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Potenza D, Belvisi L, Vasile F, Moroni E, Cossu F, Seneci P. A NMR and computational study of Smac mimics targeting both the BIR2 and BIR3 domains in XIAP protein. Org Biomol Chem 2012; 10:3278-87. [DOI: 10.1039/c2ob06979b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Vasile F, Potenza D, Marsiglia B, Maffioli S, Donadio S. Solution structure by nuclear magnetic resonance of the two lantibiotics 97518 and NAI-107. J Pept Sci 2011; 18:129-34. [PMID: 22083835 DOI: 10.1002/psc.1425] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 11/09/2022]
Abstract
Lantibiotics 97518 and NAI-107, produced by the related genera Planomonospora and Microbispora respectively, are members of a family of nisin-related compounds. They represent promising compounds to treat infections caused by multiresistant Gram-positive pathogens. Despite their similar structure and a similar antibacterial spectrum, the two lantibiotics exhibit significant differences in their potency. To gain an insight into the structure-activity relationships, their conformational properties in solution are determined by NMR. After carrying out an NOE analysis of 2D (1)H NMR spectra, high-resolution 3D structures are determined using molecular dynamics simulations.
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Potenza D, Vasile F, Belvisi L, Civera M, Araldi EMV. Cover Picture: STD and trNOESY NMR Study of Receptor-Ligand Interactions in Living Cancer Cells (ChemBioChem 5/2011). Chembiochem 2011. [DOI: 10.1002/cbic.201190015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Potenza D, Vasile F, Belvisi L, Civera M, Araldi EMV. STD and trNOESY NMR Study of Receptor-Ligand Interactions in Living Cancer Cells. Chembiochem 2011; 12:695-9. [DOI: 10.1002/cbic.201000756] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Indexed: 11/10/2022]
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da Ressurreição A, Vidu A, Civera M, Belvisi L, Potenza D, Manzoni L, Ongeri S, Gennari C, Piarulli U. Cyclic RGD-Peptidomimetics Containing Bifunctional Diketopiperazine Scaffolds as New Potent Integrin Ligands. Chemistry 2009; 15:12184-8. [DOI: 10.1002/chem.200902398] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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31
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Seneci P, Bianchi A, Battaglia C, Belvisi L, Bolognesi M, Caprini A, Cossu F, Franco ED, Matteo MD, Delia D, Drago C, Khaled A, Lecis D, Manzoni L, Marizzoni M, Mastrangelo E, Milani M, Motto I, Moroni E, Potenza D, Rizzo V, Servida F, Turlizzi E, Varrone M, Vasile F, Scolastico C. Rational design, synthesis and characterization of potent, non-peptidic Smac mimics/XIAP inhibitors as proapoptotic agents for cancer therapy. Bioorg Med Chem 2009; 17:5834-56. [DOI: 10.1016/j.bmc.2009.07.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Revised: 07/01/2009] [Accepted: 07/05/2009] [Indexed: 01/02/2023]
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Molinari F, Bertolini C, Aragozzini F, Potenza D. Selective Acylation of Monosaccharides Using Microbial Cells. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429909015225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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33
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Manzoni L, Belvisi L, Arosio D, Civera M, Pilkington-Miksa M, Potenza D, Caprini A, Araldi EM, Monferini E, Mancino M, Podestà F, Scolastico C. Cyclic RGD-Containing Functionalized Azabicycloalkane Peptides as Potent Integrin Antagonists for Tumor Targeting. ChemMedChem 2009; 4:615-32. [DOI: 10.1002/cmdc.200800422] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Maffioli SI, Potenza D, Vasile F, De Matteo M, Sosio M, Marsiglia B, Rizzo V, Scolastico C, Donadio S. Structure revision of the lantibiotic 97518. JOURNAL OF NATURAL PRODUCTS 2009; 72:605-607. [PMID: 19301921 DOI: 10.1021/np800794y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The lantibiotic 97518, produced by a Planomonospora sp., was reported as a 2194 Da polypeptide comprising 24 amino acid residues with five thioether bridges. It was assigned to the mersacidin subgroup of type B lantibiotics by Castiglione et al. (Biochemistry 2007, 46, 5884-5897) and named planosporicin. New analytical, chemical, and genetic data and reinterpretation of the published NMR chemical shifts enable structure revision of 97518. The resulting revision of the 97518 structure involves both a shift of two amino acids and a reorganization of two thioether bridges. With this revision, the lantibiotic 97518 becomes a clear member of the nisin subgroup of compounds.
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Timpano G, Tabarani G, Anderluh M, Invernizzi D, Vasile F, Potenza D, Nieto PM, Rojo J, Fieschi F, Bernardi A. Synthesis of novel DC-SIGN ligands with an alpha-fucosylamide anchor. Chembiochem 2008; 9:1921-30. [PMID: 18655085 DOI: 10.1002/cbic.200800139] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dendritic cell-specific intercellular adhesion molecule (ICAM) 3-grabbing nonintegrin (DC-SIGN) is a C-type lectin that appears to perform several different functions. Besides mediating adhesion between dendritic cells and T lymphocytes, DC-SIGN recognizes several pathogens some of which, including HIV, appear to exploit it to invade host organisms. The intriguing diversity of the roles attributed to DC-SIGN and their therapeutic implications have stimulated the search for new ligands that could be used as biological probes and possibly as lead compounds for drug development. The natural ligands of DC-SIGN consist of mannose oligosaccharides or fucose-containing Lewis-type determinants. Using the known 3D structure of the Lewis-x trisaccharide, we have identified some monovalent alpha-fucosylamides that bind to DC-SIGN with inhibitory constants 0.4-0.5 mM, as determined by SPR, and have characterized their interaction with the protein by STD NMR spectroscopy. This work establishes for the first time alpha-fucosylamides as functional mimics of chemically and enzymatically unstable alpha-fucosides and describes interesting candidates for the preparation of multivalent systems able to block the receptor DC-SIGN with high affinity and with potential biomedical applications.
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Arosio D, Belvisi L, Colombo L, Colombo M, Invernizzi D, Manzoni L, Potenza D, Serra M, Castorina M, Pisano C, Scolastico C. A Potent Integrin Antagonist from a Small Library of Cyclic RGD Pentapeptide Mimics Including Benzyl-Substituted Azabicycloalkane Amino Acids. ChemMedChem 2008; 3:1589-603. [DOI: 10.1002/cmdc.200800143] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Potenza D, Belvisi L. Transferred-NOE NMR experiments on intact human platelets: receptor-bound conformation of RGD-peptide mimics. Org Biomol Chem 2008; 6:258-62. [DOI: 10.1039/b713036h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Pistelli L, Noccioli C, Bertoli A, Scapecchi G, Potenza D. Chemical composition and volatile constituents ofAnthyllis barba-jovis. Nat Prod Res 2007; 21:418-25. [PMID: 17487613 DOI: 10.1080/14786410600577524] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Six flavonol glycosides were isolated and identified from the aerial parts of Anthyllis barba-jovis L. (Leguminosae), together with two coumarins and D-pinitol, a taxonomic marker of Leguminosae family. The structural elucidation of all compounds was based on their (1)H- and (13)C-NMR spectral data and bidimensional experiments. The total flavonoid content was also determined, according to the method described in the Italian pharmacopoeia. In order to complete the phytochemical investigation on A. barba-jovis, the essential oils from flowers and seeds were obtained by hydrodistillation and analysed by GC-MS; fresh flowers were analysed also directly by solid phase micro extraction (SPME).
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Terraneo G, Potenza D, Canales A, Jiménez-Barbero J, Baldridge KK, Bernardi A. A Simple Model System for the Study of Carbohydrate−Aromatic Interactions. J Am Chem Soc 2007; 129:2890-900. [PMID: 17309255 DOI: 10.1021/ja066633g] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A molecular scaffold was identified which enables the establishment of intramolecular interactions between a monosaccharide and a nearby phenyl ring. A group of molecules containing four different monosaccharides (glucose, galactose, N-acetyl-glucosamine, and N-acetyl-galactosamine) was synthesized and used to investigate the extent and nature of this carbohydrate-arene interaction, as well as the effect on the overall 3D structure of the molecules involved. The sugar-aromatic distance was evaluated by rigorous NMR studies supported by molecular modeling and found to be constant throughout the series, independent of the nature of the sugar and of the conformational behavior of the fragment connecting the two elements. Ab initio calculations at the B3LYP/DZV(2d,p) level of theory enable the analysis of the electronic nature of the interaction. The study shows that, given the opportunity, persistent intramolecular aromatic-sugar interactions can be established and can significantly influence overall molecular shape and energetics. These results have important implications in the design of structural mimics of oligosaccharides.
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Pistelli L, Noccioli C, Giachi I, Dimitrova B, Gevrenova R, Morelli I, Potenza D. Lupane-triterpenes from Bupleurum flavum. Nat Prod Res 2006; 19:783-8. [PMID: 16317832 DOI: 10.1080/14786410500045119] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Two new triterpenoids, lup-20(29)-en-3 alpha, 28-diol (1) and lup-20(29)-en-3 alpha, 28,30-triol (2), have been isolated from aerial parts of Bupleurum flavum, a native plant of the Eastern Mediterranean area (Bulgaria, Greece, and Turkey). Their structures were elucidated by spectral analysis. The known compounds betulin, betulinic acid, jasminol, together with the lignan nemerosin and eight flavonoids (kaempferol, isokaempferide, gossipetin, quercetin, luteolin, isorhamnetin 3-O-beta-D-glucopyranoside, isorhamnetin 3-rutinoside, and rutin) were also characterized.
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Belvisi L, Riccioni T, Marcellini M, Vesci L, Chiarucci I, Efrati D, Potenza D, Scolastico C, Manzoni L, Lombardo K, Stasi MA, Orlandi A, Ciucci A, Nico B, Ribatti D, Giannini G, Presta M, Carminati P, Pisano C. Biological and molecular properties of a new alpha(v)beta3/alpha(v)beta5 integrin antagonist. Mol Cancer Ther 2006; 4:1670-80. [PMID: 16275988 DOI: 10.1158/1535-7163.mct-05-0120] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of the present study was to identify specific alpha(v)beta3/alpha(v)beta5 integrin antagonists active on tumor-induced angiogenesis. To this purpose, in vitro integrin-binding assays were used to screen a library of conformationally constrained bicyclic lactam Arg-Gly-Asp-containing pseudopeptides. The results identified ST1646 as a high-affinity specific ligand for alpha(v)beta3 and alpha(v)beta5 integrins with negligible interacting with alpha5beta1 integrin. In all the assays, ST1646 was equipotent to or more potent than the well-characterized integrin antagonists c(RGDfV) and cyclo(Arg-Gly-Asp-d-Phe-[NMe]Val) (EMD121974). In the chorioallantoic membrane assay, topical administration of ST1646 was able to prevent the angiogenic responses elicited by recombinant fibroblast growth factor-2 or vascular endothelial growth factor. In addition, systemic administration of ST1646 in mice exerted a significant antiangiogenic activity on neovascularization triggered by mammary carcinoma MDA-MB435 cells implanted s.c. in a dorsal air sac via a (Millipore Filter Corporation, Bedford, MA) chamber. Moreover, ST1646 delivery via an osmotic pump inhibited the growth and vascularization of tumor xenografts originating from the injection of alpha(v)beta3/alpha(v)beta5-expressing human ovarian carcinoma cells in nude mice. In agreement with the biochemical and pharmacologic studies, Monte Carlo/Stochastic Dynamics simulation showed that the bicyclic scaffold in ST1646 forced the compound to assume a preferred conformation superimposable to the X-ray conformation of alpha(v)beta3-bound EMD121974. Accordingly, computer-docking studies indicated that the ST1646-alpha(v)beta3 integrin complex maintains the ligand-receptor distances and interactions observed in the crystalline EMD121974-alpha(v)beta3 integrin complex. Taken together, these observations indicate that ST1646 represents a dual alpha(v)beta3/alpha(v)beta5 integrin antagonist with interesting biochemical and biological features to be tested in cancer therapy.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Arginine/chemistry
- Aspartic Acid/chemistry
- Cattle
- Cell Adhesion
- Cell Line, Tumor
- Cell Proliferation
- Chickens
- Crystallography, X-Ray
- Dose-Response Relationship, Drug
- Endothelium, Vascular/cytology
- Fibroblast Growth Factor 2/metabolism
- Glycine/chemistry
- Guinea Pigs
- Humans
- Inhibitory Concentration 50
- Integrin alphaVbeta3/antagonists & inhibitors
- Integrins/antagonists & inhibitors
- Integrins/metabolism
- Ligands
- Mice
- Mice, Nude
- Microcirculation
- Models, Chemical
- Models, Molecular
- Molecular Conformation
- Monte Carlo Method
- Neoplasm Transplantation
- Neovascularization, Pathologic
- Oligopeptides/chemistry
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/pharmacology
- Platelet Aggregation
- Protein Binding
- Protein Conformation
- Receptors, Vitronectin/antagonists & inhibitors
- Recombinant Proteins/chemistry
- Stochastic Processes
- Vascular Endothelial Growth Factor A/metabolism
- Vitronectin/chemistry
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Belvisi L, Bernardi A, Colombo M, Manzoni L, Potenza D, Scolastico C, Giannini G, Marcellini M, Riccioni T, Castorina M, LoGiudice P, Pisano C. Targeting integrins: insights into structure and activity of cyclic RGD pentapeptide mimics containing azabicycloalkane amino acids. Bioorg Med Chem 2005; 14:169-80. [PMID: 16214345 DOI: 10.1016/j.bmc.2005.08.048] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 08/02/2005] [Indexed: 11/22/2022]
Abstract
A small library of cyclic RGD pentapeptide mimics incorporating stereoisomeric 5,6- and 5,7-fused bicyclic lactams was synthesized. This library was found to contain high-affinity ligands for the alpha(v)beta3 integrin. The aim of this study was to investigate activity, selectivity, and structure of these ligands in order to identify new specific alpha(v)-integrin antagonists that could be evaluated as tumor angiogenesis inhibitors. In vitro screening, including receptor-binding assays to purified alpha(v)beta3, alpha(v)beta5, and alpha5beta1 integrins, and platelet aggregation assay, revealed ST1646 as a potent, highly selective alpha(v)beta3/alpha(v)beta5 integrin antagonist. Structure determination of the cyclic RGD pentapeptide mimics performed by a combination of NMR spectroscopy, and molecular mechanics and dynamics calculations showed a strong dependence of the RGD cyclopeptide conformation on lactam ring size and stereochemistry. ST1646 revealed the highest ability within the library to adopt the proper RGD orientation required for binding to the alpha(v)beta3 integrin, as deduced from the recently solved crystal structure of the extracellular segment of integrin alpha(v)beta3 in complex with a cyclic pentapeptide ligand.
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Mari S, Posteri H, Marcou G, Potenza D, Micheli F, Cañada F, Jimenez-Barbero J, Bernardi A. Synthesis, Conformational Studies and Mannosidase Stability of a Mimic of 1,2-Mannobioside. European J Org Chem 2004. [DOI: 10.1002/ejoc.200400520] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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44
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Trabocchi A, Potenza D, Guarna A. Solvent-Dependent Conformational Behaviour of Model Tetrapeptides Containing a Bicyclic Proline Mimetic. European J Org Chem 2004. [DOI: 10.1002/ejoc.200400359] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Bernardi A, Arosio D, Potenza D, Sánchez-Medina I, Mari S, Cañada FJ, Jiménez-Barbero J. Intramolecular Carbohydrate-Aromatic Interactions and Intermolecular van der Waals Interactions Enhance the Molecular Recognition Ability of GM1 Glycomimetics for Cholera Toxin. Chemistry 2004; 10:4395. [PMID: 15378617 DOI: 10.1002/chem.200400084] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The design and synthesis of two GM1 glycomimetics, 6 and 7, and analysis of their conformation in the free state and when complexed to cholera toxin is described. These compounds, which include an (R)-cyclohexyllactic acid and an (R)-phenyllactic acid fragment, respectively, display significant affinity for cholera toxin. A detailed NMR spectroscopy study of the toxin/glycomimetic complexes, assisted by molecular modeling techniques, has allowed their interactions with the toxin to be explained at the atomic level. It is shown that intramolecular van der Waals and CH-pi carbohydrate-aromatic interactions define the conformational properties of 7, which adopts a three-dimensional structure significantly preorganized for proper interaction with the toxin. The exploitation of this kind of sugar-aromatic interaction, which is very well described in the context of carbohydrate/protein complexes, may open new avenues for the rational design of sugar mimics.
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Scolastico C, Belvisi L, Colombo L, Manzoni L, Potenza D. Design, Synthesis, Conformational Analysis and Application of Azabicycloalkane Amino Acids as Constrained Dipeptide Mimics. Synlett 2004. [DOI: 10.1055/s-2004-829540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Arosio D, Baretti S, Cattaldo S, Potenza D, Bernardi A. Ganglioside GM1 mimics: lipophilic substituents improve affinity for cholera toxin. Bioorg Med Chem Lett 2003; 13:3831-4. [PMID: 14552790 DOI: 10.1016/j.bmcl.2003.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ganglioside GM1 mimics including (R)-2-hydroxy-3-cyclohexylpropionic acid or (R)-2-hydroxy-3-phenylpropionic acid as replacements for NeuAc are stronger cholera toxin binders than the parent ligand 2, which includes (R)-2-hydroxy-propionic acid.
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Bernardi A, Arosio D, Manzoni L, Monti D, Posteri H, Potenza D, Mari S, Jiménez-Barbero J. Mimics of ganglioside GM1 as cholera toxin ligands: replacement of the GalNAc residue. Org Biomol Chem 2003; 1:785-92. [PMID: 12929360 DOI: 10.1039/b210503a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new cholera toxin (CT) ligands (4 and 5) are described. The new ligands were designed starting from the known GM1 mimics 2 and 3 by replacement of their GalNAc residue with the C4 isomer GlcNAc. As predicted by molecular modelling, the conformational properties of the equivalent pairs 2-4 and 3-5 are very similar and their affinity for CT is of the same order of magnitude. NMR experiments have also proved that 5 occupies the GM1-binding site of the toxin and have revealed its bound conformation.
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49
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Belvisi L, Caporale A, Colombo M, Manzoni L, Potenza D, Scolastico C, Castorina M, Cati M, Giannini G, Pisano C. Cyclic RGD Peptides Containing Azabicycloalkane Reverse-Turn Mimics. Helv Chim Acta 2002. [DOI: 10.1002/hlca.200290017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Bernardi A, Potenza D, Capelli AM, García-Herrero A, Cañada FJ, Jiménez-Barbero J. Second-generation mimics of ganglioside GM1 oligosaccharide: a three-dimensional view of their interactions with bacterial enterotoxins by NMR and computational methods. Chemistry 2002; 8:4597-612. [PMID: 12362397 DOI: 10.1002/1521-3765(20021018)8:20<4597::aid-chem4597>3.0.co;2-u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
As a step to delineate a strategy of ligand design for cholera toxin (CT), NMR studies were performed on several mimics of the GM1 ganglioside oligosaccharide. The conformation of these analogues was investigated first in solution and then upon binding to cholera toxin by transferred nuclear Overhauser effect (TR-NOE) measurements. It was demonstrated that CT selects a conformation similar to the global minima of the free saccharides from the ensemble of presented conformations. No evidence of major conformational distortions was obtained, but one or two of the available conformers of the hydroxyacid side chain appear to be selected in the bound state. The NMR data were interpreted with the aid of computer models, generated and analyzed by using a combination of different approaches (MacroModels' MC/EM and MC/SD, Autodock, and GRID). Analysis of the NMR data supported by computational studies allowed us to interpret the experimental observations and to derive workable models of the ligand:toxin complexes. These models suggest that the higher affinity of the (R)-lactic acid derivative 3 may stem from lipophilic interactions with a hydrophobic area in the toxin binding site located in the vicinity of the sialic acid side chain binding region of the CT:GM1 complex, and formed by the side chain of Ile-58 and Lys-34. Thus, the models obtained have allowed us to make useful design suggestions for the improvement of ligand affinity.
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