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El Hage K, Ribaudo G, Lagardère L, Ongaro A, Kahn PH, Demange L, Piquemal JP, Zagotto G, Gresh N. Targeting the Major Groove of the Palindromic d(GGCGCC) 2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. J Chem Inf Model 2022; 62:6649-6666. [PMID: 35895094 DOI: 10.1021/acs.jcim.2c00337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)2 sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O6/N7 of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N9-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C1G2G3G4C5G6C7C8C9G10)2. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.
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Affiliation(s)
- Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91000 Evry, France
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | - Louis Lagardère
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
| | - Alberto Ongaro
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | | | - Luc Demange
- Université Paris Cité, CiTCoM, UMR 8038 CNRS, 75006 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France.,The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas 78705, United States
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo, 35131 Padova, Italy
| | - Nohad Gresh
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
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Ongaro A, Ribaudo G, Braud E, Ethève-Quelquejeu M, De Franco M, Garbay C, Demange L, Gresh N, Zagotto G. Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) 2palindromic sequence. NEW J CHEM 2020. [DOI: 10.1039/c9nj03817e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of a peptide derivative of antitumor anthraquinones, designed to target GC-rich palindromic sequences. It has micromolar activities on three cancer cell lines and is fifty times less toxic than mitoxantrone on a healthy line.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Christiane Garbay
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Luc Demange
- Université de Paris
- CiTCoM
- UMR 8038 CNRS
- Faculté de Pharmacie
- F-75006 Paris
| | - Nohad Gresh
- Laboratoire de Chimie Théorique
- UMR 7616 CNRS
- Sorbonne Université
- Paris
- France
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
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Molecular Modeling Study of Interaction of Anthracenedione Class of Drug Mitoxantrone and Its Analogs with DNA Tetrameric Sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 696:385-400. [DOI: 10.1007/978-1-4419-7046-6_39] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Gianoncelli A, Basili S, Scalabrin M, Sosic A, Moro S, Zagotto G, Palumbo M, Gresh N, Gatto B. Rational Design, Synthesis, and DNA Binding Properties of Novel Sequence-Selective Peptidyl Congeners of Ametantrone. ChemMedChem 2010; 5:1080-91. [DOI: 10.1002/cmdc.201000106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Synthesis, DNA binding, and cytotoxicity of 1,4-bis(2-amino-ethylamino)anthraquinone–amino acid conjugates. Bioorg Med Chem 2008; 16:1006-14. [DOI: 10.1016/j.bmc.2007.10.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 10/01/2007] [Accepted: 10/04/2007] [Indexed: 11/23/2022]
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Gresh N, Perrée-Fauvet M. Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: a molecular mechanics investigation. J Comput Aided Mol Des 1999; 13:123-37. [PMID: 10091119 DOI: 10.1023/a:1008033219724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7 belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N-methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.
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Affiliation(s)
- N Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, CNRS-URA 1500, INSERM U266, Université Paris 5, France
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Takenaka S, Itakura Y, Kondo H. Control of the DNA-Binding Specificity of 9,10-Anthraquinone by the Nature and Positions of Substituents. Supramol Chem 1998. [DOI: 10.1080/10610279808034968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gatto B, Zagotto G, Sissi C, Palumbo M. Preferred interaction of D-peptidyl-anthraquinones with double-stranded B-DNA. Int J Biol Macromol 1997; 21:319-26. [PMID: 9493055 DOI: 10.1016/s0141-8130(97)00076-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The quest for more specific drugs in antitumor chemotherapy led us to the design of anthraquinone-peptide conjugates capable of selective recognition of the nucleic acid. We present here the DNA binding characteristics, sequence specificity and geometry of interaction of a pair of enantiomers containing the lysine-glycine dipeptide in the side chains. The D enantiomer binds right handed double stranded DNA more efficiently than the L form under all conditions tested. The source of higher binding affinity is not electrostatic in nature and rests in the more favorable hydrophobic contacts of the D-lysyl side chains in the drug-DNA complex. Both derivatives exhibit preference for alternating GC base sequences and intercalate into DNA in a threading mode as suggested by chiroptical and theoretical studies. The D enantiomer, being a peptidyl derivative that contains a non-natural amino acid, has the considerable advantage of being less susceptible to enzymatic hydrolysis and could therefore represent a lead compound for further development.
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Affiliation(s)
- B Gatto
- Department of Pharmaceutical Sciences, University of Padova, Italy
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Gresh N. Can a polyproline II helical motif be used in the context of sequence-selective major groove recognition of B-DNA? A molecular modelling investigation. J Biomol Struct Dyn 1996; 14:255-73. [PMID: 8913863 DOI: 10.1080/07391102.1996.10508117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Proline-rich peptides are known to adopt preferentially the extended polyproline II (PPII) helical conformation, which is involved in several protein-protein recognition events. By resorting to molecular modelling techniques, we wished to investigate the extent to which PPII helices could be used for the formation of isochelical peptide-DNA complexes leading to the selective recognition of the major groove of B-DNA. For that purpose, we have grafted to a cationic intercalator, 9-amino-acridine, an oligopeptide having the sequence: Pro- Arg-Pro-Pro-Arg-Pro-Pro-Arg-Pro-Pro-Asp-Pro-Pro. Each residue in the sequence was set in the D configuration, to prevent enzymatic hydrolysis, and each Arg residue was designed to target O6/N7 of a guanine base following the intercalation site. The Asp residue was designed to target a cytosine base, whilst simultaneously forming a bidentate complex with the Arg three residues upstream. Energy-minimization, using the JUMNA procedure, led to the following conclusions : 1) major groove binding is favoured over minor groove or exclusive binding to the phosphates by large energy differences, of over 50 and 90 kcal/mole, respectively: 2) the two best bound sequences are those having three successive guanine bases on the same DNA strand, immediately adjacent to the intercalation site. Sequence d(CGGGC G), encountered in the Primer Binding Site of the HIV retrovirus, thus ranks amongst the best-bound sequences; 3) replacement of an individual guanine amongst the three ones upstream of the intercalation site, by an adenine base, weakens by > 6 kcal/mole the binding energetics; 4) the conformational rigidity of the DNA-bound PPII helix should enable for a modulation of the base sequence selectivity, by appropriate replacements of the Arg and Asp residues. Thus sequence CGGCAAG, also encountered in the HIV genome, could be targeted by an oligopeptide having the sequence Pro-Arg-Pro-Pro-Asp-Pro-Pro-Asn-Pro-Pro-Asn-Pro-Pro-Arg-Ala.
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Affiliation(s)
- N Gresh
- Département de Pharmacochimie Moléculaire et Structurale U266 INSERM - URA D1500 CNRS UFR des Sciences Pharmaceutiques et Biologiques, Faculté de Pharmacie, Paris, France
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Routier S, Cotelle N, Catteau JP, Bernier JL, Waring MJ, Riou JF, Bailly C. Salen-anthraquinone conjugates. Synthesis, DNA-binding and cleaving properties, effects on topoisomerases and cytotoxicity. Bioorg Med Chem 1996; 4:1185-96. [PMID: 8879539 DOI: 10.1016/0968-0896(96)00082-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A series of amidoethylamino-anthraquinone derivatives bearing either one or two salen (bis(salicylidene)ethylenediamine) moieties complexed with CuII or NiII have been synthesized, and their DNA-binding and cleaving properties examined. The effects of the mono- and di-substituted anthracenedione-salen conjugates on DNA cleavage mediated by topoisomerases I and II have also been determined, as well as their cytotoxicity toward human KB cells. The anthraquinone-salen. NiII conjugates bind to GC-rich sequences in DNA, but do not cleave the macromolecule. By contrast, the anthraquinone-salen. CuII hybrids do not recognize particular nucleotide sequences but efficiently induce single-strand breaks in DNA after activation. The 5,8-dihydroxy-anthraquinone conjugates are more cytotoxic and more potent toward topoisomerase II than the non-hydroxylated analogues, but they are less cytotoxic than the salen-free anthraquinones. The attachment of a salen. CuII complex to the anthraquinone chromophore can confer DNA cleaving properties in vitro, but this is at the expense of cytotoxic activity. Anthraquinone-salen. CuII complexes may find useful employ as footprinting probes for investigating ligand-DNA interactions.
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Affiliation(s)
- S Routier
- Laboratoire de Chimie Organique Physique, URA CNRS 351, Villeneuve d'Ascq, France
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Perrée-Fauvet M, Gresh N. Molecular modelling and chemical synthesis of a bisarginyl derivative of a tricationic porphyrin designed to target the major groove of DNA. Tetrahedron Lett 1995. [DOI: 10.1016/0040-4039(95)00705-h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Gresh N, René B, Hui XW, Barsi MC, Roques BP, Garbay C. Theoretical Design, Chemical Synthesis and Footprinting Analysis of a Novel Peptide Derivative of the Intercalator 7-H Pyridocarbazole Targeted Towards the Major Groove of DNA. J Biomol Struct Dyn 1994; 12:91-110. [DOI: 10.1080/07391102.1994.10508090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Perrée-Fauvet M, Gresh N. Structure and energetics in the complexes of a double-stranded B-DNA dodecamer with netropsin derivatives of a tricationic water-soluble porphyrin: a theoretical investigation. J Biomol Struct Dyn 1994; 11:1203-24. [PMID: 7946070 DOI: 10.1080/07391102.1994.10508064] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The structural and energetical characteristics of the complexes formed between two auto-complementary DNA dodecamers, d(CGCGAATTCGCG)2, and d(GCGCAATTGCGC)2, and two novel netropsin (I) and glycine-netropsin (II) conjugates of a tricationic water-soluble porphyrin are investigated in detail by means of theoretical computations. This study was prompted by the successful chemical synthesis of II, which was recently reported (Anneheim-Herbelin, G., Perrée-Fauvet, M., Gaudemer, A., Hélissey, P., Giorgi-Renault, S. and Gresh, N., Tetrahedron Lett. 34, 7263 (1993)). The results indicate that: a) Intercalative binding of II does not entail significant distortions of the DNA backbone, and the Net moiety can bind tightly to the core of the minor groove. b) Intercalative binding of I is computed to energetically weaker than that of II. This is a consequence of the reduced length of the oligopeptide arm, such that the terminal propionamidinium group interacts less favorably with the fourth A-T base-pair than is the case with II. c) Nonintercalative binding of II produces considerable conformational distortions of the DNA. These results in a break of the DNA axis in between the fourth and the fifth base-pairs, namely, at the level where the long axis of the chromophore and of the oligopeptide intersect.
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Affiliation(s)
- M Perrée-Fauvet
- Laboratoire de Chimie Bioorganique et Bioinorganique associé au CNRS, Institut de Chimie Moléculaire d'Orsay, Université de Paris-Sud, France
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Hui X, Gresh N. Theoretical design of a bis-orthopepetide derivative of a tetracationic porphyrin targeted toward a six-base pair sequence of DNA. J Biomol Struct Dyn 1993; 11:333-44. [PMID: 8286060 DOI: 10.1080/07391102.1993.10508730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Tetra-(4-N-methylpyridyl)-porphyrin, (T4MPyP), is a tetracationic porphyrin that binds to G-C sequences of DNA by means of an intercalative mode. In order to extend its selective sequence recognition capacity for bases beyond the intercalation site, and in the major groove, we have undertaken the theoretical design of bis-ortho peptide derivatives of T4MPyP. In these, two ortho N-methylpiperidinium nitrogens are linked to a cationic residue, L-Lys, L-Orn, or L-Arg. The binding energetics of these novel compounds were compared for six distinct double-stranded palindromic hexanucleotide sequences. Four distinct modes of binding were compared: a) major, b) minor groove binding of both peptidic arms; c) a straddling mode in which each arm is in a different groove of DNA; d) exclusive binding of the arms to the sugar-phosphate backbone. For our most promising compound, that with Lys side-chains, a distinctive energetical advantage was computed in favor of an all-major groove binding to sequence d(CCCGGG)2. The corresponding complex is separated by an energy gap of 12 kcal/mol, with respect to the second-best sequence bound in the major groove, d(GGCGCC)2, and of 20 kcal/mol with respect to minor groove binding to sequence d(TACGTA)2. The results obtained with such a prototypic compound indicate that it is fully possible to design sequence selective (> 6 base-pairs) photosensitizers as peptide derivatives of T4MPyP and prompt the engineering of further, more complex analogs thereof.
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Affiliation(s)
- X Hui
- Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Paris, France
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Gresh N, Kahn PH. Theoretical design of a bistetrapeptide derivative of mitoxantrone targeted towards the double-stranded hexanucleotide sequence d(GGCGCC)2. J Biomol Struct Dyn 1991; 8:827-46. [PMID: 2059342 DOI: 10.1080/07391102.1991.10507848] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The hexanucleotide d(GGCGCC)2 is encountered in recurrent fashion within transcriptional activating sequences in retroviruses and protooncogenes. Our first theoretical design of novel oligopeptide derivatives of mitoxantrone, MTX (1), had enabled us to predict derivatives depsiGly-Lys(L) and depsiGly-Gly-Orn(D) to preferentially target the tetrameric core d(CCGG)2. Owing to the crucial importance of hexamer d(GGCGCC)2, we have attempted to extend the realm of our approach by now targeting this specific hexanucleotide. For that purpose, we undertook the design of further oligopeptide derivatives of MTX, in which each arm was identically amidated (rather than esterified as in (1)) by tri- or tetrapeptides of varying sequences and individual residue configurations. The binding affinities of these derivatives to the palindromic sequences d(GGCGCC)2, d(CGCGCG)2, d(GCCGGC)2 and d(CCCGGG)2, were compared by energy-minimization. We report here the results obtained with the most promising derivative, having the sequence Arg(L)-Gly-Val(L)-Glu(L), and displaying a considerable energy preference for d(GGCGCC)2 over the other candidate hexameric sites (referred to as I). In the corresponding complexes, the two arms are in two mutually antiparallel directions in the major groove, and adopt a beta-sheet like arrangement stabilized by two H-bonds involving the carbonyl and amide groups of the Gly residues. Each Arg side chain on a given arm chelates O6 and N7 atoms of G1, G2/G1', G2' with its imino and cis amino hydrogen, and is simultaneously bound through two amino hydrogens in a bidentate interaction with the Glu residue.
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Affiliation(s)
- N Gresh
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France
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