1
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Carstensen EV, Duynstee HI, van der Marel GA, van Boom JH, Nielsen J, Overkleeft HS, Overhand M. Synthesis of Highly Functionalized Piperidines via a Tandem Retro‐Michael‐[2 + 3]‐Cycloaddition. J Carbohydr Chem 2011. [DOI: 10.1081/car-120021703] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Howard I. Duynstee
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Gijs A. van der Marel
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Jacques H. van Boom
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - John Nielsen
- b The Royal Veterinary and Agricultural University , Thorvald Sense, VEJ‐40, DK‐1871 , Frederiksberg C , Denmark
| | - Herman S. Overkleeft
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Mark Overhand
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
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2
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Lankhorst PP, Groeneveld CM, Wille G, van Boom JH, Altona C, Haasnoot CAG. Conformational analysis of an RNA triplet in aqueous solution: m6
2
A-U-m6
2
A studied by two-dimensional nuclear magnetic resonance at 500 MHz. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19821010705] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Altona C, Koeners HJ, de Jager JR, van Boom JH, van Binst G. Adenylyl-uridine. Assignment and analysis of the 270 Mhz fast Fourier transform proton magnetic resonance spectrum. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19740930611] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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den Hartog JHJ, Altona C, van Boom JH, Reedijk J. The structure of cis
-platinum trinucleoside diphosphate species; the influence of ligand substitutions upon the conformation of the adducts. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19841031105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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van Delft FL, Rob A, Valentijn P, van der Marel GA, van Boom JH. Preparation of 2,5-Anhydrohexitols (Part Ii). Intramolecular Nucleophilic Substitution of Cyclic Sulfates. J Carbohydr Chem 2008. [DOI: 10.1080/07328309908543990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Floris L. van Delft
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - A. Rob
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - P.M. Valentijn
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Gijs A. van der Marel
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jacques H. van Boom
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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6
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van Delft FL, Rob A, Valentijn P, van der Marel GA, van Boom JH. Preparation of 2,5-Anhydrohexitols (Part I). Silicon-Directed Stereocontrolled Cyclization. J Carbohydr Chem 2008. [DOI: 10.1080/07328309908543989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Floris L. van Delft
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - A. Rob
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - P.M. Valentijn
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Gijs A. van der Marel
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jacques H. van Boom
- a Gorlaeus Laboratories , Leiden Institute of Chemistry , P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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7
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Leeuwenburgh MA, van der Marel GA, Overkleeft HS, van Boom JH. From α‐1,2‐Anhydrosugars to C‐Glycosides: The Influence of Lewis Acids and Nucleophiles on the Stereochemistry. J Carbohydr Chem 2007. [DOI: 10.1081/car-120026458] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Michiel A. Leeuwenburgh
- a Leiden Institute of Chemistry , Leiden University , P.O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Gijsbert A. van der Marel
- a Leiden Institute of Chemistry , Leiden University , P.O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Herman S. Overkleeft
- a Leiden Institute of Chemistry , Leiden University , P.O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Jacques H. van Boom
- a Leiden Institute of Chemistry , Leiden University , P.O. Box 9502, 2300 RA , Leiden , The Netherlands
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8
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van den Berg RJ, Noort D, van der Marel GA, van Boom JH, Benschop HP. SYNTHESIS OF PSEUDO-DISACCHARIDE ANALOGUES OF LIPID A: HAPTENS FOR THE GENERATION OF ANTIBODIES WITH GLYCOSIDASE ACTIVITY TOWARDS LIPID A. J Carbohydr Chem 2006. [DOI: 10.1081/car-120004331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Richard J.B.H.N. van den Berg
- a Department of Chemical Toxicology , TNO Prins Maurits Laboratory , P.O. Box 45, Rijswijk, NL-2280 AA, The Netherlands
| | - Daan Noort
- a Department of Chemical Toxicology , TNO Prins Maurits Laboratory , P.O. Box 45, Rijswijk, NL-2280 AA, The Netherlands
| | - Gijs A. van der Marel
- b Leiden Institute of Chemistry , Gorlaeus Laboratories, University of Leiden , P.O. Box 9502, Leiden, NL-2300 RA, The Netherlands
| | - Jacques H. van Boom
- b Leiden Institute of Chemistry , Gorlaeus Laboratories, University of Leiden , P.O. Box 9502, Leiden, NL-2300 RA, The Netherlands
| | - Hendrik P. Benschop
- a Department of Chemical Toxicology , TNO Prins Maurits Laboratory , P.O. Box 45, Rijswijk, NL-2280 AA, The Netherlands
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9
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Timmer MSM, Vinciano Chumillas M, Donker‐Koopman WE, Aerts JMFG, van derMarel GA, Overkleeft HS, van Boom JH. Selective Cross‐Metathesis ofC‐Allyl‐Glycosides. J Carbohydr Chem 2005. [DOI: 10.1080/07328300500174887] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Voerman G, Cavalli S, van der Marel GA, Pfleiderer W, van Boom JH, Filippov DV. 1,3-Dimethyllumazine derivatives from Limnatis nilotica. J Nat Prod 2005; 68:938-41. [PMID: 15974624 DOI: 10.1021/np049617a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Two previously unknown lumazine derivatives, 1 and 2, have been isolated from the parasitic freshwater leech Limnatis nilotica. The structures of the compounds have been elucidated by NMR and unambiguously corroborated by chemical synthesis.
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Affiliation(s)
- Gerard Voerman
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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11
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Codée JDC, Stubba B, Schiattarella M, Overkleeft HS, van Boeckel CAA, van Boom JH, van der Marel GA. A Modular Strategy Toward the Synthesis of Heparin-like Oligosaccharides Using Monomeric Building Blocks in a Sequential Glycosylation Strategy. J Am Chem Soc 2005; 127:3767-73. [PMID: 15771511 DOI: 10.1021/ja045613g] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel flexible assembly strategy is described for the modular synthesis of heparin and heparan sulfates. The reported strategy uses monomeric building blocks to construct the oligosaccharide chain to attain a maximum degree of flexibility. In the assembly, 1-hydroxyl glucosazido- and 1-thio uronic acid donors are combined in a sequential glycosylation protocol using sulfonium triflate activator systems. The key 1-thio uronic acids were obtained in an efficient manner from diacetone glucose employing a chemo- and regioselective oxidation of partially protected glucose and idose thioglycosides.
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Affiliation(s)
- Jeroen D C Codée
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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12
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Verhelst SHL, Michiels PJA, van der Marel GA, van Boeckel CAA, van Boom JH. Surface plasmon resonance evaluation of various aminoglycoside-RNA hairpin interactions reveals low degree of selectivity. Chembiochem 2005; 5:937-42. [PMID: 15239050 DOI: 10.1002/cbic.200300819] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Aminoglycoside antibiotics, which are able to selectively bind to RNA, are considered to be an important lead in RNA-targeting drug discovery. In this study, surface plasmon resonance (SPR) was employed to explore the interaction of aminoglycosides with known tobramycin-binding RNA hairpins (aptamers) and an unrelated RNA hairpin. It was established that aminoglycosides have multiple interactions with RNA hairpins. Unexpectedly, the different hairpins showed comparable affinity for a set of related aminoglycosides. The observed absence of selectivity presents an extra hurdle in the discovery of novel aminoglycosides as specific drugs that target defined RNA hairpins.
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Affiliation(s)
- Steven H L Verhelst
- Leiden Institute of Chemistry, Gorlaeus Laboratories, P. O. Box 9502, 2300 RA Leiden, The Netherlands
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13
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Timmer MS, Risseeuw MD, Verdoes M, Filippov DV, Plaisier JR, van der Marel GA, Overkleeft HS, van Boom JH. Synthesis of functionalized heterocycles via a tandem Staudinger/aza-Wittig/Ugi multicomponent reaction. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.079] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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Robillard MS, van Alphen S, Meeuwenoord NJ, J. Jansen BA, van der Marel GA, van Boom JH, Reedijk J. Solid-phase synthesis of peptide-platinum complexes using platinum-chelating building blocks derived from amino acids. NEW J CHEM 2005. [DOI: 10.1039/b411219a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Grotenbreg GM, Kronemeijer M, Timmer MSM, El Oualid F, van Well RM, Verdoes M, Spalburg E, van Hooft PAV, de Neeling AJ, Noort D, van Boom JH, van der Marel GA, Overkleeft HS, Overhand M. A practical synthesis of gramicidin s and sugar amino Acid containing analogues. J Org Chem 2004; 69:7851-9. [PMID: 15527261 DOI: 10.1021/jo0487449] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A practical gram-scale and high-yielding synthesis of the antimicrobial peptide gramicidin S is presented. An Fmoc-based solid-phase peptide synthesis protocol is employed for the generation of the linear decapeptide precursor, which is cyclized in solution to afford the target compound. The versatility of our method is demonstrated by the construction of eight gramicidin S analogues (15a-h) having nonproteinogenic sugar amino acid residues (4-7) incorporated in the turn regions.
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Affiliation(s)
- Gijsbert M Grotenbreg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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16
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Petersen L, de Koning MC, van Kuik-Romeijn P, Weterings J, Pol CJ, Platenburg G, Overhand M, van der Marel GA, van Boom JH. Synthesis and in vitro evaluation of PNA-peptide-DETA conjugates as potential cell penetrating artificial ribonucleases. Bioconjug Chem 2004; 15:576-82. [PMID: 15149186 DOI: 10.1021/bc034219p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the synthesis of novel artificial ribonucleases with potentially improved cellular uptake. The design of trifunctional conjugates 1a and 1b is based on the specific RNA-recognizing properties of PNA, the RNA-cleaving abilities of diethylenetriamine (DETA), and the peptide (KFF)(3)K for potential uptake into E. coli. The conjugates were assembled in a convergent synthetic route involving native chemical ligation of a PNA, containing an N-terminal cysteine, with the C-terminal thioester of the cell-penetrating (KFF)(3)K peptide to give 12a and 12b. These hybrids contained a free cysteine side-chain, which was further functionalized with an RNA-hydrolyzing diethylenetriamine (DETA) moiety. The trifunctional conjugates (1a, 1b) were evaluated for RNA-cleaving properties in vitro and showed efficient degradation of the target RNA at two major cleavage sites. It was also established that the cleavage efficiency strongly depended on the type of spacer connecting the PNA and the peptide.
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Affiliation(s)
- Lene Petersen
- Leiden Institute of Chemistry and ProSensa B.V., Gorlaeus Laboratories, University of Leiden, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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17
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Welters MJP, Filippov DV, van den Eeden SJF, Franken KLMC, Nouta J, Valentijn ARPM, van der Marel GA, Overkleeft HS, Lipford G, Offringa R, Melief CJM, van Boom JH, van der Burg SH, Drijfhout JW. Chemically synthesized protein as tumour-specific vaccine: immunogenicity and efficacy of synthetic HPV16 E7 in the TC-1 mouse tumour model. Vaccine 2004; 23:305-11. [PMID: 15530672 DOI: 10.1016/j.vaccine.2004.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 06/03/2004] [Accepted: 06/15/2004] [Indexed: 11/24/2022]
Abstract
Many successful candidate vaccines capable of combating tumours in animal models come to an untimely end because of the costs associated with the approval and production of the GMP-grade materials, which are usually of biological origin, for use in humans. We have used a GMP-compatible method to chemically synthesize a pure synthetic E7 protein of the human papillomavirus type 16 (HPV16-E7). This oncogen-derived protein is constitutively expressed in cervical cancer and its precursors and is thus considered as an excellent target for tumour-specific immunity. Injection of a mixture of the synthetic HPV16-E7 protein and the synthetic adjuvant CpG in mice resulted in strong functional HPV16-specific cytotoxic T-lymphocyte responses as measured by CD8+ MHC class I-tetramer staining, the detection of antigen-specific intracellular IFNgamma production and the ability to protect mice against a challenge with HPV16-E7+ TC-1 tumour cells in both prophylactic and therapeutic vaccination regimens. Our results demonstrate the potential use of pure synthetic vaccines that can be efficiently produced under GMP at low cost, which will stimulate the translation of new vaccination strategies into phase I/II clinical trials.
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Affiliation(s)
- Marij J P Welters
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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18
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Tromp RA, van Boom SSGE, Marco Timmers C, van Zutphen S, van der Marel GA, Overkleeft HS, van Boom JH, Reedijk J. The β-glucuronyl-based prodrug strategy allows for its application on β-glucuronyl-platinum conjugates. Bioorg Med Chem Lett 2004; 14:4273-6. [PMID: 15261285 DOI: 10.1016/j.bmcl.2004.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2004] [Revised: 05/12/2004] [Accepted: 06/02/2004] [Indexed: 11/28/2022]
Abstract
The use of platinum drugs in antitumour therapy is well established. An important drawback of these chemotherapeutics is the lack of selectivity for tumour cells, usually resulting in severe toxic side effects. A glucuronyl-platinum conjugate was designed and synthesised to test the compatibility of platinum compounds with beta-glucuronidase-based prodrug therapy. Instantaneous cleavage of the beta-glucuronic bond in the glucuronyl-platinum conjugate was observed upon addition of beta-glucuronidase resulting in Pt(II)(dach)(4-hydroxybenzylmalonate) and glucuronic acid.
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Affiliation(s)
- Reynier A Tromp
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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19
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van den Berg RJBHN, Korevaar CGN, Overkleeft HS, van der Marel GA, van Boom JH. Effective, High-Yielding, and Stereospecific Total Synthesis of d-erythro-(2R,3S)-Sphingosine from d-ribo-(2S,3S,4R)-Phytosphingosine. J Org Chem 2004; 69:5699-704. [PMID: 15307742 DOI: 10.1021/jo049277y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of naturally occurring D-erythro-(2R,3S,4E)-sphingosine from commercially available D-ribo-(2S,3S,4R)-phytosphingosine is described. The key step in the reaction sequence comprises TMSI/DBN promoted regio- and stereoselective oxirane opening of intermediate 2-phenyl-4-(S)-[(1S,2S)-1,2-epoxyhexadecyl]-1,3-oxazoline followed by the in situ trans-elimination of 2-phenyl-4-(S)-[(1S,2R)-1,2-dideoxy-2-iodo-1-trimethylsilyloxyhexadecyl]-1,3-oxazoline.
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20
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van Rossenberg SMW, Sliedregt-Bol KM, Prince P, van Berkel TJC, van Boom JH, van der Marel GA, Biessen EAL. A targeted peptide nucleic acid to down-regulate mouse microsomal triglyceride transfer protein expression in hepatocytes. Bioconjug Chem 2004; 14:1077-82. [PMID: 14624620 DOI: 10.1021/bc0340417] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Peptide nucleic acids (PNA's) have shown to hold potential as antisense drugs. In this study we have designed PNA drugs for the microsomal triglyceride transfer protein (MTP), which is known to play a critical role in the assembly of atherogenic lipoproteins, and have converted the most potent drug into a liver-targeted prodrug. First, we have synthesized three PNA sequences targeting domains on the mouse MTP mRNA, which were not involved in intrastrand base-pairing interactions as jugded from its secondary structure. Only one of the PNA's, PNA569, showed dose-dependent inhibition of MTP expression in a cell-free system for coupled transcription/translation of MTP. Second, to improve the cellular uptake of this PNA drug, we have conjugated PNA569 to a high affinity ligand for the asialoglycoprotein receptor, K(GalNAc)(2). As compared to the parent PNA, the prodrug PNA-K(GalNAc)(2) was found to display to a markedly improved capacity to inhibit MTP mRNA expression in parenchymal liver cells. A glycoconjugated nonsense control appeared to be ineffective. In conclusion, the design of a targeted PNA is described to reduce MTP expression in parenchymal liver cells by 70%. The presented approach for targeted tissue-specific down-regulation of genes by PNA's may be valid for other genes as well.
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Affiliation(s)
- Sabine M W van Rossenberg
- Leiden/Amsterdam Center for Drug Research, Division of Biopharmaceutics, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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21
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van Roon AMM, Pannu NS, de Vrind JPM, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP. Structure of an Anti-Lewis X Fab Fragment in Complex with Its Lewis X Antigen. Structure 2004; 12:1227-36. [PMID: 15242599 DOI: 10.1016/j.str.2004.05.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 04/28/2004] [Accepted: 05/02/2004] [Indexed: 11/25/2022]
Abstract
The Lewis X trisaccharide is pivotal in mediating specific cell-cell interactions. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, has been shown to recognize the Lewis X trisaccharide. Here we describe the structure of the Fab fragment of 291-2G3-A, with Lewis X, to 1.8 A resolution. The crystallographic analysis revealed that the antigen binding site is a rather shallow binding pocket, and residues from all six complementary determining regions of the antibody contact all sugar residues. The high specificity of the binding pocket does not result in high affinity; the K(D) determined by isothermal calorimetry is 11 microM. However, this affinity is in the same range as for other sugar-antibody complexes. The detailed understanding of the antibody-Lewis X interaction revealed by the crystal structure may be helpful in the design of better diagnostic tools for schistosomiasis and for studying Lewis X-mediated cell-cell interactions by antibody interference.
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Affiliation(s)
- Anne-Marie M van Roon
- Department of Biophysical Structural Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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22
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van den Bos LJ, Codée JDC, van der Toorn JC, Boltje TJ, van Boom JH, Overkleeft HS, van der Marel GA. Thioglycuronides: synthesis and application in the assembly of acidic oligosaccharides. Org Lett 2004. [PMID: 15200311 DOI: 10.1021/ol049380] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Partially protected thioglycuronic acids are prepared efficiently by chemo- and regioselective oxidation of the corresponding thioglycosides using the TEMPO/BAIB reagent combination. After esterification, the thioglycuronic acids proved to be useful as both donor and acceptor in sulfonium-mediated condensations toward acidic di- and trisaccharides.
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Affiliation(s)
- Leendert J van den Bos
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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23
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El Oualid F, Burm BEA, Leroy IM, Cohen LH, van Boom JH, van den Elst H, Overkleeft HS, van der Marel GA, Overhand M. Design, Synthesis, and Evaluation of Su- gar Amino Acid Based Inhibitors of Pro- tein Prenyl Transferases PFT and PGGT-1. J Med Chem 2004; 47:3920-3. [PMID: 15267228 DOI: 10.1021/jm049927q] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eleven analogues of the C-terminal Ca(1)a(2)X motif found in natural substrates of the prenyl transferases PFT and PGGT-1 were synthesized and evaluated for their inhibition potency and selectivity against PFT and PGGT-1. Replacement of the central dipeptide part a(1)a(2) by a benzylated sugar amino acid resulted in a good and highly selective PFT inhibitor (8, IC(50) = 250 +/- 20 nM). The methyl ester of 8 (13) selectively inhibited protein farnesylation in cultured cells.
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Affiliation(s)
- Farid El Oualid
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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van den Bos LJ, Codée JDC, van der Toorn JC, Boltje TJ, van Boom JH, Overkleeft HS, van der Marel GA. Thioglycuronides: Synthesis and Application in the Assembly of Acidic Oligosaccharides. Org Lett 2004; 6:2165-8. [PMID: 15200311 DOI: 10.1021/ol049380+] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Partially protected thioglycuronic acids are prepared efficiently by chemo- and regioselective oxidation of the corresponding thioglycosides using the TEMPO/BAIB reagent combination. After esterification, the thioglycuronic acids proved to be useful as both donor and acceptor in sulfonium-mediated condensations toward acidic di- and trisaccharides.
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Affiliation(s)
- Leendert J van den Bos
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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25
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IJsselstijn M, Aguilera B, van der Marel GA, van Boom JH, van Delft FL, Schoemaker HE, Overkleeft HS, Rutjes FP, Overhand M. Ring-closing alkyne metathesis mediated synthesis of cyclic β-turn mimetics. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.03.181] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Turner JJ, Sikkema FD, Erkelens K, Marel GAVD, Overkleeft HS, Boom JHV, Overhand M. Novel Reversed Chain Modified Oligopeptides via Sequential α-N-Mitsunobu Condensation of a Functionalized C-glycoside. CHEM LETT 2004. [DOI: 10.1246/cl.2004.468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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27
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Gómez-Pinto I, Cubero E, Kalko SG, Monaco V, van der Marel G, van Boom JH, Orozco M, González C. Effect of bulky lesions on DNA: solution structure of a DNA duplex containing a cholesterol adduct. J Biol Chem 2004; 279:24552-60. [PMID: 15047709 DOI: 10.1074/jbc.m311751200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional solution structure of two DNA decamers of sequence d(CCACXGGAAC)-(GTTCCGGTGG) with a modified nucleotide containing a cholesterol derivative (X) in its C1 '(chol)alpha or C1 '(chol)beta diastereoisomer form has been determined by using NMR and restrained molecular dynamics. This DNA derivative is recognized with high efficiency by the UvrB protein, which is part of the bacterial nucleotide excision repair, and the alpha anomer is repaired more efficiently than the beta one. The structures of the two decamers have been determined from accurate distance constraints obtained from a complete relaxation matrix analysis of the NOE intensities and torsion angle constraints derived from J-coupling constants. The structures have been refined with molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long range electrostatic interactions. These calculations converge to well defined structures whose conformation is intermediate between the A- and B-DNA families as judged by the root mean square deviation but with sugar puckerings and groove shapes corresponding to a distorted B-conformation. Both duplex adducts exhibit intercalation of the cholesterol group from the major groove of the helix and displacement of the guanine base opposite the modified nucleotide. Based on these structures and molecular dynamics calculations, we propose a tentative model for the recognition of damaged DNA substrates by the UvrB protein.
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Affiliation(s)
- Irene Gómez-Pinto
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, C/. Serrano 119, 28006 Madrid, Spain
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28
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van den Berg RJBHN, Donker-Koopman W, van Boom JH, Aerts HMFG, Noort D. Design and synthesis of 2-acetamidomethyl derivatives of isofagomine as potential inhibitors of human lysosomal β-hexosaminidases. Bioorg Med Chem 2004; 12:891-902. [PMID: 14980601 DOI: 10.1016/j.bmc.2003.12.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Accepted: 12/22/2003] [Indexed: 10/26/2022]
Abstract
As part of a program towards the development of specific inhibitors of human lysosomal beta-hexosaminidase for use as chemical chaperones in therapy of G(M2) gangliosidosis related diseases, the synthesis of 2-acetamidomethyl derivatives of isofagomine has been undertaken. Key event in this synthesis is the conversion of a C-2 substituted gluconolactone derivative into the corresponding lactam, followed by reduction to the corresponding amine. The 1-N-imino-2 acetamidomethyl derivative 5 proved to be a rather selective inhibitor with a K(i) of 2.4 microM for homogenate of human spleen lysosomal beta-hexosaminidase.
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Affiliation(s)
- Richard J B H N van den Berg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, PO Box 9502, Leiden NL-2300 RA, The Netherlands
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29
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Verhelst SH, Wennekes T, van der Marel GA, Overkleeft HS, van Boeckel CA, van Boom JH. Synthesis of orthogonally protected 2-deoxystreptamine stereoisomers. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.01.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Robillard MS, Bacac M, van den Elst H, Flamigni A, van der Marel GA, van Boom JH, Reedijk J. Automated parallel solid-phase synthesis and anticancer screening of a library of peptide-tethered platinum(II) complexes. ACTA ACUST UNITED AC 2004; 5:821-5. [PMID: 14606811 DOI: 10.1021/cc030011z] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The automated parallel solid-phase synthesis of a 36-member library of peptide-tethered platinum(II) complexes is described. The identity and quality of each product were confirmed by mass spectrometry and (1)H NMR. Subsequently, each compound was screened for in vitro anticancer activity by treating the A2780 (human ovarian carcinoma) cell line with two concentrations of the drugs (100 and 10 microM) in quadruplicate. The reduction of cell proliferation induced by the drugs at these concentrations was determined with the MTT colorimetric assay (MTT = 3-(4',5'-dimethylthiazol-2'-yl)-2,5-diphenyltetrazolium bromide) and compared to cisplatin. Even though no very active library members could be identified, five apparently most active (8[1], 8[4], 8[10], 8[13], and 8[24]) and two inactive complexes (8[33] and 8[34]) were purified using gel permeation chromatography and fully characterized by NMR spectroscopy ((1)H, (195)Pt) and MS. The IC(50) values of these complexes and cisplatin in A2780 cells were subsequently determined using the MTT assay in a conventional manner. All seven complexes have an IC(50) above 100 microM, confirming the results generated by the assay at 100 and 10 microM of the crude reaction products.
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Affiliation(s)
- Marc S Robillard
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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31
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Overkleeft HS, Overhand M, Grotenbreg GM, Tuin AW, Witte MD, Leeuwenburgh MA, van Boom JH, van der Marel GA. An Expeditious Route Towards Pyranopyran Sugar Amino Acids. Synlett 2004. [DOI: 10.1055/s-2004-820021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Overkleeft HS, van Boom JH, Filippov DV, van den Elst H, Tromp CM, van der Marel GA, van Boeckel CA. Parallel Solid Phase Synthesis of Tricomponent Bisubstrate Analogues as Potential Fucosyltransferase Inhibitors. Synlett 2004. [DOI: 10.1055/s-2004-817778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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van der Marel GA, Timmer MS, Codée JD, Overkleeft HS, van Boom JH. A Tandem Ring-Closing Metathesis Cleavable Linker System for Solid-Phase Oligosaccharide Synthesis. Synlett 2004. [DOI: 10.1055/s-2004-831301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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van Hooft PAV, El Oualid F, Overkleeft HS, van der Marel GA, van Boom JH, Leeuwenburgh MA. Synthesis and elaboration of functionalised carbohydrate-derived spiroketals. Org Biomol Chem 2004; 2:1395-403. [PMID: 15105932 DOI: 10.1039/b401699h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scope of a stereoselective three-step approach for the synthesis of sugar derived spiroketals is presented. The methodology consists of Grignard addition of vinyl- or allylmagnesium bromide to a carbohydrate lactone, followed by K-10 clay mediated glycosidation with a terminal alkenol and subsequent ring-closing metathesis of the resulting diene. The generality of this procedure is demonstrated by the synthesis of various pyranose- and furanose-derived spiroketals, as well as more advanced tricyclic spiroketal derivatives. It is shown that functionalisation of the double bond in the resulting spiroketals leads to fused polycyclic ethers.
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35
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Verhelst SHL, Paez Martinez B, Timmer MSM, Lodder G, van der Marel GA, Overkleeft HS, van Boom JH. A Short Route toward Chiral, Polyhydroxylated Indolizidines and Quinolizidines. J Org Chem 2003; 68:9598-603. [PMID: 14656083 DOI: 10.1021/jo0350662] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, a rapid route toward functionalized bicyclic alkaloids is presented. In only three steps, an easily accessible carbohydrate derivative was converted into iodomethyl indolizidine 13, which can equilibrate to the corresponding iodoquinolizidine 15. We provide strong evidence that this equilibration proceeds via an aziridinium ion intermediate. Furthermore, nucleophilic substitution of the iodomethyl indolizidine as well as the aziridinium intermediate gives access to highly functionalized indolizidine and quinolizidine alkaloids.
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Affiliation(s)
- Steven H L Verhelst
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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36
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Timmer MSM, Verdoes M, Sliedregt LAJM, van der Marel GA, van Boom JH, Overkleeft HS. The Use of a Mannitol-Derived Fused Oxacycle as a Combinatorial Scaffold. J Org Chem 2003; 68:9406-11. [PMID: 14629165 DOI: 10.1021/jo0349429] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient and high-yielding solid-phase synthesis of a small library of compounds containing a cis-fused pyranofuran structural motive is described. With use of the cheap and readily available D-(+)-mannitol, a highly functionalized sugar template was synthesized and immobilized on a solid support via an olefinic linker. Modification of this two-point molecular scaffold and subsequent ring-closing metathesis/cleavage gave access to a series of functionalized conformationally constrained fused oxacycles.
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Affiliation(s)
- Mattie S M Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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37
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Aguilera B, Ghauharali-van der Vlugt K, Helmond MTJ, Out JMM, Donker-Koopman WE, Groener JEM, Boot RG, Renkema GH, van der Marel GA, van Boom JH, Overkleeft HS, Aerts JMFG. Transglycosidase activity of chitotriosidase: improved enzymatic assay for the human macrophage chitinase. J Biol Chem 2003; 278:40911-6. [PMID: 12890686 DOI: 10.1074/jbc.m301804200] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chitotriosidase is a chitinase that is massively expressed by lipid-laden tissue macrophages in man. Its enzymatic activity is markedly elevated in serum of patients suffering from lysosomal lipid storage disorders, sarcoidosis, thalassemia, and visceral Leishmaniasis. Monitoring of serum chitotriosidase activity in Gaucher disease patients during progression and therapeutic correction of their disease is useful to obtain insight in changes in body burden on pathological macrophages. However, accurate quantification of chitotriosidase levels by enzyme assay is complicated by apparent substrate inhibition, which prohibits the use of saturating substrate concentrations. We have therefore studied the catalytic features of chitotriosidase in more detail. It is demonstrated that the inhibition of enzyme activity at excess substrate concentration can be fully explained by transglycosylation of substrate molecules. The potential physiological consequences of the ability of chitotriosidase to hydrolyze as well as transglycosylate are discussed. The novel insight in transglycosidase activity of chitotriosidase has led to the design of a new substrate molecule, 4-methylumbelliferyl-(4-deoxy)chitobiose. With this substrate, which is no acceptor for transglycosylation, chitotriosidase shows normal Michaelis-Menten kinetics, resulting in major improvements in sensitivity and reproducibility of enzymatic activity measurements. The novel convenient chitotriosidase enzyme assay should facilitate the accurate monitoring of Gaucher disease patients receiving costly enzyme replacement therapy.
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Affiliation(s)
- Begoña Aguilera
- Department of Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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38
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de Koning MC, Filippov DV, van der Marel GA, van Boom JH, Overhand M. Synthesis of macrocyclic peptide nucleic acid derivatives via intramolecular chemical ligation. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.08.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Luca S, White JF, Sohal AK, Filippov DV, van Boom JH, Grisshammer R, Baldus M. The conformation of neurotensin bound to its G protein-coupled receptor. Proc Natl Acad Sci U S A 2003; 100:10706-11. [PMID: 12960362 PMCID: PMC196868 DOI: 10.1073/pnas.1834523100] [Citation(s) in RCA: 200] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2003] [Indexed: 11/18/2022] Open
Abstract
G protein-coupled receptors (GPCRs) mediate the perception of smell, light, taste, and pain. They are involved in signal recognition and cell communication and are some of the most important targets for drug development. Because currently no direct structural information on high-affinity ligands bound to GPCRs is available, rational drug design is limited to computational prediction combined with mutagenesis experiments. Here, we present the conformation of a high-affinity peptide agonist (neurotensin, NT) bound to its GPCR NTS-1, determined by direct structural methods. Functional receptors were expressed in Escherichia coli, purified in milligram amounts by using optimized procedures, and subsequently reconstituted into lipid vesicles. Solid-state NMR experiments were tailored to allow for the unequivocal detection of microgram quantities of 13C,15N-labeled NT(8-13) in complex with functional NTS-1. The NMR data are consistent with a disordered state of the ligand in the absence of receptor. Upon receptor binding, the peptide undergoes a linear rearrangement, adopting a beta-strand conformation. Our results provide a viable structural template for further pharmacological investigations.
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Affiliation(s)
- Sorin Luca
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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40
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van Well RM, Marinelli L, Altona C, Erkelens K, Siegal G, van Raaij M, Llamas-Saiz AL, Kessler H, Novellino E, Lavecchia A, van Boom JH, Overhand M. Conformational analysis of furanoid epsilon-sugar amino acid containing cyclic peptides by NMR spectroscopy, molecular dynamics simulation, and X-ray crystallography: evidence for a novel turn structure. J Am Chem Soc 2003; 125:10822-9. [PMID: 12952461 DOI: 10.1021/ja035461+] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sugar amino acids (SAAs) are useful building blocks for the design of peptidomimetics and peptide scaffolds. The three-dimensional structures of cyclic hybrid molecules containing the furanoid epsilon-SAA III and several amino acids were elucidated to study the preferred conformation of such an epsilon-SAA and its conformational influence on the backbone of cyclic peptides. NMR-based molecular dynamics simulations and empirical calculations of the cyclic tetramer 1, consisting of two copies of the SAA residue and two amino acids, revealed that it is conformationally restrained. The two SAA residues adopt different conformations. One of them forms an unusual turn, stabilized by an intraresidue nine-member hydrogen bond. The methylene functionalities of the other SAA residue are positioned in such a way that an intraresidue H bond is not possible. The X-ray crystal structure of 1 strongly resembles the solution conformation. Molecular dynamics calculations in combination with NMR analysis were also performed for compounds 2 and 3, which contain the RGD (Arg-Gly-Asp) consensus sequence and were previously shown to inhibit alpha(IIb)beta(3)-receptor-mediated platelet aggregation. The biologically most active compound 2 adopts a preferred conformation with the single SAA residue folded into the nine-member H bond-containing turn. Compound 3, containing an additional valine residue, as compared with compound 2, is conformational flexible. Our studies demonstrate that the furanoid epsilon-SAA III is able to introduce an unusual intraresidue hydrogen bond-stabilized beta-turn-like conformation in two of the three cyclic structures.
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Affiliation(s)
- Renate M van Well
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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41
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Abstract
The sequence specificity and intensity of DNA damage induced by six peptide-tethered platinum complexes was compared to cisplatin and Pt(en)Cl(2). DNA damage was investigated in pUC19 plasmid and in intact HeLa cells, and quantitatively analyzed using a Taq DNA polymerase/linear amplification assay. The DNA sequence specificity of the peptide-platinum compounds was found to be very similar to cisplatin and Pt(en)Cl(2), with runs of consecutive guanines being the most intensely damaged sites. The observed reactivity of the peptide-platinum complexes towards plasmid DNA was lower compared to cisplatin and Pt(en)Cl(2), with the glycine-tethered complex 3 and the phenylalanine-tethered complex 4 producing the highest relative damage intensity, followed by (in decreasing order) lysine-tethered (5), arginine-tethered (6), serine-tethered (7) and glutamate-tethered (8). The reactivity of the peptide-platinum complexes towards cellular DNA was also lower compared to cisplatin and Pt(en)Cl(2). For most investigated complexes, the relative damage intensities were found to be similar in cells compared to plasmid DNA, but were greatly reduced for 3 and 4. The lysine-tethered 5 complex produced the highest DNA damage intensity in cells followed by (in decreasing order) 6, 7, 3, 4 and 8.
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Affiliation(s)
- Marc S Robillard
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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van Rossenberg SMW, Sliedregt-Bol KM, Koning G, van den Elst H, van Berkel TJC, van Boom JH, van der Marel GA, Biessen EAL. Improvement of hepatocyte-specific gene expression by a targeted colchicine prodrug. Chembiochem 2003; 4:633-9. [PMID: 12851933 DOI: 10.1002/cbic.200300582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Colchicine, an established tubulin inhibitor, interferes with the trafficking of endocytotic vesicles and thereby promotes the escape of lysosome-entrapped compounds. To improve its potency and cell specificity, a targeted prodrug of colchicine was synthesized by conjugation to a high-affinity ligand (di-N(alpha),N(epsilon)-(5-(2-acetamido-2-deoxy-beta-D-galactopyranosyloxy)pentanomido)lysine, K(GalNAc)(2)) for the asialoglycoprotein receptor on parenchymal liver cells. The resulting colchicine-K(GalNAc)(2) conjugate bound to this receptor with an affinity of 4.5 nM. Confocal microscopy studies confirmed rapid uptake and receptor dependency of a prodrug conjugated with fluorescein isothiocyanate. Colchicine-K(GalNAc)(2) substantially increased the transfection efficiency of polyplexed DNA in parenchymal liver cells in a concentration- and receptor-dependent fashion. Colchicine-K(GalNAc)(2) was found to enhance the transfection efficiency by 50-fold at 1 nM, whereas the parental colchicine was ineffective. In conclusion, this nontoxic colchicine-K(GalNAc)(2) conjugate can be a useful tool to improve the transfection efficiency of hepatic nonviral gene transfer vehicles.
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Affiliation(s)
- Sabine M W van Rossenberg
- Division of Biopharmaceutics, Leiden/Amsterdam Center for Drug Research, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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Grotenbreg GM, Spalburg E, de Neeling AJ, van der Marel GA, Overkleeft HS, van Boom JH, Overhand M. Synthesis and biological evaluation of novel turn-modified gramicidin S analogues. Bioorg Med Chem 2003; 11:2835-41. [PMID: 12788356 DOI: 10.1016/s0968-0896(03)00219-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The synthesis of novel gramicidin S analogues having additional functionalities in the turn region by employing a biomimetic approach is described. The preservation of beta-sheet character in all analogues was established by NMR and the biological activity was evaluated.
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Affiliation(s)
- Gijsbert M Grotenbreg
- Leiden Institute of Chemistry, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
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44
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Codée JDC, van den Bos LJ, Litjens REJN, Overkleeft HS, van Boom JH, van der Marel GA. Sequential one-pot glycosylations using 1-hydroxyl and 1-thiodonors. Org Lett 2003; 5:1947-50. [PMID: 12762693 DOI: 10.1021/ol034528v] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A novel sequential glycosylation procedure is described that combines the use of 1-hydroxyl and thiodonors. The Ph(2)SO/Tf(2)O-mediated dehydrative condensation of 1-hydroxyl donors with thioglycosides affords in good yield the thiodisaccharides, which in turn can be activated by the same activator system to furnish trisaccharides. The alpha-Gal epitope and a hyaluronan trisaccharide were efficiently assembled in a one-pot procedure.
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Affiliation(s)
- Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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45
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Codée JDC, Litjens REJN, den Heeten R, Overkleeft HS, van Boom JH, van der Marel GA. Ph2SO/Tf2O: a powerful promotor system in chemoselective glycosylations using thioglycosides. Org Lett 2003; 5:1519-22. [PMID: 12713313 DOI: 10.1021/ol034312t] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diphenylsulfoxide in combination with triflic anhydride provides a very potent thiophilic glycosylation promotor system, capable of activating disarmed thioglycosides. The usefulness of this novel thiophilic activator is illustrated in a successful chemoselective glycosylation sequence in which the donor thioglycoside in the first condensation step may be either armed or disarmed. [reaction: see text]
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Affiliation(s)
- Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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46
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Heetebrij RJ, de Kort M, Meeuwenoord NJ, den Dulk H, van der Marel GA, van Boom JH, Reedijk J. A versatile approach towards regioselective platinated DNA sequences. Chemistry 2003; 9:1823-7. [PMID: 12698440 DOI: 10.1002/chem.200390209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Undesired N(7) platination of 2'-deoxyguanosine residues at predetermined sites in an oligodeoxynucleotide (ODN) sequence is prevented by applying the sterically demanding diphenylcarbamoyl (DPC) as an O(6)-protecting group. The presence of a base-labile oxalyl linker between the immobilized 3'-nucleotide and controlled pore glass (CPG) allows cleavage of the protected ODN from the support and leaves DPC protection unaffected. This method provides an ODN with specifically blocked guanine-N(7) sites for platination. In the hexanucleotides prepared in this study, 5'-GGBGGT-3'(for B=T, C and A), a platinum GG adduct is introduced at G4,G5. These site-specific platinated hexamers were isolated in a yield of 65 %, and were fully characterized by using reversed-phase HPLC (high performance liquid chromotography), LCMS (liquid chromatography-mass spectrometry), MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), PAGE (polyacrylamide gel electrophoresis) and Maxam-Gilbert sequencing analysis.
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Affiliation(s)
- Robert J Heetebrij
- Leiden Institute of Chemistry Gorlaeus Laboratories, Leiden University, P.O. Box 9502, The Netherlands
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van Well RM, Meijer ME, Overkleeft HS, van Boom JH, van der Marel GA, Overhand M. Synthesis of bridged sugar amino acids: a new entry into conformationally locked δ- and ε-amino acids. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00288-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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48
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van Well RM, Overkleeft HS, van der Marel GA, Bruss D, Thibault G, de Groot PG, van Boom JH, Overhand M. Solid-phase synthesis of cyclic RGD-furanoid sugar amino acid peptides as integrin inhibitors. Bioorg Med Chem Lett 2003; 13:331-4. [PMID: 12565923 DOI: 10.1016/s0960-894x(02)01022-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The solid-phase synthesis of cyclic RGD peptides containing either one or two furanoid sugar amino acids (SAAs) is reported. Using a cyclization-cleavage approach five peptides were successfully assembled and consecutively tested on their ability to bind to the integrin receptors alpha(v)beta(3) and alpha(IIb)beta(3). The cyclic tetrapeptide c[RGD-SAA] (1) showed the most promising activity in an inhibition assay with an IC(50) of 1.49 microM for the alpha(v)beta(3) receptor and 384 nM for the alpha(IIb)beta(3) receptor.
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Affiliation(s)
- Renate M van Well
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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van den Bos LJ, Codée JDC, van Boom JH, Overkleeft HS, van der Marel GA. A novel strategy towards the synthesis of orthogonally functionalised 4-aminoglycosides. Org Biomol Chem 2003; 1:4160-5. [PMID: 14685319 DOI: 10.1039/b309823k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tethered nucleophilic substitution strategy for the stereoselective introduction of axially oriented amino functions on suitably protected gluco- and mannopyranosides is presented. The obtained oxazine is a versatile building block, which after some manipulation, could be used in the construction of highly functionalised oligosaccharides.
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Affiliation(s)
- Leendert J van den Bos
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, PO Box 9502, 2300 RA Leiden, The Netherlands
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50
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Paul AV, Peters J, Mugavero J, Yin J, van Boom JH, Wimmer E. Biochemical and genetic studies of the VPg uridylylation reaction catalyzed by the RNA polymerase of poliovirus. J Virol 2003; 77:891-904. [PMID: 12502805 PMCID: PMC140777 DOI: 10.1128/jvi.77.2.891-904.2003] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The first step in poliovirus (PV) RNA synthesis is the covalent linkage of UMP to the terminal protein VPg. This reaction can be studied in vitro with two different assays. The simpler assay is based on a poly(A) template and requires synthetic VPg, purified RNA polymerase 3D(pol), UTP, and a divalent cation. The other assay uses specific viral sequences [cre(2C)] as a template for VPg uridylylation and requires the addition of proteinase 3CD(pro). Using one or both of these assays, we analyzed the VPg specificities and metal requirements of the uridylylation reactions. We determined the effects of single and double amino acid substitutions in VPg on the abilities of the peptides to serve as substrates for 3D(pol). Mutations in VPg, which interfered with uridylylation in vitro, were found to abolish viral growth. A chimeric PV containing the VPg of human rhinovirus 14 (HRV14) was viable, but substitutions of HRV2 and HRV89 VPgs for PV VPg were lethal. Of the three rhinoviral VPgs tested, only the HRV14 peptide was found to function as a substrate for PV1(M) 3D(pol) in vitro. We also examined the metal specificity of the VPg uridylylation reaction on a poly(A) template. Our results show a strong preference of the RNA polymerase for Mn(2+) as a cofactor compared to Mg(2+) or other divalent cations.
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Affiliation(s)
- Aniko V Paul
- Department of Molecular Genetics and Microbiology, State University of New York at Stony Brook, 11794, USA
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