Abstract
In this paper, a computational approach to model conformational and spectroscopic properties of doxorubicin in aqueous environment is presented. We show that our approach, rooted in DFT and TD-DFT with the further inclusion of solvent effects within the polarizable continuum model, is able to describe the main features of vibrational resonance Raman spectra, as well as IR and UV–Vis spectra. Also, in order to get more insight, the limitations of the continuum approach to solvation, and to explain some of the discrepancies between calculations and experiments, a detailed analysis of the solvated system through molecular dynamics is presented.
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References
Brayfield A (ed) (2013) “Doxorubicin”. Martindale: the complete drug reference. Pharmaceutical Press, London
Arcamone F, Cassinelli G, Fantini G et al (1969) Adriamycin, 14-hydroxydaunomycin, a new antitumor antibiotic from S. peucetius var. caesius. Biotechnol Bioeng 11:1101–1110
Kersten H, Kersten W (1974) Inhibitors of nucleic acid synthesis. Springer, New York
Airoldi M, Barone G, Gennaro G, Giuliani AM, Giustini M (2014) Interaction of doxorubicin with polynucleotides. A spectroscopic study. Biochemistry 53:2197–2207
Fiallo MML, Tayeb H, Suarato A, Garnier-Suillerot A (1998) Circular dichroism studies on anthracycline antitumor compounds. Relationship between the molecular structure and the spectroscopic data. J Pharm Sci 8:967
Drechsel H, Fiallo M, Garnier-Suillerot A, Matzanke BF, Schunemann V (2001) Spectroscopic studies on iron complexes of different anthracyclines in aprotic solvent systems. Inorg Chem 40:5324–5333
Kizek R, Adam V, Hrabeta J, Eckschlager T, Smutny S, Burda JV, Frei E, Stiborova M (2012) Anthracyclines and ellipticines as DNA-damaging anticancer drugs: recent advances. Pharmacol Ther 133:26–39
Lu Y, Lv J, Zhang G, Wang G, Liu Q (2010) Interaction of an anthracycline disaccharide with ctDNA: investigation by spectroscopic technique and modeling studies spectrochim. Acta Mol Biomol Spectrosc 75:1511–1515
Temperini C, Messori L, Orioli P, Di Bugno C, Animati F, Ughetto G (2003) The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes. Nucleic Acids Res 31:1464–1469
Quigley GJ, Wang AHJ, Ughetto G, Van Der Marel G, Van Boom JH, Rich A (1980) Molecular structure of an anticancer drug-DNA complex: daunomycin plus d(CpGpTpApCpG). Proc Natl Acad Sci USA 77:7204–7208
Post GC, Barthel BL, Burkhart DJ, Hagadorn JR, Koch TH (2005) Doxazolidine, a proposed active metabolite of doxorubicin that cross-links DNA. J Med Chem 48:7648–7657
Manfait M, Alix AJP, Jeannesson P, Jardillier J-C, Theophanides T (1982) Interaction of adriamycin with DNA as studied by resonance Raman spectroscopy. Nucleic Acids Res 10:3803
Lee CJ, Kang JS, Kim MS, Lee KP, Lee MS (2004) The study of doxorubicin and its complex with DNA by SERS and UV-resonance Raman spectroscopy. Bull Korean Chem Soc 25:1211
Smulevich G, Mantini AR, Feis A, Marzocchi MP (2001) Resonance Raman spectra and transform analysis of anthracyclines and their complexes with DNA. J Raman Spectrosc 32:565–578
Yan Q, Priebe W, Chaires JB, Czernuszewicz RS (1997) Interaction of doxorubicin and its derivatives with DNA: elucidation by resonance Raman and surface-enhanced resonance Raman spectroscopy. Biospectroscopy 3:307–316
Butler CA, Cooney RP, Denny WA (1994) Resonance Raman study of the binding of the anticancer drug amsacrine to DNA. Appl Spectrosc 48:822
Beljebbar A, Sockalingum GD, Angiboust JF, Manfait M (1995) Comparative FT SERS, resonance Raman and SERRS studies of doxorubicin and its complex with DNA. Spectrochim Acta Mol Biomol Spectrosc 51:2083–2090
Das G, Nicastri A, Coluccio ML, Gentile F, Candeloro P, Cojoc G, Liberale C, De Angelis F, Di Fabrizio E (2010) FT-IR, Raman, RRS measurements and DFT calculation for doxorubicin. Microsc Res Tech 73:991–995
Rygula A, Majzner K, Marzec KM, Kaczor A, Pilarczyka M, Baranska M (2013) Raman spectroscopy of proteins: a review. J Raman Spectrosc 44:1061–1076
Maiti NC, Apetri MM, Zagorski MG, Carey PR, Anderson VE (2004) Raman spectroscopic characterization of secondary structure in natively unfolded proteins: \(\alpha\)-synuclein. J Am Chem Soc 126:2399–2408
Hillig KW, Morris MD (1976) Pre-resonance Raman spectra of adriamycin. Biochem Biophys Res Commun 71:1228–1233
Huang C-Y, Balakrishnan G, Spiro TG (2006) Protein secondary structure from deep-UV resonance Raman spectroscopy. J Raman Spectrosc 37:277–282
Chi Z, Chen XG, Holtz JSW, Asher SA (1998) UV resonance raman-selective amide vibrational enhancement: quantitative methodology for determining protein secondary structure. Biochemistry 37:2854–2864
Oladepo SA, Xiong K, Hong Z, Asher SA, Handen J, Lednev IK (2012) UV resonance raman investigations of peptide and protein structure and dynamics. Chem Rev 112:2604–2628
Hong Z, Wert J, Asher SA (2013) UV resonance Raman and DFT studies of arginine side chains in peptides: insights into arginine hydration. J Phys Chem B 117:7145–7156
Cho N, Asher SA (1993) UV resonance Raman studies of DNA-pyrene interactions: optical decoupling Raman spectroscopy selectively examines external site bound pyrene. J Am Chem Soc 115(14):6349–6356
Chen TI, Morris MD (1983) Resonance inverse Raman spectroscopic study of proflavin-DNA intercalation. J Phys Chem 87:2314–2317
Stanicova J, Fabriciova G, Chinsky L, Sutiak V, Miskovsky P (1999) Amantadine–DNA interaction as studied by classical and resonance Raman spectroscopy. J Mol Struct 478:129–138
Mariam YH, Chantranupong L (2000) DFT computational studies of intramolecular hydrogen-bonding interactions in a model system for 5-iminodaunomycin. J Mol Struct (Theochem) 529:83–97
Mortier J, Rakers C, Bermudez M, Murgueitio MS, Riniker S, Wolber G (2015) The impact of molecular dynamics on drug design: applications for the characterization of ligand- macromolecule complexes. Drug Discov Today 1:686–702
Lei H, Wanga X, Wu C (2012) Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Model 38:279–289
Wilhelm M, Mukherjee A, Bouvier B, Zakrzewska K, Hynes JT, Lavery R (2012) Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA. J Am Chem Soc 134:8588–8596
Trieb M, Rauch C, Wibowo FR, Wellenzohn B, Liedl KR (2004) Cooperative effects on the formation of intercalation sites. Nucleic Acids Res 32:4696–4703
Poupaert JH, Couvreur P (2003) A computationally derived structural model of doxorubicin interacting with oligomeric polyalkylcyanoacrylate in nanoparticles. J Control Release 92:19–26
Jacquemin D, Brémond E, Planchat A, Ciofini I, Adamo C (2011) TD-DFT vibronic couplings in anthraquinones: from basis set and functional benchmarks to applications for industrial dyes. J Chem Theory Comput 7:1882–1892
Jacquemin D, Brémond E, Ciofini I, Adamo C (2012) Impact of vibronic couplings on perceived colors: two anthraquinones as a working example. J Phys Chem Lett 3:468–471
Egidi F, Cappelli C (2015) Calculation of molecular properties in solution. In: Reference module in chemistry, molecular sciences and chemical engineering. Elsevier
Barone V, Baiardi A, Biczysko M, Bloino J, Cappelli C, Lipparini F (2012) Implementation and validation of a multi-purpose virtual spectrometer for large systems in complex environments. Phys Chem Chem Phys 14:12404–12422
Mennucci B, Cappelli C, Cammi R, Tomasi J (2007) A quantum mechanical polarizable continuum model for the calculation of resonance Raman spectra in condensed phase. Theor Chem Acc 117:1029–1039
Santoro F, Cappelli C, Barone V (2011) Effective time-independent calculations of vibrational resonance Raman spectra of isolated and solvated molecules including Duschinsky and Herzberg-Teller effects. J Chem Theory Comput 7:1824–1839
Egidi F, Bloino J, Cappelli C, Barone V (2014) A robust and effective time-independent route to the calculation of resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects. J Chem Theory Comput 10:346–363
Avila Ferrer FJ, Barone V, Cappelli C, Santoro F (2013) Duschinsky, Herzberg-Teller, and multiple electronic resonance interferential effects in resonance Raman spectra and excitation profiles. The case of pyrene. J Chem Theory Comput 9:3597–3611
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H,Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G,Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J,Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T,Montgomery JA, Jr., Peralta JE, Ogliaro F, Bearpark M, Heyd JJ,Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J,Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M,Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C,Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R,Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, VothGA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö,Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian 09Revision C.01. Gaussian Inc. Wallingford CT
Gaussian Development Version, Revision I.02, Frisch MJ, Trucks GW,Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, BaroneV, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X,Hratchian HP, Bloino J, Janesko BG, Izmaylov AF, Lipparini F, ZhengG, Sonnenberg JL, Liang W, Hada M, Ehara M, Toyota K, Fukuda R,Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, VrevenT, Throssell K, Montgomery JA, Jr., Peralta JE, Ogliaro F, BearparkM, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Keith T, KobayashiR, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS,Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB,Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O,Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K,Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S,Parandekar PV, Mayhall NJ, Daniels AD, Farkas O, Foresman JB, OrtizJV, Cioslowski J, Fox DJ (2014) Gaussian, Inc., Wallingford CT
Yanai T, Tew DP, Handy NC (2004) A new hybrid exchange-correlation functional using the coulomb-attenuating method (cam-b3lyp). Chem Phys Lett 393:51–57
Limacher PA, Mikkelsen KV, Luthi HP (2009) On the accurate calculation of polarizabilities and second hyperpolarizabilities of polyacetylene oligomer chains using the CAM-B3LYP density functional. J Chem Phys 130:194114
Bulik IW, Zalesny R, Bartkowiak W, Luis JM, Kirtman B, Scuseria GE, Avramopoulos A, Reis H, Papadopoulos MG (2013) Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities. J.Comput Chem 34:1775–1784
Baranowska-Laczkowska A, Bartkowiak W, Gora RW, Pawlowski F, Zalesny R (2013) On the performance of long-range-corrected density functional theory and reduced-size polarized LPol-n basis sets in computations of electric dipole (hyper)polarizabilities of \(\pi\)-conjugated molecules. J Comput Chem 34:819–826
RCSB Protein Data Bank. (http://www.rcsb.org/pdb/home/home.do)
Marvin 15.6.15.0, 2015, ChemAxon. (http://www.chemaxon.com)
Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3094
Mennucci B (2012) Polarizable continuum model. WIREs Comput Mol Sci 2:386–404
Bondi A (1964) van der Waals volumes and radii. J Phys Chem 68:441
Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378–6396
Barone V, Cimino P, Stendardo E (2008) Development and validation of the B3LYP/N07D computational model for structural parameter and magnetic tensors of large free radicals. J Chem Theory Comput 4:751–764
van der Spoel D, Lindahl E, Hess B, van Buuren AR, Apol E, Meulenhoff P, Tieleman D, Sijbers A, Feenstra K, van Drunen R, Berendsen H (2010) Gromacs4.5. Gromacs User Manual version 4.5.4. www.gromacs.org
Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) Application of the multimolecule and multiconformational RESP methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J Comput Chem 11:1357–1377
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general AMBER force field. J Comput Chem 25:1157–1174
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
Hummer G, Pratt LR, Garcia AE (1998) Molecular theories and simulation of ions and polar molecules in water. J Phys Chem A 41:7885–7895
Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463
Bussi G, Donadio D, Parrinello M (2013) Canonical sampling through velocity rescaling. J Chem Phys 126:014101
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38
Luzar A (2000) Resolving the hydrogen bond dynamics conundrum. J Chem Phys 113:10663
Foresman JB, Keith TA, Wiberg KB, Snoonian J, Frisch MJ (1996) Influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations. J Phys Chem 100:16098
Wong MW, Wiberg KB, Frisch MJ (1995) Ab initio calculation of molar volumes: comparison with experiment and use in solvation models. J Comput Chem 16:385
Cappelli C, Mennucci B, da Silva CO, Tomasi J (2000) Refinements on solvation continuum models: hydrogen-bond effects on the OH stretch in liquid water and methanol. J Chem Phys 112:5382–5392
Barone V, Cossi M, Tomasi J (1997) A new definition of cavities for the computation of solvation free energies by the polarizable continuum model. J Chem Phys 107:3210
Tomasi J, Bonaccorsi R (1992) Methodological aspects of the solvation models based on continuous solvent distributions. Croat Chem Acta 65:29
West RC (ed) (2005) Handbook of chemistry and physics. Chemical Rubber Company, Cleveland, p 198
Jacquemin D, Wathelet V, Perpète EA, Adamo C (2009) Extensive TD-DFT benchmark: singlet-excited states of organic molecules. J Chem Theory Comput 5:2420–2435
Cave RJ, Burke K, Castner EW (2002) Theoretical investigation of the ground and excited states of coumarin 151 and coumarin 120. J Phys Chem A 106:9294–9305
Fabian J (2010) TDDFT-calculations of Vis/NIR absorbing compounds. Dyes Pigm 84:36–53
Orio M, Pantazis DA, Neese F (2009) Density functional theory. Photosynth Res 102:443–453
Avila Ferrer FJ, Cerezo J, Stendardo E, Improta R, Santoro F (2013) Insights for an accurate comparison of computational data to experimental absorption and emission spectra: beyond the vertical transition approximation. J Chem Theory Comput 9:2072–2082
Runge E, Gross EKU (1984) Density-functional theory for time-dependent systems. Phys Rev Lett 52:997
Santoro F, Improta R, Lami A, Bloino J, Barone V (2007) Effective method to compute Franck–Condon integrals for optical spectra of large molecules in solution. J Chem Phys 126:084509/1-13
Dierksen M, Grimme S (2005) An efficient approach for the calculation of Franck-Condon integrals of large molecules. J Chem Phys 122:244101
Bloino J, Biczysko M, Santoro F, Barone V (2010) General approach to compute vibrationally resolved one-photon electronic spectra. J Chem Theory Comput 6:1256
Peticolas L, Rush T (1995) Ab initio calculations of the ultraviolet resonance Raman spectrum of Uracil. J Comput Chem 16:1261–1270
Heller EJ, Lee S-Y (1979) Time dependent theory of Raman scattering. J Chem Phys 71:4777–4788
Heller EJ, Sundberg RL, Tannor D (1982) Simple aspects of Raman scattering. J Phys Chem 86:1822–1833
Yoshida Z, Takabayashi F (1968) Electronic spectra of mono-substituted anthraquinones and solvent effects. Tetrahedron 24:913–943
Issa IM, Issa RM, El-Ezaby MS, Ahmed Y-Z (1969) Spectrophotometric studies on acid in solutions of varying pH. Z Phys Chem 242:169–176
Kuboyama A, Wada K (1966) The \(\pi\)-electronic excitation energies of anthraquinone. Bull Chem Soc Jpn 2:1874–1877
Rick SW, Stuart SJ, Berne BJ (1994) Dynamical fluctuating charge force fields: application to liquid water. J Chem Phys 101:6141
Lipparini F, Barone V (2011) Polarizable force fields and polarizable continuum model: a fluctuating charges/PCM approach. 1. theory and implementation. J Chem Theory Comput 7:3711
Mortier WJ, Van Genechten K, Gasteiger J (1985) Electronegativity equalization: application and parametrization. J Am Chem Soc 107:829
Rappe A, Goddard W (1991) Charge equilibration for molecular dynamics simulations. J Phys Chem 95:3358
Lipparini F, Cappelli C, Scalmani G, De Mitri N, Barone V (2012) Analytical first and second derivatives for a fully polarizable QM/Classical hamiltonian. J Chem Theory Comput 8:4270
Lipparini F, Cappelli C, Barone V (2013) A gauge invariant multiscale approach to magnetic spectroscopies in condensed phase: general three-layer model, computational implementation and pilot applications. J Chem Phys 138:234108
Lipparini F, Cappelli C, Barone V (2012) Linear response theory and electronic transition energies for a fully polarizable QM/classical Hamiltonian. J Chem Theory Comput 8:4153
Lipparini F, Egidi F, Cappelli C, Barone V (2013) The optical rotation of methyloxirane in aqueous solution: a never ending story? J Chem Theory Comput 9:1880
Egidi F, Russo R, Carnimeo I, D’Urso A, Mancini G, Cappelli C (2015) The electronic circular dichroism of nicotine in aqueous solution: a test case for continuum and mixed explicit-continuum solvation approaches. J Phys Chem A 119:5396
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MO and CC acknowledge support from the Italian MIUR (PRIN 2012 NB3KLK002) and COST CMST-Action CM1405 MOLecules In Motion (MOLIM).
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Olszówka, M., Russo, R., Mancini, G. et al. A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution. Theor Chem Acc 135, 27 (2016). https://doi.org/10.1007/s00214-015-1781-9
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DOI: https://doi.org/10.1007/s00214-015-1781-9