Rational Design, Synthesis, and Computational Investigation of Dihydropyridine [2,3-d] Pyrimidines as Polyphenol Oxidase Inhibitors with Improved Potency.

Publisher: Springer Country of Publication: Netherlands NLM ID: 101212092 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1875-8355 (Electronic) Linking ISSN: 15723887 NLM ISO Abbreviation: Protein J Subsets: MEDLINE

Publication: 2005- : Dordrecht : Springer
Original Publication: Dordrecht, The Netherlands ; New York : Kluwer Academic/Plenum, c2004-

Catechol Oxidase*/chemistry ; Catechol Oxidase*/antagonists & inhibitors ; Catechol Oxidase*/metabolism ; Molecular Docking Simulation* ; Drug Design* ; Enzyme Inhibitors*/chemistry ; Enzyme Inhibitors*/pharmacology ; Enzyme Inhibitors*/chemical synthesis ; Pyrimidines*/chemistry; Musa/chemistry ; Musa/enzymology ; Plant Proteins/chemistry ; Plant Proteins/antagonists & inhibitors ; Dihydropyridines/chemistry ; Dihydropyridines/pharmacology ; Structure-Activity Relationship

Polyphenol oxidase (PPO) is an industrially important enzyme associated with browning reactions. In the present study, a set of ten new dihydropyridine [2,3-d] pyrimidines (TD-Hid-1-10) were synthesized and was found to be proven characteristically by ¹ H NMR, ¹³ C NMR, IR, elemental analysis, and assessed as possible PPO inhibitors. PPO was purified from banana using three-phase partitioning, achieving an 18.65-fold purification and 136.47% activity recovery. Enzyme kinetics revealed that the compounds TD-Hid-6 and TD-Hid-7 are to be the most potent inhibitors, exhibiting mixed-type inhibition profile with IC 50 values of 1.14 µM, 5.29 µM respectively against purified PPO enzyme. Electronic structure calculations at the B3LYP/PBE0 level of theories using def-2 SVP, def2-TZVP basis sets with various molecular descriptors characterized the electronic behavior of studied derivatives TD-Hid-1-10. Molecular electrostatic potential (MEP) and reduced density gradient analyses of RDG-NCI provided insights into charge distributions and weak intermolecular interactions. Docking study simulations predicted binding poses within crucial amino acid sequence in the 2y9x enzyme's active site, which is typically similar in sequence to the PPO form is not allowed. Ligands were analysed in terms of binding energies, inhibitor concentrations (mM) and various molecular interactions such as H-bonds, H-carbon, π-carbon, π-sigma, π-sigma, π-π T-shaped, π-π stacked, π-alkyl, Van der Waals and Cu interactions. The lowest binding energy (-7.83 kcal/mol) and the highest inhibitory effect (1.83 mM) were shown by the ligand Td-Hid-6, which forms H-bonds with Met280 and Asn260, exhibits π-sigma interactions with His61 and π-alkyl interactions with Val283. Other ligands also showed different interactions with various amino acids; for example, the Td-Hid-1 ligand formed H-bonds with His244 and showed π-sigma interactions with His244 and Val283.
(© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Zhou L, Liao T, Liu W, Zou L, Liu C, Terefe NS (2020) Inhibitory effects of organic acids on polyphenol oxidase: from model systems to food systems. Crit Rev Food Sci Nutr 60:3594–3621. https://doi.org/10.1080/10408398.2019.1702500. (PMID: 10.1080/10408398.2019.170250031858810)
Sabarre DC, Yagonia-Lobarbio CF (2021) Extraction and characterization of polyphenol oxidase from plant materials: a review. J Appl Biotechnol Rep 8:83–95. https://doi.org/10.30491/JABR.2021.255549.1308. (PMID: 10.30491/JABR.2021.255549.1308)
Tang M, Zhang S, Xiong L, Zhou J, Huang J, Zhao A, Liu Z, Liu A (2023) A comprehensive review of polyphenol oxidase in tea (Camellia sinensis): physiological characteristics, oxidation manufacturing, and biosynthesis of functional constituents. Compr Rev Food Sci 22:2267–2291. https://doi.org/10.1111/1541-4337.13146. (PMID: 10.1111/1541-4337.13146)
Fan X (2023) Chemical inhibition of polyphenol oxidase and cut surface browning of fresh-cut apples. Crit Rev Food Sci Nutr 63:8737–8751. https://doi.org/10.1080/10408398.2022.2061413. (PMID: 10.1080/10408398.2022.206141335416745)
Tilley A, McHenry MP, McHenry JA, Solah V, Bayliss K (2023) Enzymatic browning: the role of substrates in polyphenol oxidase mediated browning. Curr Res Food Sci 7:100623. https://doi.org/10.1016/j.crfs.2023.100623. (PMID: 10.1016/j.crfs.2023.1006233795491510637886)
Zhang S (2023) Recent advances of polyphenol oxidases in plants. Molecules 28:2158. https://doi.org/10.3390/molecules28227517. (PMID: 10.3390/molecules282275173690340310004730)
Arnau J, Lauritzen C, Petersen GE, Pedersen J (2006) Current strategies for the use of affinity tags and tag removal for the purification of recombinant proteins. Protein Expr Purif 48:1–13. https://doi.org/10.1016/j.pep.2005.12.002. (PMID: 10.1016/j.pep.2005.12.00216427311)
Bayrak S, Öztürk C, Demir Y, Alım Z, Küfrevioglu Öİ (2020) Purification of polyphenol oxidase from potato and investigation of the inhibitory effects of phenolic acids on enzyme activity protein. Pept Lett 27:187–192. https://doi.org/10.2174/0929866526666191002142301. (PMID: 10.2174/0929866526666191002142301)
de Carvalho LR, Santos DR, dos Santos Lima CS, Peralta RM, de Souza CGM, Uetanabaro APT, da Silva EGP, da Costa AM (2024) Stable polyphenol oxidase produced by pleurotus pulmonarius from fermented peach-palm and cocoa wastes. Bioenergy Res 17:198–207. https://doi.org/10.1007/s12155-023-10628-0. (PMID: 10.1007/s12155-023-10628-0)
Salehi S, Abdollahi K, Panahi R, Rahmanian N, Shakeri N, Mokhtarani B (2021) Applications of biocatalysts for sustainable oxidation of phenolic pollutants: a review. Sustainability 13:8620. https://doi.org/10.3390/su13158620. (PMID: 10.3390/su13158620)
Kheireddine S, Annabelle C, Noureddine N, Rachida M, Mahmoud A, Abdeltif A (2022) Peroxidase enzymes as green catalysts for bioremediation and biotechnological applications: a review. Sci Total Environ 806(2):150500. https://doi.org/10.1016/j.scitotenv.2021.150500. (PMID: 10.1016/j.scitotenv.2021.150500)
Gagaoua M, Hafid K (2016) Three phase partitioning system, an emerging non-chromatographic tool for proteolytic enzymes recovery and purification. Biosens J 5:1. https://doi.org/10.4172/2090-4967.1000134. (PMID: 10.4172/2090-4967.1000134)
Dennison C, Lovrien R (1997) Three phase partitioning: concentration and purification of proteins. Protein Expr Purif 11:149–161. https://doi.org/10.1006/prep.1997.0779. (PMID: 10.1006/prep.1997.07799367811)
Chaiwut P, Pintathong P, Rawdkuen S (2010) Extraction and three-phase partitioning behavior of proteases from papaya peels. Process Biochem 45:1172–1175. https://doi.org/10.1016/j.procbio.2010.03.019. (PMID: 10.1016/j.procbio.2010.03.019)
Yan JK, Wang YY, Qiu WY, Ma H, Wang ZB, Wu JY (2018) Three-phase partitioning as an elegant and versatile platform applied to nonchromatographic bioseparation processes. Crit Rev Food Sci Nutr 58:2416–2431. https://doi.org/10.1080/10408398.2017.1327418. (PMID: 10.1080/10408398.2017.132741828609145)
Dennison C, Rex L (1997) Three phase partitioning: concentration and purification of proteins. Protein Exp Purif 11:149–161. https://doi.org/10.1006/prep.1997.0779. (PMID: 10.1006/prep.1997.0779)
Mohammed G, Nawel B, Amel B, Ferhat Z, Sabrina N, Kahina H, Hiba-Ryma B (2014) Three-phase partitioning as an efficient method for the purification and recovery of ficin from Mediterranean fig (Ficus carica L.) latex, separation and Purification Technology,volume 132: 461–467. https://doi.org/10.1016/j.seppur.2014.05.050.
Huang X, Su J, Rao AU, Tang H, Zhou W, Zhu X, Chen X, Liu Z, Huang Y, Degrado S, Xiao D, Qin J, Aslanian R, McKittrick BA, Greenfeder S, van Heek M, Chintala M, Palani A (2012) SAR studies of C2 ethers of 2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones as nicotinic acid receptor (NAR) agonist. Bioorg Med Chem Lett 22:854–858. https://doi.org/10.1016/j.bmcl.2011.12.041. (PMID: 10.1016/j.bmcl.2011.12.04122209457)
Abdelghani E, Said SA, Assy MG, Hamid AMA (2017) Synthesis and antimicrobial evaluation of some new pyrimidines and condensed pyrimidines. Arab J Chem 10:2926–2933. https://doi.org/10.1016/j.arabjc.2013.11.025. (PMID: 10.1016/j.arabjc.2013.11.025)
Grivsky EM, Lee S, Sigel CW, Duch DS, Nichol CA (1980) Synthesis and antitumor activity of 2,4-diamino-6-(2,5-dimethoxybenzyl)-5-methylpyrido[2,3-d]pyrimidine. J Med Chem 23:327–329. https://doi.org/10.1021/jm00177a025. (PMID: 10.1021/jm00177a0256928967)
Krall RL, Penry JK, White BG, Kupferberg HJ, Swinyard EA (1978) Swinyard, antiepileptic drug development: II. Anticonvulsant drug screening. Epilepsia 19:409–428. https://doi.org/10.1111/j.1528-1157.1978.tb04507.x. (PMID: 10.1111/j.1528-1157.1978.tb04507.x699894)
Piaz VD, Castellana MC, Vergelli C, Giovannoni MP, Gavaldà A, Segarra V, Beleta J, Ryder H, Palacios JM (2002) Synthesis and evaluation of some pyrazolo[3,4-d]pyridazinones and analogues as pde 5 ınhibitors potentially useful as peripheral vasodilator agents. J Enzyme Inhib Med Chem 17:227–233. https://doi.org/10.1080/1475636021000008494. (PMID: 10.1080/1475636021000008494)
Mohamed SF, Abd-Elghaffar HS, Amr AEGE, Elnaggar DH, Abou-Amra ES, Hosny HM, Mohamed AM, Abd El-Shafy DN (2023) New poly heterocyclic compounds based on pyrimidine-2-thiones: synthesis, evaluation of putative antiviral agents, DFT calculation, and molecular modeling. J Mol Struct 1291:136083. https://doi.org/10.1016/j.molstruc.2023.136083. (PMID: 10.1016/j.molstruc.2023.136083)
Alsharif A, Allahyani M, Aljuaid A, Alsaiari AA, Almehmadi MM, Asif M (2023) Diverse pharmacological potential of various substituted pyrimidine derivatives. Curr Org Chem 27:1779–1798. https://doi.org/10.2174/0113852728266665231101112129. (PMID: 10.2174/0113852728266665231101112129)
Kumar S, Deep A, Narasimhan B (2019) A review on synthesis, anticancer and antiviral potentials of pyrimidine derivatives. Curr Bioact Compd 15:289–303. https://doi.org/10.2174/1573407214666180124160405. (PMID: 10.2174/1573407214666180124160405)
de Jesus Rivas N, Whitaker JR (1973) Purification and some properties of two polyphenol oxidases from bartlett pears. Plant Physiol 52:501–507. https://doi.org/10.1104/pp.52.5.501. (PMID: 10.1104/pp.52.5.50116658592366532)
Dong L, He L, Huo D (2020) Three phase partitioning as a rapid and efficient method for purification of plant-esterase from wheat flour. Pol J Chem Technol 22:42–49. https://doi.org/10.2478/pjct-2020-0015. (PMID: 10.2478/pjct-2020-0015)
Flurkey WH (1986) Polyphenoloxidase in higher plants. Plant Physiol 81:614–618. https://doi.org/10.1104/pp.81.2.614. (PMID: 10.1104/pp.81.2.614166648651075386)
Bradford M (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254. https://doi.org/10.1006/abio.1976.9999. (PMID: 10.1006/abio.1976.9999942051)
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685. https://doi.org/10.1038/227680a0. (PMID: 10.1038/227680a05432063)
Spector T (1978) Refinement of the Coomassie blue method of protein quantitation. Anal Biochem 86:142–146. https://doi.org/10.1016/0003-2697(78)90327-5. (PMID: 10.1016/0003-2697(78)90327-5655375)
Sedmak JJ, Grossberg SE (1977) A rapid, sensitive, and versatile assay for protein using Coomassie brilliant blue G250. Anal Biochem 79:544–552. https://doi.org/10.1016/0003-2697(77)90428-6. (PMID: 10.1016/0003-2697(77)90428-668686)
Eissa HA, Fadel HHM, Ibrahim GE, Hassan IM, Elrashid AA (2006) Thiol containing compounds as controlling agents of enzymatic browning in some apple products. F Res Int 39:855–863. https://doi.org/10.1016/j.foodres.2006.04.004. (PMID: 10.1016/j.foodres.2006.04.004)
Neese F (2022) Software update: the < scp > ORCA program system—version 5.0, WIREs. Comput Mol Sci 12. https://doi.org/10.1002/wcms.1606.
Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98:5648–5652. https://doi.org/10.1063/1.464913. (PMID: 10.1063/1.464913)
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. https://doi.org/10.1103/PhysRevB.37.785. (PMID: 10.1103/PhysRevB.37.785)
Stephens PC, Devlin FJ, Chabalowski CF, Frisch MJ (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J Phys Chem 98:11623–11627. https://doi.org/10.1021/j100096a001. (PMID: 10.1021/j100096a001)
Vosko SH, Wilk L, Nusair M (1980) Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can J Phys 58:1200–1211. https://doi.org/10.1139/p80-159. (PMID: 10.1139/p80-159)
Weigend F (2006) Accurate coulomb-fitting basis sets for H to Rn. Phys Chem Chem Phys 8:1057. https://doi.org/10.1039/b515623h. (PMID: 10.1039/b515623h16633586)
Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001. https://doi.org/10.1021/jp9716997. (PMID: 10.1021/jp9716997)
Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010) Revealing noncovalent interactions. J Am Chem Soc 132:6498–6506. https://doi.org/10.1021/ja100936w. (PMID: 10.1021/ja100936w203944282864795)
Lu T, Chen F (2012) A multifunctional wavefunction analyser. J Comput Chem 33:580–592. https://doi.org/10.1002/jcc.22885. (PMID: 10.1002/jcc.2288522162017)
Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38. https://doi.org/10.1016/0263-7855(96)00018-5. (PMID: 10.1016/0263-7855(96)00018-58744570)
Hanwell MD, Curtis DE, Lonie DC, Vandermeersch T, Zurek E, Hutchison GR (2012) Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform 4:17. https://doi.org/10.1186/1758-2946-4-17. (PMID: 10.1186/1758-2946-4-17228893323542060)
Cornell T, Hutchison (2018) GR Avogadro Chemistry; Last modified July 24.
Eybek A, Kaya MO, Güleç Ö, Demirci T, Musatat AB, Özdemir O, Öner MNK, Kaya Y, Arslan M (2024) Bovine carbonic anhydrase (bCA) inhibitors: synthesis, molecular docking and theoretical studies of bisoxadiazole-substituted sulfonamide derivatives. Int J Biol Macromol 267:1. https://doi.org/10.1016/j.ijbiomac.2024.131489. (PMID: 10.1016/j.ijbiomac.2024.131489)
Musatat AB, Atahan A, Ergün A, Çıkrıkcı K, Gençer N, Arslan O, Zengin M (2023) Synthesis, enzyme inhibition, and molecular docking studies of a novel chalcone series bearing benzothiazole scaffold. Biotechnol Appl Biochem 70:1357–1370. https://doi.org/10.1002/bab.2445. (PMID: 10.1002/bab.244536722438)
Musatat AB, Kılıçcıoğlu İ, Kurman Y, Dülger G, Alpay M, Yağcı R, Atahan A, Durmuş S (2023) Antimicrobial, antiproliferative effects and docking studies of methoxy group enriched coumarin-chalcone hybrids. Chem Biodivers e 202200973. https://doi.org/10.1002/cbdv.202200973.
Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and develop- ment settings. Adv Drug Delivery Rev 23:3–25. https://doi.org/10.1016/S0169-409X(96)00423-1. (PMID: 10.1016/S0169-409X(96)00423-1)
Muegge I, Heald SL, Brittelli D (2001) Simple selection criteria for drug-like chemical matter. J Med Chem 44:1841–1846. https://doi.org/10.1021/jm015507e. (PMID: 10.1021/jm015507e11384230)
Egan WJ, Merz KM, Baldwin JJ (2000) Prediction of drug absorption using multivariate statistics. J Med Chem 43:3867–3877. https://doi.org/10.1021/jm000292e. (PMID: 10.1021/jm000292e11052792)
Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1.A. qualitative and quantitative characterization of known drug databases. J Comb Chem 1:55–68. https://doi.org/10.1021/cc9800071. (PMID: 10.1021/cc980007110746014)
Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717. https://doi.org/10.1038/srep42717. (PMID: 10.1038/srep42717282565165335600)
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AS (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785–2791. https://doi.org/10.1002/jcc.21256. (PMID: 10.1002/jcc.21256193997802760638)
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33. https://doi.org/10.1186/1758-2946-3-33. (PMID: 10.1186/1758-2946-3-33219823003198950)
Iraji A, Adelpour T, Edraki N, Khoshneviszadeh M, Miri R, Khoshneviszadeh M (2020) Synthesis, biological evaluation and molecular docking analysis of aniline–benzylidenehydrazine hybrids as potent tyrosinase inhibitors. BMC Chem 14:28. https://doi.org/10.1186/s13065-020-00679-1. (PMID: 10.1186/s13065-020-00679-1322809497137441)
Ismaya WT, Rozeboom HJ, Weijn A, Mes JJ, Fusetti F, Wichers HJ, Dijkstra B (2011) Crystal structure of Agaricus Bisporus mushroom tyrosinase: identity of the tetramer subunits and ınteraction with tropolone. Biochemistry 50:5477–5486. https://doi.org/10.1021/bi200395t. (PMID: 10.1021/bi200395t21598903)
Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—A visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612. https://doi.org/10.1002/jcc.20084. (PMID: 10.1002/jcc.2008415264254)
Biovia M, Discovery Studio Client version 20.1.0.19295, Biovia Discovery Studio Visualizer, Dassault Systèmes Corporate, Waltham, MA, USA., n.d.
Panadare D, Rathod VK (2018) Extraction and purification of polyphenol oxidase: a review. Biocatal Agric Biotechnol 14:431–437. https://doi.org/10.1016/j.bcab.2018.03.010. (PMID: 10.1016/j.bcab.2018.03.010)
Öztürk C, Aksoy M, Küfrevioğlu Öİ (2020) Purification of tea leaf (Camellia sinensis) polyphenol oxidase by using affinity chromatography and investigation of its kinetic properties. J Food Meas Charact 14:31–38. (PMID: 10.1007/s11694-019-00264-8)
Benaceur F, Gouzi H, Meddah B, Neifar A, Guergouri A (2019) Purification and characterization of catechol oxidase from Tadela (Phoenix dactylifera L.) date fruit. Int J Biol Macromol 125:1248–1256. https://doi.org/10.1016/j.ijbiomac.2018.09.101. (PMID: 10.1016/j.ijbiomac.2018.09.10130236755)
Sharma A, Gupta MN (2001) Three phase partitioning as a large-scale separation method for purification of a wheat germ bifunctional protease/amylase inhibitor. Process Biochem 37:193–196. https://doi.org/10.1016/S0032-9592(01)00199-6. (PMID: 10.1016/S0032-9592(01)00199-6)
Delaney JS (2004) ESOL: estimating aqueous solubility directly from molecular structure. J Chem Inf Comput Sci 44:1000–1005. https://doi.org/10.1021/ci034243x. (PMID: 10.1021/ci034243x15154768)
Alıcı EH, Arabacı G (2016) Purification of polyphenol oxidase from borage (Trachystemon Orientalis L.) by using three-phase partitioning and investigation of kinetic properties. Int J Biol Macromol 93:1051–1056. https://doi.org/10.1016/j.ijbiomac.2016.09.070. (PMID: 10.1016/j.ijbiomac.2016.09.07027664922)
Veisi H, Maleki A, Farokhzad Y (2017) Electron as potential and green catalyst in the multicomponent synthesis of pyrano[2,3-d]pyrimidine derivatives. Iran Chem Commun 5:217–226. http://icc.journals.pnu.ac.ir.
Yüzügüllü Karakus Y, Yıldırım B, Acemi A (2021) Characterization of polyphenol oxidase from fennel (Foeniculum vulgare Mill.) Seeds as a promising source. Int J Biol Macromol 170:261–271. https://doi.org/10.1016/j.ijbiomac.2020.12.147. (PMID: 10.1016/j.ijbiomac.2020.12.14733359609)

(2012-02-04-033/2016-50-02-002) This work was supported by the Research Fund of Sakarya University

Keywords: 1,4-Dihydropyridine; DFT; Molecular Docking; Molecular Electronic Potential; Polyphenol Oxidase

EC 1.10.3.1 (Catechol Oxidase)
0 (Enzyme Inhibitors)
0 (Pyrimidines)
0 (Plant Proteins)
0 (Dihydropyridines)

Date Created: 20240804 Date Completed: 20240825 Latest Revision: 20240825

20240826

10.1007/s10930-024-10220-1

39097848