Quantum Chemical Benchmark Study on Valdecoxib, a Potent and Selective Inhibitor of COX-2, and its Hydroxylated Derivative

Sümeyya Serin; Öznur Doğan Ulu

doi:10.17776/csj.1086277

Research Article

Year 2022, , 221 - 231, 29.06.2022

Sümeyya Serin , Öznur Doğan Ulu

https://doi.org/10.17776/csj.1086277

Cited By: 1

Abstract

References

[1] Vane J.R., Inhibition of Prostaglandin Synthesis as a Mechanism of Action for Aspirin-like Drugs, Nature New Biol., 231 (1971) 232–235.
[2] Fu J. R., Masferrer J. L., Seibert K., Raz A., Needle-man P., The induction and suppression of prostaglandin H2 synthase (cyclooxygenase) in human monocytes, J. Biol. Chem., 265 (1990) 265 16737-16740.
[3] Battistini B., Botting B., Bakhle Y., SCOX-1 and COX-2:Toward the development of more selective NSAİDs, Drug News Perspect., 7 (1994) 501.
[4] Sayed G., Abou-seri S.M., Kamel G., Moawad M., Celecoxib analogs bearing ben- zofuran moiety as cyclooxygenase-2 inhibitors : design, synthesis and evalua- tion as potential anti-inflammatory agents, Eur. J. Med. Chem., 76 (2014) 482–493.
[5] Abdelall E.K.A., Lamie P.F., Ahmed A.K.M., El-nahass E., COX-1/COX-2 inhibi- tion assays and histopathological study of the new designed anti-inflammatory agent with a pyrazolopyrimidine core, Bioorg. Chem., 86 (2019) 235–253.
[6] Raz A., Wyche A., Siegel N., Needleman P., Regulation of fibroblast cyclooxygenase synthesis by interleukin-1, J. Biol.Chem., 263 (1988) 263 3022-3028.
[7] Wang C., Chen F., Qian P., Cheng J., Recent advances in the Rh-catalyzed cascade arene C–H bond activation/annulation toward diverse heterocyclic compounds, Org. Biomol. Chem., 19 (2021) 1705-1721.
[8] Mermer A., Keleş T., Şirin Y., Recent studies of nitrogen containing heterocyclic compounds as novelantiviral agents: A review, Bioorg. Chem., 114 (2021) 105076.
[9] Zhu Jun J., Hong-zhi M., Yao L., Chen Y., Sun H., The recent progress of isoxazole in medicinal chemistry, Bioorg. Med. Chem., 26 (2018) 3065–3075.
[10] Scheen A.J., Malaise M., Le medicament du mois.Valdecoxib (Bextra), Rev. Med. Liege, 59 (2004) 251-254.
[11] Erdelyi P., Fodor t., Varga A.K., Czugler M., Gere A., Fischer J., Chemical and biological investigation of N-hydroxy-valdecoxib:An active metabolite of valdecoxib, Bioorg. Med. Chem., 16 (2008) 5322–5330.
[12] Talley J.J., Brown D.L., Carter J.S., Graneto M.J., Koboldt C.M., Masferrer J.L., Perkins W.E., Rogers R.SShaffer A.F., Zhang Y.Y., Zweifel B.S., Seibert K., 4-[5-Methyl-3-phenylisoxazol-4-yl]-benzenesulfonamide, Valdecoxib: A potent and selective Inhibitor of COX-2, J. Med. Chem., 43 (2000), 775-777.
[13] Van De Waterbeemd H., Gifford E., ADMET in silico modelling: towards prediction paradise?, Nat. Rev. Drug Discov., 3 (2003) 192-204.
[14] Borges R. M., Colby S. M., Das S., Edison A. S., Fiehn O., Kind T., Lee J., Merrill A. T., Merz K. M. Jr., Metz T. O., Nunez J. R., Tantillo D. J., Wang L. P., Wang S., Renslow R. S., Quantum chemistry calculations for metabolomics., Chem. Rev., 121 (2021), 5633–5670.
[15] Genç F, Kandemirli S. G., Kandemirli F., Theoretical B3LYP study on electronic structure of contrast agent ıopamidol, Acta Chim. Slov., 68 (2021) 320-331.
[16] Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Petersson G.A., Nakatsuji H., et.al., Gaussian 16 Rev. B.01, Wallingford, CT, 2016.
[17] Dennington R., Keith T.A., Millam J.M., GaussView, Version 6 Semichem Inc., Shawnee Mission, KS. 2016.
[18] Becke A.D., A new mixing of Hartree–Fock and local density‐functional theories, J. Chem. Phys., 98 (1993) 1372–1377.
[19] Lee C., Yang W., Parr R.G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B., 37 (1988) 785–789.
[20] Becke A.D., Density‐functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98 (1993) 5648–5652.
[21] Marenich A.V., Cramer C.J., Truhlar D.G., universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions, J. Phys. Chem. B., 113 (8) (2009) 6378-6396.
[22] Molinspiration Cheminformatics free web services, https://www.molinspiration.com, Slovensky Grob, Slovakia.
[23] Gaillard P., Carrupt P.A., Testa B., Boudon A., Molecular lipophilicity potential, a tool in 3D QSAR: method and applications, J. Comput. Aided Mol. Des., 8 (1994) 83−96.
[24] Koopmans T., Über die zuordnung von wellenfunktionen und eigenwerten zu den einzelnen elektronen eines atoms, Physica, 1(6) (1934) 104-113.
[25] Parr R. G., Pearson R. G.,. Absolute hardness: companion parameter to absolute electronegativity, J. Am. Chem. Soc., 105 (1983) 7512-7516.
[26] Pearson R. G., Absolute electronegativity and hardness correlated with the molecular orbital theory, Proc. Natl. Acad. Sci. U.S.A., 83 (1986) 8440-8441.
[27] Parr R. G., Szentpaly L. V., Liu, S., Electrophilicity Index, J. Am. Chem. Soc., 121 (1999) 1922-1924.
[28] Perdew J. P., Levy M., Physical content of the exact Kohn-Sham orbital energies: band gaps and derivative iscontinuities, Phys. Rev. Lett., 51(20) (1983). 1884-1887.
[29] Perdew J. P., Parr R. G., Levy M., Balduz J. L. Jr., Density functional theory for fractional particle number: derivative discontinuities of the energy, Phys. Rev. Lett., 49 (23) (1982) 1691-1694.
[30] Malathy Sony S. M., Charles P., Ponnuswamya M. N., Yathirajan H. S., Valdecoxib, a non-steroidal anti-inflammatory drug, Acta Cryst., 61 (2005) 108-110.
[31] Kaushal A.M., Chakraborti A.K., Bansal A.K., FTIR Studies on differential ıntermolecular association in crystalline and amorphous states of structurally related non-steroidal anti-ınflammatory drugs, Molecular Pharmaceutıcs, 6 (2008) 937–945.
[32] Sundaraganesan N., Ilakiamani S., Salem H., Wojciechowski P. M., Michalska D., FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine, Spectrochim. Acta A Mol. Biomol. Spectrosc., 61 (2005) 2995–3001.
[33] Arıcı K., Vibrational Spectra of 4-hydroxy-3-cyano-7-chloro-quinoline by density functional theory and ab initio Hartree-Fock Calculations, Int. J. Chem. Technol., 1 (2017) 24-29.
[34] Erdoğan M., Serdaroğlu G., New Hybrid (E)-4-((pyren-1-ylmethylene) amino)-N-(thiazol-2-yl)benzenesulfonamide as a potential drug candidate: Spectroscopy, TD-DFT, NBO, FMO, and MEP studies, ChemistrySelect, 6 (2021) 9369–938.
[35] Fukui K., Role of frontier orbitals in chemical reactions, Science., 218 (1982) 747–754.
[36] Baybas D., Serdaroglu G., Semerci B., The composite microbeads of alginate, carrageenan, gelatin, and poly(lactic-co-glycolic acid): Synthesis, characterization and density functional theory calculations, Int. J. Biol. Macromol., 181 (2021) 322–338.
[37] Sayin K., Üngördü A., Investigations of structural, spectral and electronic properties of enrofloxacin and boron complexes via quantum chemical calculation and molecular docking, Spectrochim. Acta A Mol. Biomol. Spectrosc., 220 (2019)117102.
[38] Brahmia A., Bejaoui L., Rolicek J., Hassen R.B., Serdaroğlu G., Kaya S., Synthesis, crystal structure, Hirshfeld surface analysis and DFT calculations of 2, 2, 2-tribromo-1-(3,5-dibromo-2-hydroxyphenyl)ethanone, J. Mol. Struct., 1248 (2022) 131313.
[39] Blake J. F., Chemoinformatics - predicting the physicochemical properties of ′drug-like′ molecules, Curr. Opin. Biotechnol., 11 (2000) 104-107.
[40] Lipinski C. A. ,Lombardo F., Dominy B. W., Feeney,P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Delivery Rev., 23 (1997) 3-25.
[41] Mulliken R.S., Electron population analysis on LCAO-MO molecular wave functions, J. Chem. Phys., (1955) 1833-1841.
[42] Reed A.E., Weinstock R.B., Weinhold F., Natural atomic orbitals and natural population analysis, J. Chem. Phys., 83 (1985) 735−746.
[43] Weinhold F., Landis C.R., Glendening E.D., What is NBO analysis and how is it useful?, Int. Rev. Phys. Chem., 35 (2016) 399-440.
[44] Reed A.E., Curtiss L.A., Weinhold F., Intermolecular ınteractions from a natural bond orbital, donor-acceptor viewpoint, Chem. Rev., 88(1988) 899-926.
[45] Murray J.S., Politzer P., The electrostatic potential: an overview, Wiley Interdiscip. Rev. Comput. Mol. Sci., 1 (2011) 153-163.

Quantum Chemical Benchmark Study on Valdecoxib, a Potent and Selective Inhibitor of COX-2, and its Hydroxylated Derivative

Year 2022, , 221 - 231, 29.06.2022

Sümeyya Serin , Öznur Doğan Ulu

https://doi.org/10.17776/csj.1086277

Cited By: 1

Abstract

In this work, quantum chemical calculations were performed on valdecoxib (VLB), a highly selective and potent COX-2 inhibitor, and its hydroxylated derivative (1H-VLB), an active metabolite. The geometry optimizations and frequency calculations were carried out by using density functional theory (DFT)/B3LYP functional with the 6-311++G (d, p) basis set. To define water phase behaviors, calculations were renewed by using universal SMD solvation model for both molecules. Structural and thermodynamic parameters, FT-IR analysis, Mulliken population analysis (MPA), frontier molecular orbital (FMO) analysis, natural bond orbital (NBO) analysis, and electrostatic surface properties were investigated in detail. Quantum chemical reactivity identifiers were calculated separately for both vacuum and water environment in order to evaluate the bioactivity tendency of both mentioned compounds. When the bioactivity of VLB and 1H-VLB molecules were compared based on quantum chemical reactivity identifiers, it was observed that the VLB molecule was more active. Moreover, drug-likeness properties of studied molecules were predicted by means of Molinspiration cheminformatics software. Molecular lipophilicity potential (MLP) maps that exhibit the accumulative lipophilic contributions of each atom in studied molecules were visualized.

Keywords

Valdecoxib, DFT, Lipophilicity, NBO

References

[1] Vane J.R., Inhibition of Prostaglandin Synthesis as a Mechanism of Action for Aspirin-like Drugs, Nature New Biol., 231 (1971) 232–235.
[2] Fu J. R., Masferrer J. L., Seibert K., Raz A., Needle-man P., The induction and suppression of prostaglandin H2 synthase (cyclooxygenase) in human monocytes, J. Biol. Chem., 265 (1990) 265 16737-16740.
[3] Battistini B., Botting B., Bakhle Y., SCOX-1 and COX-2:Toward the development of more selective NSAİDs, Drug News Perspect., 7 (1994) 501.
[4] Sayed G., Abou-seri S.M., Kamel G., Moawad M., Celecoxib analogs bearing ben- zofuran moiety as cyclooxygenase-2 inhibitors : design, synthesis and evalua- tion as potential anti-inflammatory agents, Eur. J. Med. Chem., 76 (2014) 482–493.
[5] Abdelall E.K.A., Lamie P.F., Ahmed A.K.M., El-nahass E., COX-1/COX-2 inhibi- tion assays and histopathological study of the new designed anti-inflammatory agent with a pyrazolopyrimidine core, Bioorg. Chem., 86 (2019) 235–253.
[6] Raz A., Wyche A., Siegel N., Needleman P., Regulation of fibroblast cyclooxygenase synthesis by interleukin-1, J. Biol.Chem., 263 (1988) 263 3022-3028.
[7] Wang C., Chen F., Qian P., Cheng J., Recent advances in the Rh-catalyzed cascade arene C–H bond activation/annulation toward diverse heterocyclic compounds, Org. Biomol. Chem., 19 (2021) 1705-1721.
[8] Mermer A., Keleş T., Şirin Y., Recent studies of nitrogen containing heterocyclic compounds as novelantiviral agents: A review, Bioorg. Chem., 114 (2021) 105076.
[9] Zhu Jun J., Hong-zhi M., Yao L., Chen Y., Sun H., The recent progress of isoxazole in medicinal chemistry, Bioorg. Med. Chem., 26 (2018) 3065–3075.
[10] Scheen A.J., Malaise M., Le medicament du mois.Valdecoxib (Bextra), Rev. Med. Liege, 59 (2004) 251-254.
[11] Erdelyi P., Fodor t., Varga A.K., Czugler M., Gere A., Fischer J., Chemical and biological investigation of N-hydroxy-valdecoxib:An active metabolite of valdecoxib, Bioorg. Med. Chem., 16 (2008) 5322–5330.
[12] Talley J.J., Brown D.L., Carter J.S., Graneto M.J., Koboldt C.M., Masferrer J.L., Perkins W.E., Rogers R.SShaffer A.F., Zhang Y.Y., Zweifel B.S., Seibert K., 4-[5-Methyl-3-phenylisoxazol-4-yl]-benzenesulfonamide, Valdecoxib: A potent and selective Inhibitor of COX-2, J. Med. Chem., 43 (2000), 775-777.
[13] Van De Waterbeemd H., Gifford E., ADMET in silico modelling: towards prediction paradise?, Nat. Rev. Drug Discov., 3 (2003) 192-204.
[14] Borges R. M., Colby S. M., Das S., Edison A. S., Fiehn O., Kind T., Lee J., Merrill A. T., Merz K. M. Jr., Metz T. O., Nunez J. R., Tantillo D. J., Wang L. P., Wang S., Renslow R. S., Quantum chemistry calculations for metabolomics., Chem. Rev., 121 (2021), 5633–5670.
[15] Genç F, Kandemirli S. G., Kandemirli F., Theoretical B3LYP study on electronic structure of contrast agent ıopamidol, Acta Chim. Slov., 68 (2021) 320-331.
[16] Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Scalmani G., Barone V., Petersson G.A., Nakatsuji H., et.al., Gaussian 16 Rev. B.01, Wallingford, CT, 2016.
[17] Dennington R., Keith T.A., Millam J.M., GaussView, Version 6 Semichem Inc., Shawnee Mission, KS. 2016.
[18] Becke A.D., A new mixing of Hartree–Fock and local density‐functional theories, J. Chem. Phys., 98 (1993) 1372–1377.
[19] Lee C., Yang W., Parr R.G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B., 37 (1988) 785–789.
[20] Becke A.D., Density‐functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98 (1993) 5648–5652.
[21] Marenich A.V., Cramer C.J., Truhlar D.G., universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions, J. Phys. Chem. B., 113 (8) (2009) 6378-6396.
[22] Molinspiration Cheminformatics free web services, https://www.molinspiration.com, Slovensky Grob, Slovakia.
[23] Gaillard P., Carrupt P.A., Testa B., Boudon A., Molecular lipophilicity potential, a tool in 3D QSAR: method and applications, J. Comput. Aided Mol. Des., 8 (1994) 83−96.
[24] Koopmans T., Über die zuordnung von wellenfunktionen und eigenwerten zu den einzelnen elektronen eines atoms, Physica, 1(6) (1934) 104-113.
[25] Parr R. G., Pearson R. G.,. Absolute hardness: companion parameter to absolute electronegativity, J. Am. Chem. Soc., 105 (1983) 7512-7516.
[26] Pearson R. G., Absolute electronegativity and hardness correlated with the molecular orbital theory, Proc. Natl. Acad. Sci. U.S.A., 83 (1986) 8440-8441.
[27] Parr R. G., Szentpaly L. V., Liu, S., Electrophilicity Index, J. Am. Chem. Soc., 121 (1999) 1922-1924.
[28] Perdew J. P., Levy M., Physical content of the exact Kohn-Sham orbital energies: band gaps and derivative iscontinuities, Phys. Rev. Lett., 51(20) (1983). 1884-1887.
[29] Perdew J. P., Parr R. G., Levy M., Balduz J. L. Jr., Density functional theory for fractional particle number: derivative discontinuities of the energy, Phys. Rev. Lett., 49 (23) (1982) 1691-1694.
[30] Malathy Sony S. M., Charles P., Ponnuswamya M. N., Yathirajan H. S., Valdecoxib, a non-steroidal anti-inflammatory drug, Acta Cryst., 61 (2005) 108-110.
[31] Kaushal A.M., Chakraborti A.K., Bansal A.K., FTIR Studies on differential ıntermolecular association in crystalline and amorphous states of structurally related non-steroidal anti-ınflammatory drugs, Molecular Pharmaceutıcs, 6 (2008) 937–945.
[32] Sundaraganesan N., Ilakiamani S., Salem H., Wojciechowski P. M., Michalska D., FT-Raman and FT-IR spectra, vibrational assignments and density functional studies of 5-bromo-2-nitropyridine, Spectrochim. Acta A Mol. Biomol. Spectrosc., 61 (2005) 2995–3001.
[33] Arıcı K., Vibrational Spectra of 4-hydroxy-3-cyano-7-chloro-quinoline by density functional theory and ab initio Hartree-Fock Calculations, Int. J. Chem. Technol., 1 (2017) 24-29.
[34] Erdoğan M., Serdaroğlu G., New Hybrid (E)-4-((pyren-1-ylmethylene) amino)-N-(thiazol-2-yl)benzenesulfonamide as a potential drug candidate: Spectroscopy, TD-DFT, NBO, FMO, and MEP studies, ChemistrySelect, 6 (2021) 9369–938.
[35] Fukui K., Role of frontier orbitals in chemical reactions, Science., 218 (1982) 747–754.
[36] Baybas D., Serdaroglu G., Semerci B., The composite microbeads of alginate, carrageenan, gelatin, and poly(lactic-co-glycolic acid): Synthesis, characterization and density functional theory calculations, Int. J. Biol. Macromol., 181 (2021) 322–338.
[37] Sayin K., Üngördü A., Investigations of structural, spectral and electronic properties of enrofloxacin and boron complexes via quantum chemical calculation and molecular docking, Spectrochim. Acta A Mol. Biomol. Spectrosc., 220 (2019)117102.
[38] Brahmia A., Bejaoui L., Rolicek J., Hassen R.B., Serdaroğlu G., Kaya S., Synthesis, crystal structure, Hirshfeld surface analysis and DFT calculations of 2, 2, 2-tribromo-1-(3,5-dibromo-2-hydroxyphenyl)ethanone, J. Mol. Struct., 1248 (2022) 131313.
[39] Blake J. F., Chemoinformatics - predicting the physicochemical properties of ′drug-like′ molecules, Curr. Opin. Biotechnol., 11 (2000) 104-107.
[40] Lipinski C. A. ,Lombardo F., Dominy B. W., Feeney,P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Delivery Rev., 23 (1997) 3-25.
[41] Mulliken R.S., Electron population analysis on LCAO-MO molecular wave functions, J. Chem. Phys., (1955) 1833-1841.
[42] Reed A.E., Weinstock R.B., Weinhold F., Natural atomic orbitals and natural population analysis, J. Chem. Phys., 83 (1985) 735−746.
[43] Weinhold F., Landis C.R., Glendening E.D., What is NBO analysis and how is it useful?, Int. Rev. Phys. Chem., 35 (2016) 399-440.
[44] Reed A.E., Curtiss L.A., Weinhold F., Intermolecular ınteractions from a natural bond orbital, donor-acceptor viewpoint, Chem. Rev., 88(1988) 899-926.
[45] Murray J.S., Politzer P., The electrostatic potential: an overview, Wiley Interdiscip. Rev. Comput. Mol. Sci., 1 (2011) 153-163.

There are 45 citations in total.

Details

Primary Language	English
Journal Section	Natural Sciences
Authors	Sümeyya Serin 0000-0002-4637-1734 Öznur Doğan Ulu 0000-0002-5561-227X
Publication Date	June 29, 2022
Submission Date	March 11, 2022
Acceptance Date	May 27, 2022
Published in Issue	Year 2022

Cite

APA	Serin, S., & Doğan Ulu, Ö. (2022). Quantum Chemical Benchmark Study on Valdecoxib, a Potent and Selective Inhibitor of COX-2, and its Hydroxylated Derivative. Cumhuriyet Science Journal, 43(2), 221-231. https://doi.org/10.17776/csj.1086277

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