. 32.

    Ouellet H, Guan S, Johnston JB, Chow ED, Kells PM, Burlingame AL, Cox JS, Podust LM, de Montellano PR (2010) Mycobacterium tuberculosis CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one. Mol Microbiol 77:730–742

    CAS  Article  Google Scholar 

  33. 33.

    van der Kamp MW, Mulholland AJ (2013) Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology. Biochemistry 52:2708–2728

    Article  Google Scholar 

  34. 34.

    Singh UC, Kollman PA (1986) A combined Ab Iinitio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: applications to the CH3Cl + Cl exchange reaction and gas phase protonation of polyethers. J Comput Chem 7:718–730

    CAS  Article  Google Scholar 

  35. 35.

    Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227–249

    CAS  Article  Google Scholar 

  36. 36.

    Field MJ, Bash PA, Karplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11:700–733

    CAS  Article  Google Scholar 

  37. 37.

    Thèry V, Rinaldi D, Rivail J-L, Maigret B, Ferenczy GG (1994) Quantum mechanical computations on very large molecular systems: The local self-consistent field method. J Comput Chem 15:269–282

    Article  Google Scholar 

  38. 38.

    Ferenczy Gy G (2013) Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation. J Comput Chem 34:854–861

    CAS  Article  Google Scholar 

  39. 39.

    Ferenczy Gy G (2013) Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part II. Application of the local basis equation. J Comput Chem 34:862–869

    CAS  Article  Google Scholar 

  40. 40.

    Kästner J, Thiel S, Senn HM, Sherwood P, Thiel W (2007) Exploiting QM/MM capabilities in geometry optimization: a microiterative approach using electrostatic embedding. J Chem Theory Comput 3:1064–1072

    Article  Google Scholar 

  41. 41.

    Kumar S, Rosenberg JM, Bouzida D, Swendsen RH, Kollman PA (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comput Chem 13:1011–1021

    CAS  Article  Google Scholar 

  42. 42.

    Prasad BR, Plotnikov NV, Lameira J, Warshel A (2013) Quantitative exploration of the molecular origin of the activation of GTPase. Proc Natl Acad Sci USA 110:20509–20514

    Article  Google Scholar 

  43. 43.

    Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A (2013) Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant Ab Initio QM/MM free-energy surfaces. J Phys Chem B 117:12807–12819

    CAS  Article  Google Scholar 

  44. 44.

    Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99:12562–12566

    CAS  Article  Google Scholar 

  45. 45.

    Plotnikov NV, Kamerlin SC, Warshel A (2011) Paradynamics: an effective and reliable model for Ab Initio QM/MM free-energy calculations and related tasks. J Phys Chem B 115:7950–7962

    CAS  Article  Google Scholar 

  46. 46.

    Krámos B, Oláh J (2014) Enolization as an alternative proton delivery pathway in human aromatase (P450 19A1). J Phys Chem B 118:390–405

    Article  Google Scholar 

  47. 47.

    Zheng JJ, Wang D, Thiel W, Shaik S (2006) QM/MM study of mechanisms for compound I formation in the catalytic cycle of cytochrome P450cam. J Am Chem Soc 128:13204–13215

    CAS  Article  Google Scholar 

  48. 48.

    Groves JT, Gross Z, Stern MK (1994) Preparation and reactivity of oxoiron(IV) porphyrins. Inorg Chem 33:5065–5072

    CAS  Article  Google Scholar 

  49. 49

    He K, Falick AM, Chen B, Nilsson F, Correia MA (1996) Identification of the heme adduct and an active site peptide modified during mechanism-based inactivation of rat liver cytochrome P450 2B1 by secobarbital. Chem Res Toxicol 9:614–622

    CAS  Article  Google Scholar 

  50. 50.

    de Visser SP, Kumar D, Shaik S (2004) How do aldehyde side products occur during alkene epoxidation by cytochrome P450? Theory reveals a state-specific multi-state scenario where the high-spin component leads to all side products. J Inorg Biochem 98:1183–1193

    Article  Google Scholar 

  51. 51.

    Ogliaro F, Cohen S, de Visser SP, Shaik S (2000) Medium polarization and hydrogen bonding effects on compound I of cytochrome P450: what kind of a radical is it really? J Am Chem Soc 122:12892–12893

    CAS  Article  Google Scholar 

  52. 52.

    Ogliaro F, de Visser SP, Cohen S, Kaneti J, Shaik S (2001) The experimentally elusive oxidant of cytochrome P450: a theoretical, “trapping” defining more closely the “real” species. ChemBioChem 2:848–851

    CAS  Article  Google Scholar 

  53. 53.

    Bathelt CM, Zurek J, Mulholland AJ, Harvey JN (2005) Electronic structure of compound i in human isoforms of cytochrome P450 from QM/MM modeling. J Am Chem Soc 127:12900–12908

    CAS  Article  Google Scholar 

  54. 54.

    Ogliaro F, Cohen S, Filatov M, Harris N, Shaik S (2000) The high-valent compound of cytochrome P450: the nature of the Fe–S bond and the role of the thiolate ligand as an internal electron donor. Angew Chem Int Ed 39:3851–3855

    CAS  Article  Google Scholar 

  55. 55.

    Ogliaro F, Cohen S, Filatov M, Harris N, Shaik S (2001) The high-valent compound of cytochrome P450: the nature of the Fe–S bond and the role of the thiolate ligand as an internal electron donor. Angew Chem Int Ed 40:647

    CAS  Article  Google Scholar 

  56. 56.

    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA et al (2009) Gaussian 09, revision A.1. Gaussian Inc, Wallingford, CT

    Google Scholar 

  57. 57.

    Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652

    CAS  Article  Google Scholar 

  58. 58.

    Altun A, Kumar D, Neese F, Thiel W (2008) Multireference Ab Initio quantum mechanics/molecular mechanics study on intermediates in the catalytic cycle of cytochrome P450cam. J Phys Chem A 112:12904–12910

    CAS  Article  Google Scholar 

  59. 59

    Dolg M, Wedig U, Stoll H, Preuss H (1987) Energy-adjusted ab initio pseudopotentials for the first row transition elements. J. Chem. Phys. 86:866–872

    CAS  Article  Google Scholar 

  60. 60.

    Andrae D, Haussermann U, Dolg M, Stoll H, Preuss H (1990) Energy-adjusted ab initio pseudopotentials for the second and third row transition elements. Theor Chim Acta 77:123–141

    CAS  Article  Google Scholar 

  61. 61.

    Krámos B, Menyhárd DK, Oláh J (2012) Direct hydride shift mechanism and stereoselectivity of P450nor confirmed by QM/MM calculations. J Phys Chem B 116:872–885

    Article  Google Scholar 

  62. 62.

    Grimme S, Antony J, Ehrlich S, Krieg H (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104

    Article  Google Scholar 

  63. 63.

    NBO 5.9, Glendening ED, Badenhoop JK, Reed AE, Carpenter JE, Bohmann JA, Morales C, Weinhold F (2009) Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 2009. http://www.chem.wisc.edu/~nbo5. Accessed Nov 4, 2013

  64. 64.

    Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Acc 120:215–241

    CAS  Article  Google Scholar 

  65. 65.

    Tao JM, Perdew JP, Staroverov VN, Scuseria GE (2003) Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids. Phys Rev Lett 91:146401

    Article  Google Scholar 

  66. 66.

    Lee C, Yang W, Parr RG (1988) Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789

    CAS  Article  Google Scholar 

  67. 67.

    Chai JD, Head-Gordon M (2008) Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections. Phys Chem Chem Phys 10:6615–6620

    CAS  Article  Google Scholar 

  68. 68.

    Miertuš S, Scrocco E, Tomasi J (1981) Electrostatic interaction of a solute with a continuum. a direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 55:117–129

    Article  Google Scholar 

  69. 69.

    Pascual-Ahuir JL, Silla E, Tuñón I (1994) GEPOL: an improved description of molecular-surfaces. 3. A new algorithm for the computation of a solvent-excluding surface. J Comp Chem 15:1127–1138

    CAS  Article  Google Scholar 

  70. 70.

    Ghosh D, Griswold J, Erman M, Pangborn W (2009) Structural basis for androgen specificity and oestrogen synthesis in human aromatase. Nature 457:219–223

    CAS  Article  Google Scholar 

  71. 71.

    Altun A, Guallar V, Friesner RA, Shaik S, Thiel W (2006) The effect of heme environment on the hydrogen abstraction reaction of camphor in P450cam catalysis: a QM/MM study. J Am Chem Soc 128:3924–3925

    CAS  Article  Google Scholar 

  72. 72.

    Altun A, Shaik S, Thiel W (2006) Systematic QM/MM investigation of factors that affect the cytochrome P450-catalyzed hydrogen abstraction of camphor. J Comput Chem 27:1324–1337

    CAS  Article  Google Scholar 

  73. 73.

    MacKerell AD Jr, Banavali N, Foloppe N (2000) Development and current status of the CHARMM Force field for nucleic acids. Biopolymers 56:257–265

    CAS  Article  Google Scholar 

  74. 74.

    Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614

    CAS  Article  Google Scholar 

  75. 75.

    Harvey JN (2004) Spin-forbidden CO ligand recombination in myoglobin. Faraday Discuss. 127:165–177

    CAS  Article  Google Scholar 

  76. 76.

    TINKER—Home Page. Tinker—software tools for molecular design. http://dasher.wustl.edu/tinker/. Accessed October 5, 2011

  77. 77.

    Ren P, Wu C, Ponder JW (2011) Polarizable atomic multipole-based molecular mechanics for organic molecules. J Chem Theory Comput 7:3143–3161

    CAS  Article  Google Scholar 

  78. 78.

    Lonsdale R, Harvey JN, Mulholland AJ (2010) Inclusion of dispersion effects significantly improves accuracy of calculated reaction barriers for cytochrome P450 catalyzed reactions. J Phys Chem Lett 1:3232–3237

    CAS  Article  Google Scholar 

  79. 79.

    Lonsdale R, Harvey JN, Mulholland AJ (2012) Effects of dispersion in density functional based quantum mechanical/molecular mechanical calculations on cytochrome P450 catalyzed reactions. J Chem Theory Comput 8:4637–4645

    CAS  Article  Google Scholar 

  80. 80.

    Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799

    CAS  Article  Google Scholar 

  81. 81.

    Schaftenaar G, Noordik JH (2000) Molden: a pre- and post-processing program for molecular and electronic structures. J Comput-Aided Mol Design 14:123–134

    CAS  Article  Google Scholar 

  82. 82.

    Humphrey W, Dalke A, Schulten K (1996) VMD - Visual Molecular Dynamics. J Mol Graphics 14:33–38

    CAS  Article  Google Scholar 

  83. 83.

    Schöneboom JC, Cohen S, Lin H, Shaik S, Thiel W (2004) Quantum mechanical/molecular mechanical investigation of the mechanism of C–H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism. J Am Chem Soc 126:4017–4034

    Article  Google Scholar 

  84. 84.

    Meigs RA, Ryan KJ (1971) Enzymatic aromatization of steroids I. Effects of oxygen and carbon monoxide on the intermediate steps of estrogen biosynthesis. J Biol Chem 246:83–87

    CAS  Google Scholar 

  85. 85.

    Townsley JD, Brodi HJ (1968) Mechanism of estrogenbiosynthesis. III. Stereochemistry of aromatization of C19 and C18 steroids. Biochemistry 7:33–40

    CAS  Article  Google Scholar 

  86. 86.

    Conradie J, Abhik Ghosh A (2007) DFT calculations on the spin-crossover complex Fe(salen)(NO): a quest for the best functional. J Phys Chem B 111:12621–12624

    CAS  Article  Google Scholar 

  87. 87.

    Harvey JN (2006) On the accuracy of density functional theory in transition metal chemistry. Annu Rep Prog Chem C 102:203–226

    CAS  Article  Google Scholar 

  88. 88.

    Radoń M (2014) Revisiting the role of exact exchange in DFT spin-state energetics of transition metal complexes. Phys Chem Chem Phys 16:14479–14488

    Article  Google Scholar 

  89. 89.

    Frushicheva MP, Warshel A (2012) Towards quantitative computer-aided studies of enzymatic enantioselectivity: the case of candida Antarctica lipase A. ChemBioChem 13:215–223

    CAS  Article  Google Scholar 

  90. 90.

    Lonsdale R, Hoyle S, Grey DT, Ridder L, Mulholland AJ (2012) Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling. Biochemistry 51:1774–1786

    CAS  Article  Google Scholar 

  91. 91.

    Torrie GM, Valleau JP (1974) Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett 28:578–581

    CAS  Article  Google Scholar 

  92. 92.

    Car R, Parrinello M (1985) Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55:2471–2474

    CAS  Article  Google Scholar 

  93. 93.

    Ufimtsev IS, Martínez TJ (2008) Quantum chemistry on graphical processing units. 1. Strategies for two-electron integral evaluation. J Chem Theory Comput 4:222–231

    CAS  Article  Google Scholar 

  94. 94.

    Sisto A, Glowacki DR, Martinez TJ (2014) Ab Initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework. Acc Chem Res 47:2857–2866

    CAS  Article  Google Scholar 

  95. 95.

    Lonsdale R, Houghton KT, Żurek J, Bathelt CM, Foloppe N, de Groot MJ, Harvey JN, Mulholland AJ (2013) Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9. J Am Chem Soc 135:8001–8015

    CAS  Article  Google Scholar 

  96. 96.

    Oláh J, Mulholland AJ, Harvey JN (2011) Understanding the Determinants of Selectivity in Drug Metabolism through Modeling of Dextromethorphan Oxidation by Cytochrome P450. Proc Natl Acad Sci USA 108:6050–6055

    Article  Google Scholar 

  97. 97.

    Ranaghan KE, Mulholland AJ (2010) Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. Int Rev Phys Chem 29:65–133

    CAS  Article  Google Scholar 

  98. 98.

    Klähn M, Braun-Sand S, Rosta E, Warshel A (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J Phys Chem B 109:15645–15650

    Article  Google Scholar 

  99. 99.

    Harvey JN, Bathelt CM, Mulholland AJ (2006) QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase. J Comput Chem 27:1352–1362

    CAS  Article  Google Scholar 

  100. 100.

    Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MH (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210–3235

    CAS  Article  Google Scholar 

  101. 101.

    Warshel A (1978) Energetics of enzyme catalysis. Proc Natl Acad Sci USA 75:5250–5254

    CAS  Article  Google Scholar 

Download references

Acknowledgments

The authors thank Prof. Jeremy Harvey (University of Bristol. UK) for useful discussions, Dóra K. Menyhárd for proof-reading of the manuscript, and the financial support of the New Széchenyi Plan (TÁMOP-4.2.2/B-10/1-2010-0009) and of OTKA Grant No. 108721. JO acknowledges receipt of an EU Marie Curie ERG Fellowship (Project “Oestrometab”). Part of this work was supported by the COST Action CM1305 (ECOSTBio).

Author information

Affiliations

Authors

Corresponding author

Correspondence to Julianna Oláh.

Electronic supplementary material

Below is the link to the electronic supplementary material.

SUPPORTING INFORMATION.

Selected geometrical parameters and fragment charges for QM-only optimized structures using various basis sets, and details of all reactants, TS, and product complexes obtained in QM/MM calculations. Furthermore, total energies and Cartesian coordinates of all QM-only structures, geometries of the QM region of the QM/MM structures belonging to profile 1, and MM parameters for the 19-oxo-ASD are also provided in the SI together with tables and figures indicated in the text. (DOC 2789 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Krámos, B., Oláh, J. The mechanism of human aromatase (CYP 19A1) revisited: DFT and QM/MM calculations support a compound I-mediated pathway for the aromatization process. Struct Chem 26, 279–300 (2015). https://doi.org/10.1007/s11224-014-0545-9

Download citation

Keywords

  • Deformylation
  • Androstenedione
  • QM/MM
  • Reaction mechanism
  • C–C bond fission