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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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Ali K, Mishra P, Kumar A, Reddy DN, Chowdhury S, Panda G. Reactivity vs. selectivity of quinone methides: synthesis of pharmaceutically important molecules, toxicity and biological applications. Chem Commun (Camb) 2022; 58:6160-6175. [PMID: 35522910 DOI: 10.1039/d2cc00838f] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Quinone methides (QMs) are considered to be highly reactive intermediates because of their aromatization both in chemical and biological systems. Being highly accessible, quinone methides (QMs) have been widely exploited and their concurrent use has been manifested for the synthesis of tertiary and quaternary carbon centers of bioactives, drugs and drug-like molecules. In this feature article, the synthetic routes, structure-reactivity relationships and synthetic applications of quinone methides are discussed. Formation of the intermediates during bioactivation of different chemical entities and possible chemical manifestations leading to their toxicity in biological systems are also covered.
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Affiliation(s)
- Kasim Ali
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
| | - Prajjval Mishra
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Awnish Kumar
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Damodara N Reddy
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
| | - Sushobhan Chowdhury
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India.
| | - Gautam Panda
- Medicinal & Process Chemistry Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Sector 10, Lucknow 226031, UP, India. .,Academy of Scientific & Industrial Research (AcSIR), Ghaziabad, Uttar Pradesh-201 002, India
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Erben A, Sviben I, Mihaljević B, Piantanida I, Basarić N. Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment. Molecules 2021; 26:molecules26144315. [PMID: 34299591 PMCID: PMC8306964 DOI: 10.3390/molecules26144315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.
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Affiliation(s)
- Antonija Erben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Igor Sviben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Branka Mihaljević
- Department of Material Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
- Correspondence:
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Pérez-Ruiz R, Molins-Molina O, Lence E, González-Bello C, Miranda MA, Jiménez MC. Photogeneration of Quinone Methides as Latent Electrophiles for Lysine Targeting. J Org Chem 2018; 83:13019-13029. [PMID: 30274513 DOI: 10.1021/acs.joc.8b01559] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Latent electrophiles are nowadays very attractive chemical entities for drug discovery, as they are unreactive unless activated upon binding with the specific target. In this work, the utility of 4-trifluoromethyl phenols as precursors of latent electrophiles, quinone methides (QM), for lysine-targeting is demonstrated. These Michael acceptors were photogenerated for specific covalent modification of lysine residues using human serum albumin (HSA) as a model target. The reactive QM-type intermediates I or II, generated upon irradiation of 4-trifluoromethyl-1-naphthol (1)@HSA or 4-(4-trifluorometylphenyl)phenol (2)@HSA complexes, exhibited chemoselective reactivity toward lysine residues leading to amide adducts, which was confirmed by proteomic analysis. For ligand 1, the covalent modification of residues Lys106 and Lys414 (located in subdomains IA and IIIA, respectively) was observed, whereas for ligand 2, the modification of Lys195 (in subdomain IIA) took place. Docking and molecular dynamics simulation studies provided an insight into the molecular basis of the selectivity of 1 and 2 for these HSA subdomains and the covalent modification mechanism. These studies open the opportunity of performing protein silencing by generating reactive ligands under very mild conditions (irradiation) for specific covalent modification of hidden lysine residues.
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Affiliation(s)
- Raúl Pérez-Ruiz
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain.,Photoactivated Processes Unit , IMDEA Energy Institute , Av. Ramón de la Sagra 3 , 28935 Móstoles, Madrid , Spain
| | - Oscar Molins-Molina
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica , Universidade de Santiago de Compostela , Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica , Universidade de Santiago de Compostela , Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Miguel A Miranda
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
| | - M Consuelo Jiménez
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
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Yang Y, Ma Y, Zhao Y, Zhao Y, Li Y. Theoretical Investigation of the Reaction Mechanism of Photodeamination Induced by Excited-State Intramolecular Proton Transfer of Cresol Derivatives. J Phys Chem A 2018; 122:1011-1018. [DOI: 10.1021/acs.jpca.7b11571] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yunfan Yang
- Department of Physics, Liaoning University, Shenyang 110036, P. R. China
- State Key Laboratory of Molecular Reaction
Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yanzhen Ma
- Department of Physics, Liaoning University, Shenyang 110036, P. R. China
| | - Yu Zhao
- Department of Physics, Liaoning University, Shenyang 110036, P. R. China
| | - Yanliang Zhao
- School of Physics and Optoelectronics Engineering, Ludong University, Yantai 264025, P. R. China
| | - Yongqing Li
- Department of Physics, Liaoning University, Shenyang 110036, P. R. China
- State Key Laboratory of Molecular Reaction
Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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