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Baeriswyl S, Javor S, Stocker A, Darbre T, Reymond J. X‐Ray Crystal Structure of a Second‐Generation Peptide Dendrimer in Complex with
Pseudomonas aeruginosa
Lectin LecB. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Stéphane Baeriswyl
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Sacha Javor
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Achim Stocker
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Tamis Darbre
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
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2
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Dereven’kov IA, Tsaba LV, Pokrovskaya EA, Makarov SV. Studies on the interaction of aquacobalamin with cysteinesulfinic and cysteic acids, hypotaurine and taurine. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1515927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ilia A. Dereven’kov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - Lubov V. Tsaba
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - Elizaveta A. Pokrovskaya
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
| | - Sergei V. Makarov
- Department of Food Chemistry, Ivanovo State University of Chemistry and Technology, Ivanovo, Russian Federation
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3
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Filipe LCS, Machuqueiro M, Darbre T, Baptista AM. Exploring the Structural Properties of Positively Charged Peptide Dendrimers. J Phys Chem B 2016; 120:11323-11330. [PMID: 27739676 DOI: 10.1021/acs.jpcb.6b09156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report a combined experimental and computational approach to study the structural behavior of positively charged peptide dendrimers. Third-generation dendrimers containing combinations of positive/neutral amino acid residues in the different dendrimer generations were synthesized and their overall size evaluated using diffusion NMR. Molecular dynamics simulations were performed to obtain a comprehensive description of the molecular-level phenomena substantiating the structural differences observed. Comparison of the results presented with previous findings reveals a striking charge-dependent tendency in these systems, where the simple number and placement of charged amino acids in the sequence allows an extensive control over the exhibited structural features. Indeed, we observe that peptide dendrimers bearing progressively higher amounts of charged residues are characterized by an increasing structural plasticity, with a myriad of conformational states equally accessible to them. On the other hand, dendrimers containing only small amounts of charged residues evidence, to some extent, a characteristic structural rigidity.
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Affiliation(s)
- Luís C S Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - António M Baptista
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, EAN, 2780-157 Oeiras, Portugal
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4
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Filipe LCS, Campos SRR, Machuqueiro M, Darbre T, Baptista AM. Structuring Peptide Dendrimers through pH Modulation and Substrate Binding. J Phys Chem B 2016; 120:10138-10152. [DOI: 10.1021/acs.jpcb.6b05905] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Luís C. S. Filipe
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Sara R. R. Campos
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Tamis Darbre
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, 3012 Bern, Switzerland
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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Stach M, Siriwardena TN, Köhler T, van Delden C, Darbre T, Reymond JL. Combining topology and sequence design for the discovery of potent antimicrobial peptide dendrimers against multidrug-resistant Pseudomonas aeruginosa. Angew Chem Int Ed Engl 2014; 53:12827-31. [PMID: 25346278 DOI: 10.1002/anie.201409270] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Indexed: 11/07/2022]
Abstract
Multidrug-resistant opportunistic bacteria, such as Pseudomonas aeruginosa, represent a major public health threat. Antimicrobial peptides (AMPs) and related peptidomimetic systems offer an attractive opportunity to control these pathogens. AMP dendrimers (AMPDs) with high activity against multidrug-resistant clinical isolates of P. aeruginosa and Acinetobacter baumannii were now identified by a systematic survey of the peptide sequences within the branches of a distinct type of third-generation peptide dendrimers. Combined topology and peptide sequence design as illustrated here represents a new and general strategy to discover new antimicrobial agents to fight multidrug-resistant bacterial pathogens.
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Affiliation(s)
- Michaela Stach
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern (Switzerland)
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6
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Stach M, Siriwardena TN, Köhler T, van Delden C, Darbre T, Reymond JL. Combining Topology and Sequence Design for the Discovery of Potent Antimicrobial Peptide Dendrimers against Multidrug-ResistantPseudomonas aeruginosa. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Tripp S, Appelhans D, Striegler C, Voit B. Oligosaccharide Shells as a Decisive Factor for Moderate and Strong Ionic Interactions of Dendritic Poly(ethylene imine) Scaffolds under Shear Forces. Chemistry 2014; 20:8314-9. [DOI: 10.1002/chem.201402147] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Indexed: 12/16/2022]
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8
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Filipe LCS, Machuqueiro M, Darbre T, Baptista AM. Unraveling the Conformational Determinants of Peptide Dendrimers Using Molecular Dynamics Simulations. Macromolecules 2013. [DOI: 10.1021/ma401574b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luís C. S. Filipe
- Instituto de Tecnologia Química
e Biológica, Universidade Nova de Lisboa, Av. da República,
EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C8, 1749-016 Lisboa, Portugal
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - António M. Baptista
- Instituto de Tecnologia Química
e Biológica, Universidade Nova de Lisboa, Av. da República,
EAN, 2780-157 Oeiras, Portugal
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9
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Reymond JL, Bergmann M, Darbre T. Glycopeptide dendrimers as Pseudomonas aeruginosa biofilm inhibitors. Chem Soc Rev 2013; 42:4814-22. [PMID: 23370573 DOI: 10.1039/c3cs35504g] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthetic glycopeptide dendrimers composed of a branched oligopeptide tree structure appended with glycosidic groups at its multiple N-termini were investigated for binding to the Pseudomonas aeruginosa lectins LecB and LecA. These lectins are partly responsible for the formation of antibiotic resistant biofilms in the human pathogenic bacterium P. aeruginosa, which causes lethal airway infections in immune-compromised and cystic fibrosis patients. Glycopeptide dendrimers with high affinity to the lectins were identified by screening of combinatorial libraries. Several of these dendrimers, in particular the LecB specific glycopeptide dendrimers FD2 and D-FD2 and the LecA specific glycopeptide dendrimers GalAG2 and GalBG2, also efficiently block P. aeruginosa biofilm formation and induce biofilm dispersal in vitro. Structure-activity relationship and structural studies are reviewed, in particular the observation that multivalency is essential to the anti-biofilm effect in these dendrimers.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freistrasse 3, 3012 Berne, Switzerland.
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Geotti-Bianchini P, Darbre T, Reymond JL. pH-tuned metal coordination and peroxidase activity of a peptide dendrimer enzyme model with a Fe(II)bipyridine at its core. Org Biomol Chem 2012; 11:344-52. [PMID: 23172354 DOI: 10.1039/c2ob26551f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide dendrimer BP1 was obtained by double thioether bond formation between 5,5'-bis(bromomethyl)-2,2'-bipyridine and two equivalents of peptide dendrimer N1 (Ac-Glu-Ser)(8)(Dap-Glu-Ala)(4)(Dap-Amb-Tyr)(2)Dap-Cys-Asp-NH(2) (Dap = branching 2,3-diaminopropanoic acid, Amb = 4-aminomethyl-benzoic acid). At pH 4.0 BP1 bound Fe(ii) to form the expected tris-coordinated complex [Fe(II)(BP1)(3)] (K(f) = 2.1 × 10(15) M(-3)). At pH 6.5 a monocoordinated complex [Fe(II)(BP1)] was formed instead (K(f) = 2.1 × 10(5) M(-1)) due to electrostatic repulsion between the polyanionic dendrimer branches, as confirmed by the behavior of three analogues where glutamates were partially or completely replaced by neutral glutamines or positive lysines. [Fe(II)(BP1)] catalyzed the oxidation of o-phenylenediamine with H(2)O(2) with enzyme-like kinetics (k(cat) = 1.0 min(-1), K(M) = 1.5 mM, k(cat)/k(uncat) = 90 000) and multiple turnover, while Fe(2+) or [Fe(bipy)(3)](2+) were inactive. The labile coordination positions allowing coordination to H(2)O(2) and to the substrate are likely responsible for the enhanced peroxidase activity of the metallopeptide dendrimer.
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Affiliation(s)
- Piero Geotti-Bianchini
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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11
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Affiliation(s)
- Jingjing Hu
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, People’s
Republic of China
| | - Tongwen Xu
- CAS Key Laboratory of Soft Matter
Chemistry, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230026, People’s
Republic of China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory
Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, People’s Republic of China
- Shanghai
Key Laboratory of Magnetic
Resonance, Department of Physics, East China Normal University, Shanghai, 200062, P.R.China
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12
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Reymond JL, Darbre T. Peptide and glycopeptide dendrimer apple trees as enzyme models and for biomedical applications. Org Biomol Chem 2012; 10:1483-92. [PMID: 22274649 DOI: 10.1039/c2ob06938e] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solid phase peptide synthesis (SPPS) provides peptides with a dendritic topology when diamino acids are introduced in the sequences. Peptide dendrimers with one to three amino acids between branches can be prepared with up to 38 amino acids (MW ~ 5,000 Da). Larger peptide dendrimers (MW ~ 30,000) were obtained by a multivalent chloroacetyl cysteine (ClAc) ligation. Structural studies of peptide dendrimers by CD, FT-IR, NMR and molecular dynamics reveal molten globule states containing up to 50% of α-helix. Esterase and aldolase peptide dendrimers displaying dendritic effects and enzyme kinetics (k(cat)/k(uncat) ~ 10(5)) were designed or discovered by screening large combinatorial libraries. Strong ligands for Pseudomonas aeruginosa lectins LecA and LecB able to inhibit biofilm formation were obtained with glycopeptide dendrimers. Efficient ligands for cobalamin, cytotoxic colchicine conjugates and antimicrobial peptide dendrimers were also developed showing the versatility of dendritic peptides. Complementing the multivalency, the amino acid composition of the dendrimers strongly influenced the catalytic or biological activity obtained demonstrating the importance of the "apple tree" configuration for protein-like function in peptide dendrimers.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland.
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13
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Stach M, Maillard N, Kadam RU, Kalbermatter D, Meury M, Page MGP, Fotiadis D, Darbre T, Reymond JL. Membrane disrupting antimicrobial peptide dendrimers with multiple amino termini. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00272d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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14
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Maillard N, Biswas R, Darbre T, Reymond JL. Combinatorial discovery of peptide dendrimer enzyme models hydrolyzing isobutyryl fluorescein. ACS COMBINATORIAL SCIENCE 2011; 13:310-20. [PMID: 21438622 DOI: 10.1021/co200006z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two 6750-membered one-bead-one-compound peptide dendrimer combinatorial libraries L (X(4))(8)(LysX(3))(4)(LysX(2))(2)LysX(1) (X(1-4) = 14 different amino acids or deletion, Lys = branching lysine residue) and AcL (with N-terminal acetylation) were prepared by split-and-mix solid phase peptide synthesis. Screening toward fluorogenic substrates for esterase and aldolase activities using the in silica off-bead assay (N. Maillard et al., J. Comb. Chem. 2009, 11, 667-675) and bead decoding by amino acid analysis revealed histidine containing sequences active against fluorescein diacetate. Isobutyryl fluorescein, a related hydrophobic fluorogenic substrate, was preferentially hydrolyzed by dendrimers from library AcL containing hydrophobic residues such as AcH3 (AcHis)(8)(LysLeu)(4)(LysVal)(2)LysLysOH, compared to simple oligohistidine peptides as reference catalysts. Polycationic dendrimers from library L with multiple free N-termini such as H8 (His)(8)(LysβAla)(4)(LysThr)(2)LysaProNH(2) (aPro = (2S,4S)-4-aminoproline) showed stronger reactivity toward 8-acetoxypyrene-1,3,6-trisulfonate with partial acylation of N-termini. These experiments highlight the role of noncatalytic amino acids to determine substrate selectivity in peptide dendrimer esterase models.
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Affiliation(s)
- Noélie Maillard
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | - Rasomoy Biswas
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
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Synthesis of glycopeptide dendrimers, dimerization and affinity for Concanavalin A. Bioorg Med Chem 2011; 19:2879-87. [DOI: 10.1016/j.bmc.2011.03.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 03/08/2011] [Accepted: 03/18/2011] [Indexed: 12/17/2022]
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16
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Filipe LCS, Machuqueiro M, Baptista AM. Unfolding the Conformational Behavior of Peptide Dendrimers: Insights from Molecular Dynamics Simulations. J Am Chem Soc 2011; 133:5042-52. [DOI: 10.1021/ja111001v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Luís C. S. Filipe
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
- Centro de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, C5, 1749-016 Lisboa, Portugal
| | - António M. Baptista
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal
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Euzen R, Reymond JL. Glycopeptide dendrimers: tuning carbohydrate–lectin interactions with amino acids. ACTA ACUST UNITED AC 2011; 7:411-21. [DOI: 10.1039/c0mb00177e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Uhlich NA, Darbre T, Reymond JL. Peptide dendrimer enzyme models for ester hydrolysis and aldolization prepared by convergent thioether ligation. Org Biomol Chem 2011; 9:7071-84. [DOI: 10.1039/c1ob05877k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Johansson EMV, Dubois J, Darbre T, Reymond JL. Glycopeptide dendrimer colchicine conjugates targeting cancer cells. Bioorg Med Chem 2010; 18:6589-97. [PMID: 20674369 DOI: 10.1016/j.bmc.2010.04.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 03/15/2010] [Accepted: 04/07/2010] [Indexed: 02/08/2023]
Abstract
Screening of a 65,536-member one-bead-one-compound (OBOC) combinatorial library of glycopeptide dendrimers of structure ((betaGal)(n)(+1)X(8)X(7)X(6)X(5))(2)DapX(4)X(3)X(2)X(1)(beta-Gal)(m) (betaGal=beta-galactosyl-thiopropionic acid, X(8-1)=variable amino acids, Dap=l-2,3-diaminopropionic acid, n, m=0, or 1 if X(8)=Lys resp. X(1)=Lys) for binding of Jurkat cells to the library beads in cell culture, resynthesis and testing lead to the identification of dendrimer J1 (betaGal-Gly-Arg-His-Ala)(2)Dap-Thr-Arg-His-Asp-CysNH(2) and related analogues as delivery vehicles. Cell targeting is evidenced by FACS with fluorescein conjugates such as J1F. The colchicine conjugate J1C is cytotoxic with LD(50)=1.5 microM. The beta-galactoside groups are necessary for activity, as evidenced by the absence of cell-binding and cytotoxicity in the non-galactosylated, acetylated analogue AcJ1F and AcJ1C, respectively. The pentagalactosylated dendrimer J4 betaGal(4)(Lys-Arg-His-Leu)(2)Dap-Thr-Tyr-His-Lys(betaGal)-Cys) selectively labels Jurkat cell as the fluorescein derivative J4F, but its colchicine conjugate J4C lacks cytotoxicity. Tubulin binding assays show that the colchicine dendrimer conjugates do not bind to tubulin, implying intracellular degradation of the dendrimers releasing the active drug.
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Affiliation(s)
- Emma M V Johansson
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
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