101
|
Caumes C, Hjelmgaard T, Roy O, Reynaud M, Servent D, Taillefumier C, Faure S. Synthesis and binding affinities for sst receptors of cyclic peptoid SRIF-mimetics. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20265d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthesis of the first all-peptoid SRIF (Somatotropin Release-Inhibiting Factor) analogues and evaluation of their binding affinities for the five human somatostatin receptors (hsst1–5).
Collapse
Affiliation(s)
- Cécile Caumes
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Thomas Hjelmgaard
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Olivier Roy
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Morgane Reynaud
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Denis Servent
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Claude Taillefumier
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Sophie Faure
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| |
Collapse
|
102
|
Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
| | | |
Collapse
|
103
|
Whitby LR, Ando Y, Setola V, Vogt PK, Roth BL, Boger DL. Design, synthesis, and validation of a β-turn mimetic library targeting protein-protein and peptide-receptor interactions. J Am Chem Soc 2011; 133:10184-94. [PMID: 21609016 DOI: 10.1021/ja201878v] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design and synthesis of a β-turn mimetic library as a key component of a small-molecule library targeting the major recognition motifs involved in protein-protein interactions is described. Analysis of a geometric characterization of 10,245 β-turns in the protein data bank (PDB) suggested that trans-pyrrolidine-3,4-dicarboxamide could serve as an effective and synthetically accessible library template. This was confirmed by initially screening select compounds against a series of peptide-activated GPCRs that recognize a β-turn structure in their endogenous ligands. This validation study was highlighted by identification of both nonbasic and basic small molecules with high affinities (K(i) = 390 and 23 nM, respectively) for the κ-opioid receptor (KOR). Consistent with the screening capabilities of collaborators and following the design validation, the complete library was assembled as 210 mixtures of 20 compounds, providing a total of 4200 compounds designed to mimic all possible permutations of 3 of the 4 residues in a naturally occurring β-turn. Unique to the design and because of the C(2) symmetry of the template, a typical 20 × 20 × 20-mix (8000 compounds prepared as 400 mixtures of 20 compounds) needed to represent 20 variations in the side chains of three amino acid residues reduces to a 210 × 20-mix, thereby simplifying the library synthesis and subsequent screening. The library was prepared using a solution-phase synthetic protocol with liquid-liquid or liquid-solid extractions for purification and conducted on a scale that insures its long-term availability for screening campaigns. Screening the library against the human opioid receptors (KOR, MOR, and DOR) identified not only the activity of library members expected to mimic the opioid receptor peptide ligands but also additional side-chain combinations that provided enhanced receptor binding selectivities (>100-fold) and affinities (as low as K(i) = 80 nM for KOR). A key insight to emerge from the studies is that the phenol of Tyr in endogenous ligands bearing the H-Tyr-Pro-Trp/Phe-Phe-NH(2) β-turn is important for MOR binding but may not be important for KOR (accommodated, but not preferred) and that the resulting selectivity for KOR observed with its removal can be increased by replacing the phenol OH with a chlorine substituent, further enhancing KOR affinity.
Collapse
Affiliation(s)
- Landon R Whitby
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | | | | | | | |
Collapse
|
104
|
Pinsker A, Einsiedel J, Härterich S, Waibel R, Gmeiner P. A Highly Efficient Type I β-Turn Mimetic Simulating an Asx-Pro-Turn-Like Structure. Org Lett 2011; 13:3502-5. [DOI: 10.1021/ol201313q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Andrea Pinsker
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Jürgen Einsiedel
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Steffen Härterich
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Reiner Waibel
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstrasse 19, 91052 Erlangen, Germany
| |
Collapse
|
105
|
Seebach D, Lukaszuk A, Patora-Komisarska K, Podwysocka D, Gardiner J, Ebert MO, Reubi JC, Cescato R, Waser B, Gmeiner P, Hübner H, Rougeot C. On the Terminal Homologation of Physiologically Active Peptides as a Means of Increasing Stability in Human Serum - Neurotensin, Opiorphin, B27-KK10 Epitope, NPY. Chem Biodivers 2011; 8:711-39. [DOI: 10.1002/cbdv.201100093] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
106
|
Use of secondary structure element information in drug design: polypharmacology and conserved motifs in protein–ligand binding and protein–protein interfaces. Future Med Chem 2011; 3:699-708. [DOI: 10.4155/fmc.11.26] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The structure-based design of small-molecule inhibitors of protein–ligand and protein–protein interfaces is a key component of drug discovery. The underlying protein interactions can be regarded based on structural similarity of the secondary structure elements: similarities around the binding site (‘ligand-sensing cores’) or in the protein interface (‘interface-sensing surfaces’) in otherwise unrelated proteins can be useful in predicting polypharmacology and identifying new lead structures. Even small conserved motifs can provide similar interaction patterns in proteins with a completely different fold and function. The identification of these structural similarities can help in the design of new drugs by guiding further optimization. Here, the concepts and ideas based on secondary structure element similarities and their successful applications in drug design are reviewed and discussed.
Collapse
|
107
|
Guitot K, Larregola M, Pradhan TK, Vasse JL, Lavielle S, Bertus P, Szymoniak J, Lequin O, Karoyan P. The Combination of Prolinoamino Acids and Cyclopropylamino Acids Leads to Fully Functionalized, Stable β-Turns in Water. Chembiochem 2011; 12:1039-42. [DOI: 10.1002/cbic.201000707] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Indexed: 12/17/2022]
|
108
|
Gruber CW, Muttenthaler M, Freissmuth M. Ligand-based peptide design and combinatorial peptide libraries to target G protein-coupled receptors. Curr Pharm Des 2011; 16:3071-88. [PMID: 20687879 DOI: 10.2174/138161210793292474] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 07/21/2010] [Indexed: 01/20/2023]
Abstract
G protein-coupled receptors (GPCRs) are considered to represent the most promising drug targets; it has been repeatedly said that a large fraction of the currently marketed drugs elicit their actions by binding to GPCRs (with cited numbers varying from 30-50%). Closer scrutiny, however, shows that only a modest fraction of (≈60) GPCRs are, in fact, exploited as drug targets, only ≈20 of which are peptide-binding receptors. The vast majority of receptors in the humane genome have not yet been explored as sites of action for drugs. Given the drugability of this receptor class, it appears that opportunities for drug discovery abound. In addition, GPCRs provide for binding sites other than the ligand binding sites (referred to as the "orthosteric site"). These additional sites include (i) binding sites for ligands (referred to as "allosteric ligands") that modulate the affinity and efficacy of orthosteric ligands, (ii) the interaction surface that recruits G proteins and arrestins, (iii) the interaction sites of additional proteins (GIPs, GPCR interacting proteins that regulate G protein signaling or give rise to G protein-independent signals). These sites can also be targeted by peptides. Combinatorial and natural peptide libraries are therefore likely to play a major role in identifying new GPCR ligands at each of these sites. In particular the diverse natural peptide libraries such as the venom peptides from marine cone-snails and plant cyclotides have been established as a rich source of drug leads. High-throughput screening and combinatorial chemistry approaches allow for progressing from these starting points to potential drug candidates. This will be illustrated by focusing on the ligand-based drug design of oxytocin (OT) and vasopressin (AVP) receptor ligands using natural peptide leads as starting points.
Collapse
Affiliation(s)
- Christian W Gruber
- Institute of Pharmacology, Center of Biomolecular Medicine & Pharmacology, Medical University of Vienna, Waehringer Str. 13a, A-1090 Vienna, Austria
| | | | | |
Collapse
|
109
|
Sacchetti A, Silvani A, Lesma G, Pilati T. Phe-Ala-Based Diazaspirocyclic Lactam as Nucleator of Type II′ β-Turn. J Org Chem 2011; 76:833-9. [DOI: 10.1021/jo1019927] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Alessandro Sacchetti
- Politecnico di Milano, Dipartimento di Chimica, Materiali ed Ingegneria Chimica ‘Giulio Natta’, via Mancinelli 7, 20131 Milano, Italy
| | - Alessandra Silvani
- Dipartimento di Chimica Organica e Industriale, Università degli Studi di Milano, via G. Venezian 21, 20133 Milano, Italy
| | - Giordano Lesma
- Dipartimento di Chimica Organica e Industriale, Università degli Studi di Milano, via G. Venezian 21, 20133 Milano, Italy
| | - Tullio Pilati
- Istituto di Scienze e Tecnologie Molecolari − CNR, Via Golgi 19, 20133 Milano, Italy
| |
Collapse
|
110
|
Gayen A, Goswami SK, Mukhopadhyay C. NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:127-39. [DOI: 10.1016/j.bbamem.2010.09.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 08/24/2010] [Accepted: 09/22/2010] [Indexed: 01/30/2023]
|
111
|
Belen’kii L, Gramenitskaya V, Evdokimenkova Y. The Literature of Heterocyclic Chemistry, Part X, 2005–2007. ADVANCES IN HETEROCYCLIC CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-385464-3.00001-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
112
|
Harrison RS, Ruiz-Gómez G, Hill TA, Chow SY, Shepherd NE, Lohman RJ, Abbenante G, Hoang HN, Fairlie DP. Novel helix-constrained nociceptin derivatives are potent agonists and antagonists of ERK phosphorylation and thermal analgesia in mice. J Med Chem 2010; 53:8400-8. [PMID: 21067234 DOI: 10.1021/jm101139f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nociceptin opioid peptide receptor (NOP, NOR, ORL-1) is a GPCR that recognizes nociceptin, a 17-residue peptide hormone. Nociceptin regulates pain transmission, learning, memory, anxiety, locomotion, cardiovascular and respiratory stress, food intake, and immunity. Nociceptin was constrained using an optimized helix-inducing cyclization strategy to produce the most potent NOP agonist (EC50 = 40 pM) and antagonist (IC50 = 7.5 nM) known. Alpha helical structures were measured in water by CD and 2D (1)H NMR spectroscopy. Agonist and antagonist potencies, evaluated by ERK phosphorylation in mouse neuroblastoma cells natively expressing NOR, increased 20-fold and 5-fold, respectively, over nociceptin. Helix-constrained peptides with key amino acid substitutions had much higher in vitro activity, serum stability, and thermal analgesic activity in mice, without cytotoxicity. The most potent agonist increased hot plate contact time from seconds up to 60 min; the antagonist prevented this effect. Such helix-constrained peptides may be valuable physiological probes and therapeutics for treating some forms of pain.
Collapse
Affiliation(s)
- Rosemary S Harrison
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
113
|
Allin SM, Towler J, Gaskell SN, Saha B, Martin WP, Page PCB, Edgar M. Enolate amination and derivatization of a pyrroloisoquinoline template: towards novel peptidomimetics. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
114
|
Proteau-Gagné A, Bournival V, Rochon K, Dory YL, Gendron L. Exploring the Backbone of Enkephalins To Adjust Their Pharmacological Profile for the δ-Opioid Receptor. ACS Chem Neurosci 2010; 1:757-69. [PMID: 22778812 DOI: 10.1021/cn1000759] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 09/08/2010] [Indexed: 12/23/2022] Open
Abstract
The role of each of the four amide bonds in Leu(5)-enkephalin was investigated by systematically and sequentially replacing each with its corresponding trans-alkene. Six Leu(5)-enkephalin analogs based on six dipeptide surrogates and two Met(5)-enkephalin analogs were synthesized and thoroughly tested using a δ-opioid receptor internalization assay, an ERK1/2 activation assay, and a competition binding assay to evaluate their biological properties. We observed that an E-alkene can efficiently replace the first amide bond of Leu(5)- and Met(5)-enkephalin without significantly affecting biological activity. By contrast, the second amide bond was found to be highly sensitive to the same modification, suggesting that it is involved in biologically essential intra- or intermolecular interactions. Finally, we observed that the affinity and activity of analogs containing an E-alkene at either the third or fourth position were partially reduced, indicating that these amide bonds are less important for these intra- or intermolecular interactions. Overall, our study demonstrates that the systematic and sequential replacement of amide bonds by E-alkene represents an efficient way to explore peptide backbones.
Collapse
Affiliation(s)
| | | | | | - Yves L. Dory
- Laboratoire de synthèse supramoléculaire, Département de chimie,
| | | |
Collapse
|
115
|
Mayorov AV, Cai M, Palmer ES, Liu Z, Cain JP, Vagner J, Trivedi D, Hruby VJ. Solid-phase peptide head-to-side chain cyclodimerization: discovery of C(2)-symmetric cyclic lactam hybrid α-melanocyte-stimulating hormone (MSH)/agouti-signaling protein (ASIP) analogues with potent activities at the human melanocortin receptors. Peptides 2010; 31:1894-905. [PMID: 20688117 PMCID: PMC3041174 DOI: 10.1016/j.peptides.2010.06.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/23/2010] [Accepted: 06/23/2010] [Indexed: 02/05/2023]
Abstract
A novel hybrid melanocortin pharmacophore was designed based on the pharmacophores of the agouti-signaling protein (ASIP), an endogenous melanocortin antagonist, and α-melanocyte-stimulating hormone (α-MSH), an endogenous melanocortin agonist. The designed hybrid ASIP/MSH pharmacophore was explored in monomeric cyclic, and cyclodimeric templates. The monomeric cyclic disulfide series yielded peptides with hMC3R-selective non-competitive binding affinities. The direct on-resin peptide lactam cyclodimerization yielded nanomolar range (25-120 nM) hMC1R-selective full and partial agonists in the cyclodimeric lactam series which demonstrates an improvement over the previous attempts at hybridization of MSH and agouti protein sequences. The secondary structure-oriented pharmacophore hybridization strategy will prove useful in development of unique allosteric and orthosteric melanocortin receptor modulators. This report also illustrates the utility of peptide cyclodimerization for the development of novel GPCR peptide ligands.
Collapse
Affiliation(s)
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Erin S. Palmer
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Zhihua Liu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - James P. Cain
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Josef Vagner
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Dev Trivedi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, USA
| |
Collapse
|
116
|
Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions. J Comput Aided Mol Des 2010; 24:917-34. [PMID: 20862601 DOI: 10.1007/s10822-010-9384-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/31/2010] [Indexed: 12/22/2022]
Abstract
Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.
Collapse
|
117
|
Sellers RP, Alexander LD, Johnson VA, Lin CC, Savage J, Corral R, Moss J, Slugocki TS, Singh EK, Davis MR, Ravula S, Spicer JE, Oelrich JL, Thornquist A, Pan CM, McAlpine SR. Design and synthesis of Hsp90 inhibitors: exploring the SAR of Sansalvamide A derivatives. Bioorg Med Chem 2010; 18:6822-56. [PMID: 20708938 PMCID: PMC2933939 DOI: 10.1016/j.bmc.2010.07.042] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/13/2010] [Accepted: 07/19/2010] [Indexed: 01/10/2023]
Abstract
Utilizing the structure-activity relationship we have developed during the synthesis of the first two generations and mechanism of action studies that point to the interaction of these molecules with the key oncogenic protein Hsp90, we report here the design of 32 new Sansalvamide A derivatives and their synthesis. Our new structures, designed from previously reported potent compounds, were tested for cytotoxicity on the HCT116 colon cancer cell line, and their binding to the biological target was analyzed using computational studies involving blind docking of derivatives using Autodock. Further, we show new evidence that our molecules bind directly to Hsp90 and modulate Hsp90's binding with client proteins. Finally, we demonstrate that we have integrated good ADME properties into a new derivative.
Collapse
Affiliation(s)
- Robert P. Sellers
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Leslie D. Alexander
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Victoria A. Johnson
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Chun-Chieh Lin
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Jeremiah Savage
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Ricardo Corral
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Jason Moss
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Tim S. Slugocki
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Erinprit K. Singh
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Melinda R. Davis
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Suchitra Ravula
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Jamie E. Spicer
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Jenna L. Oelrich
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Andrea Thornquist
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Chung-Mao Pan
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| | - Shelli R. McAlpine
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030. Tel: 619-594-5580, fax: 619-594-4634
| |
Collapse
|
118
|
Di Cianni A, Carotenuto A, Brancaccio D, Novellino E, Reubi JC, Beetschen K, Papini AM, Ginanneschi M. Novel Octreotide Dicarba-analogues with High Affinity and Different Selectivity for Somatostatin Receptors. J Med Chem 2010; 53:6188-97. [DOI: 10.1021/jm1005868] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alessandra Di Cianni
- Laboratory of Peptides & Proteins, Chemistry & Biology, University of Firenze, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 5-13, I-50019, Sesto Fiorentino, Italy
| | - Alfonso Carotenuto
- Department of Pharmaceutical Chemistry and Toxicology, University of Napoli, Via Domenico Montesano 49, I-80131 Napoli, Italy
| | - Diego Brancaccio
- Department of Pharmaceutical Chemistry and Toxicology, University of Napoli, Via Domenico Montesano 49, I-80131 Napoli, Italy
| | - Ettore Novellino
- Department of Pharmaceutical Chemistry and Toxicology, University of Napoli, Via Domenico Montesano 49, I-80131 Napoli, Italy
| | - Jean Claude Reubi
- Division of Cell Biology and Experimental Cancer Research, Institute of Pathology, University of Berne, Murtenstrasse 31, CH-3010 Berne, Switzerland
| | - Karin Beetschen
- Division of Cell Biology and Experimental Cancer Research, Institute of Pathology, University of Berne, Murtenstrasse 31, CH-3010 Berne, Switzerland
| | - Anna Maria Papini
- Laboratory of Peptides & Proteins, Chemistry & Biology, University of Firenze, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 5-13, I-50019, Sesto Fiorentino, Italy
| | - Mauro Ginanneschi
- Laboratory of Peptides & Proteins, Chemistry & Biology, University of Firenze, Via della Lastruccia 13, I-50019 Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 5-13, I-50019, Sesto Fiorentino, Italy
| |
Collapse
|
119
|
Sawai Y, Yamane T, Ikeuchi M, Kawaguchi S, Yamada M, Yamano M. Process for the Preparation of an Amorphous, Peptide-like Diabetes Drug: Approach to a Chromatography-Free Process. Org Process Res Dev 2010. [DOI: 10.1021/op100084r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yasuhiro Sawai
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Taihei Yamane
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Motoki Ikeuchi
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Shinji Kawaguchi
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Masatoshi Yamada
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| | - Mitsuhisa Yamano
- Chemical Development Laboratories, CMC Center, Takeda Pharmaceutical Company Limited, 17-85, Jusohonmachi 2-chome, Yodogawa-ku, Osaka 532-8686, Japan
| |
Collapse
|
120
|
Cupido T, Spengler J, Ruiz-Rodriguez J, Adan J, Mitjans F, Piulats J, Albericio F. Amide-to-ester substitution allows fine-tuning of the cyclopeptide conformational ensemble. Angew Chem Int Ed Engl 2010; 49:2732-7. [PMID: 20213784 DOI: 10.1002/anie.200907274] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Tommaso Cupido
- Institute for Research in Biomedicine (IRB), Barcelona Science Park (PCB) and CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, PCB Baldiri Reixac 10, 08028 Barcelona, Spain.
| | | | | | | | | | | | | |
Collapse
|
121
|
Lim HA, Kang C, Chia CSB. Solid-Phase Synthesis and NMR Structural Studies of the Marine Antibacterial Cyclic Tetrapeptide: Cyclo[GSPE]. Int J Pept Res Ther 2010. [DOI: 10.1007/s10989-010-9216-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
122
|
Scully CCG, Blakeney JS, Singh R, Hoang HN, Abbenante G, Reid RC, Fairlie DP. Selective Hexapeptide Agonists and Antagonists for Human Complement C3a Receptor. J Med Chem 2010; 53:4938-48. [DOI: 10.1021/jm1003705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Conor C. G. Scully
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jade S. Blakeney
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ranee Singh
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Giovanni Abbenante
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert C. Reid
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|
123
|
Lesma G, Landoni N, Sacchetti A, Silvani A. The spiropiperidine-3,3′-oxindole scaffold: a type II β-turn peptide isostere. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.04.077] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
124
|
Macaluso NM, Glen R. Exploring the ‘RPRL’ Motif of Apelin-13 through Molecular Simulation and Biological Evaluation of Cyclic Peptide Analogues. ChemMedChem 2010; 5:1247-53. [DOI: 10.1002/cmdc.201000061] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
125
|
Yang D, Liu GJ, Hao Y, Li W, Dong ZM, Zhang DW, Zhu NY. Conformational Studies on Peptides of α-Aminoxy Acids with Functionalized Side Chains. Chem Asian J 2010; 5:1356-63. [DOI: 10.1002/asia.200900636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
126
|
Cupido T, Spengler J, Ruiz-Rodriguez J, Adan J, Mitjans F, Piulats J, Albericio F. Amide-to-Ester Substitution Allows Fine-Tuning of the Cyclopeptide Conformational Ensemble. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
127
|
Pérez de Vega MJ, García-Aranda MI, González-Muñiz R. A role for ring-closing metathesis in medicinal chemistry: Mimicking secondary architectures in bioactive peptides. Med Res Rev 2010; 31:677-715. [DOI: 10.1002/med.20199] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
128
|
Endothelin-A receptor antagonism attenuates carcinoma-induced pain through opioids in mice. THE JOURNAL OF PAIN 2010; 11:663-71. [PMID: 20071245 DOI: 10.1016/j.jpain.2009.10.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 09/10/2009] [Accepted: 10/08/2009] [Indexed: 12/17/2022]
Abstract
UNLABELLED We previously reported that endothelin A (ET-A) receptor antagonism attenuates carcinoma-induced pain in a cancer pain mouse model. In this study, we investigated the mechanism of ET-A receptor-mediated antinociception and evaluated the role of endogenous opioid analgesia. Squamous cell carcinoma (SCC) cell culture treated with the ET-A receptor antagonist (BQ-123) at 10(-6) M and 10(-5) M significantly increased production and secretion of beta-endorphin and leu-enkephalin, respectively. Behavioral studies were performed by inducing tumors in the hind paw of female nude mice with local injection of cells derived from a human oral SCC. Significant pain, as indicated by reduction in withdrawal thresholds in response to mechanical stimulation, began at 4 days after SCC inoculation and lasted to 18 days, the last day of measurement. Local administration of either naloxone methiodide (500 microg/kg), selective antagonists for mu-opioid receptor (CTOP, 500 microg/kg), or delta-opioid receptor (naltrindole, 11 mg/kg) but not kappa-opioid receptor (nor-BNI, 2.5 mg/kg) significantly reversed antinociception observed from ET-A receptor antagonism (BQ-123, 92 mg/kg) in cancer animals. These results demonstrate that antagonism of peripheral ET-A receptor attenuates carcinoma pain by modulating release of endogenous opioids to act on opioid receptors in the cancer microenvironment. PERSPECTIVE This article proposes a novel mechanism for ET-A receptor antagonist drugs in managing cancer-induced pain. An improved understanding of the role of innate opioid analgesia in ET-A receptor-mediated antinociception might provide novel alternatives to morphine therapy for the treatment of cancer pain.
Collapse
|
129
|
|
130
|
Mothes C, Larregola M, Quancard J, Goasdoué N, Lavielle S, Chassaing G, Lequin O, Karoyan P. Prolinoamino Acids as Tools to Build Bifunctionalized, Stable β-Turns in Water. Chembiochem 2009; 11:55-8. [DOI: 10.1002/cbic.200900572] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
131
|
DeLorbe JE, Clements JH, Teresk MG, Benfield AP, Plake HR, Millspaugh LE, Martin SF. Thermodynamic and Structural Effects of Conformational Constraints in Protein−Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. J Am Chem Soc 2009; 131:16758-70. [DOI: 10.1021/ja904698q] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- John E. DeLorbe
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - John H. Clements
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Martin G. Teresk
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Aaron P. Benfield
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Hilary R. Plake
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Laura E. Millspaugh
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| | - Stephen F. Martin
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, and The Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, Texas 78712
| |
Collapse
|
132
|
Grauer A, König B. Peptidomimetics – A Versatile Route to Biologically Active Compounds. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900599] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andreas Grauer
- Institute für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany, Fax: +49‐941‐943‐1717
| | - Burkhard König
- Institute für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany, Fax: +49‐941‐943‐1717
| |
Collapse
|
133
|
Tetrahydroisoquinoline-Based Spirocyclic Lactam as a Type II′ β-Turn Inducing Peptide Mimetic. J Org Chem 2009; 74:8098-105. [DOI: 10.1021/jo901480d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
134
|
Langelaan DN, Rainey JK. Headgroup-dependent membrane catalysis of apelin-receptor interactions is likely. J Phys Chem B 2009; 113:10465-71. [PMID: 19708686 PMCID: PMC2736645 DOI: 10.1021/jp904562q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 06/11/2009] [Indexed: 12/18/2022]
Abstract
Apelin is the peptidic ligand for the G-protein-coupled receptor APJ. The apelin-APJ system is important in cardiovascular regulation, fluid homeostasis, and angiogenesis, among other roles. In this study, we investigate interactions between apelin and membrane-mimetic micelles of the detergents sodium dodecyl sulfate (SDS), dodecylphosphocholine (DPC), and 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG). Far-ultraviolet circular dichroism spectropolarimetry and diffusion-ordered spectroscopy indicate that apelin peptides bind to micelles of the anionic detergents SDS and LPPG much more favorably than to zwitterionic DPC micelles. Nuclear magnetic resonance spectroscopy allowed full characterization of the interactions of apelin-17 with SDS micelles. Titration with paramagnetic agents and structural determination of apelin-17 in SDS indicate that R6-K12 is highly structured, with R6-L9 directly interacting with headgroups of the micelle. Type I beta-turns are initiated between R6 and L9, and a well-defined type IV beta-turn is initiated at S10. Furthermore, binding of apelin-17 to SDS micelles causes structuring of M15-F17, with no evidence for direct binding of this region to the micelles. These results are placed into the context of the membrane catalysis hypothesis for peptide-receptor binding, and a hypothetical mechanism of APJ binding and activation by apelin is advanced.
Collapse
Affiliation(s)
| | - Jan K. Rainey
- To whom correspondence should be addressed. Phone: (902) 494-4632. Fax: (902) 494-1355. E-mail:
| |
Collapse
|
135
|
Pan PS, Vasko RC, Lapera SA, Johnson VA, Sellers RP, Lin CC, Pan CM, Davis MR, Ardi VC, McAlpine SR. A comprehensive study of Sansalvamide A derivatives: The structure-activity relationships of 78 derivatives in two pancreatic cancer cell lines. Bioorg Med Chem 2009; 17:5806-25. [PMID: 19643615 DOI: 10.1016/j.bmc.2009.07.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/09/2009] [Accepted: 07/10/2009] [Indexed: 11/18/2022]
Abstract
We report an extensive structure-activity relationship (SAR) of 78 compounds active against two pancreatic cancer cell lines. Our comprehensive evaluation of these compounds utilizes SAR that allow us to evaluate which features of potent compounds play a key role in their cytotoxicity. This is the first report of 19 new second-generation structures, where these new compounds were designed from the first generation of 59 compounds. These 78 structures were tested for their cytotoxicity and this is the first report of their activity against two pancreatic cancer cell lines. Our results show that out of 78 compounds, three compounds are worth pursuing as leads, as they show potency of 55% in both cancer cell lines. These three compounds all have a common structural motif, two consecutive d-amino acids and an N-methyl moiety. Further, of these three compounds, two are second-generation structures, indicating that we can incorporate and utilize data from the first generation to design potency into the second generation. Finally, one analog is in the mid nanomolar range, and has the lowest IC(50) of any reported San A derivative. These analogs share no structural homology to current pancreatic cancer drugs, and are cytotoxic at levels on par with existing drugs treating other cancers. Thus, we have established Sansalvamide A as an excellent lead for killing multiple pancreatic cancer cell lines.
Collapse
Affiliation(s)
- Po-Shen Pan
- Department of Chemistry and Biochemistry, San Diego State University, CA 92182-1030, United States
| | | | | | | | | | | | | | | | | | | |
Collapse
|
136
|
Nanga RPR, Brender JR, Xu J, Hartman K, Subramanian V, Ramamoorthy A. Three-dimensional structure and orientation of rat islet amyloid polypeptide protein in a membrane environment by solution NMR spectroscopy. J Am Chem Soc 2009; 131:8252-61. [PMID: 19456151 PMCID: PMC4163022 DOI: 10.1021/ja9010095] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Islet amyloid polypeptide (IAPP or amylin) is a 37-residue peptide hormone associated with glucose metabolism that is cosecreted with insulin by beta-cells in the pancreas. Since human IAPP is a highly amyloidogenic peptide, it has been suggested that the formation of IAPP amyloid fibers is responsible for the death of beta-cells during the early stages of type II diabetes. It has been hypothesized that transient membrane-bound alpha-helical structures of human IAPP are precursors to the formation of these amyloid deposits. On the other hand, rat IAPP forms transient alpha-helical structures but does not progress further to form amyloid fibrils. To understand the nature of this intermediate state and the difference in toxicity between the rat and human versions of IAPP, we have solved the high-resolution structure of rat IAPP in the membrane-mimicking detergent micelles composed of dodecylphosphocholine. The structure is characterized by a helical region spanning the residues A5 to S23 and a disordered C-terminus. A distortion in the helix is seen at R18 and S19 that may be involved in receptor binding. Paramagnetic quenching NMR experiments indicate that rat IAPP is bound on the surface of the micelle, in agreement with other nontoxic forms of IAPP. A comparison to the detergent-bound structures of other IAPP variants indicates that the N-terminal region may play a crucial role in the self-association and toxicity of IAPP by controlling access to the putative dimerization interface on the hydrophobic face of the amphipathic helix.
Collapse
|
137
|
Lee JY, Im I, Webb TR, McGrath D, Song MR, Kim YC. Combinatorial synthesis and biological evaluation of peptide-binding GPCR-targeted library. Bioorg Chem 2009; 37:90-5. [DOI: 10.1016/j.bioorg.2009.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 03/30/2009] [Accepted: 04/09/2009] [Indexed: 01/09/2023]
|
138
|
Saavedra C, Hernández R, Boto A, Álvarez E. Catalytic, One-Pot Synthesis of β-Amino Acids from α-Amino Acids. Preparation of α,β-Peptide Derivatives. J Org Chem 2009; 74:4655-65. [DOI: 10.1021/jo9004487] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Carlos Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain, and Instituto de Investigaciones Químicas (CSIC-USe), Isla de la Cartuja, Avda. Américo Vespucio 49, 41092-Sevilla, Spain
| | - Rosendo Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain, and Instituto de Investigaciones Químicas (CSIC-USe), Isla de la Cartuja, Avda. Américo Vespucio 49, 41092-Sevilla, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain, and Instituto de Investigaciones Químicas (CSIC-USe), Isla de la Cartuja, Avda. Américo Vespucio 49, 41092-Sevilla, Spain
| | - Eleuterio Álvarez
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206-La Laguna, Tenerife, Spain, and Instituto de Investigaciones Químicas (CSIC-USe), Isla de la Cartuja, Avda. Américo Vespucio 49, 41092-Sevilla, Spain
| |
Collapse
|
139
|
Gentilucci L, Cardillo G, Tolomelli A, De Marco R, Garelli A, Spampinato S, Spartà A, Juaristi E. Synthesis and Conformational Analysis of Cyclotetrapeptide Mimetic β-Turn Templates and Validation as 3D Scaffolds. ChemMedChem 2009; 4:517-23. [DOI: 10.1002/cmdc.200800407] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
140
|
Weill N, Rognan D. Development and Validation of a Novel Protein−Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands. J Chem Inf Model 2009; 49:1049-62. [DOI: 10.1021/ci800447g] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathanael Weill
- Structural Chemogenomics Group, Laboratory of Therapeutic Inovation, UMR 7200 CNRS-UdS (Université de Strasbourg), 74 route du Rhin, B.P.24, F-67400 Illkirch, France
| | - Didier Rognan
- Structural Chemogenomics Group, Laboratory of Therapeutic Inovation, UMR 7200 CNRS-UdS (Université de Strasbourg), 74 route du Rhin, B.P.24, F-67400 Illkirch, France
| |
Collapse
|
141
|
Jackson GE, Mabula AN, Stone SR, Gäde G, Kövér KE, Szilágyi L, van der Spoel D. Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP). Peptides 2009; 30:557-64. [PMID: 19103242 DOI: 10.1016/j.peptides.2008.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 11/21/2008] [Accepted: 11/21/2008] [Indexed: 11/27/2022]
Abstract
The solution structure of crustacean cardioactive peptide (CCAP), a cyclic amidated nonapeptide neurohormone, was studied using molecular dynamics techniques, with constraints derived from NMR studies in water and water/dodecylphosphocholine micellar medium. This peptide, found in various invertebrates, has the primary sequence Pro(1) Phe(2) Cys(3) Asn(4) Ala(5) Phe(6) Thr(7) Gly(8) Cys(9) NH(2), with an intramolecular disulfide bridge between the two cysteine residues. In aqueous solution the peptide was found to have a type(IV) beta-turn between residues 5-8. In a water/decane biphasic medium a type(IV) beta-turn between residues 3 and 6 and two classic gamma-turns between residues 4-6 and 7-9, were found. Analysis of the (1)H and (13)C NMR chemical shifts data showed that the model free S(2) order parameter of the residues varied between 0.65 and 0.9. The molecular dynamic root mean square fluctuations of structural ensembles of the backbone varied between 0.5 and 2.2 with the central residues showing the least fluctuations.
Collapse
Affiliation(s)
- Graham E Jackson
- Chemistry Department, University of Cape Town, Private Bag, 7701 Rondebosch, Cape Town, South Africa.
| | | | | | | | | | | | | |
Collapse
|
142
|
De Wachter R, Brans L, Ballet S, Van den Eynde I, Feytens D, Keresztes A, Toth G, Urbanczyk-Lipkowska Z, Tourwé D. Influence of ring substitution on the conformation and β-turn mimicry of 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one peptide mimetics. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.01.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
143
|
Koch O, Klebe G. Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions. Proteins 2009; 74:353-67. [DOI: 10.1002/prot.22185] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
144
|
Langelaan DN, Bebbington EM, Reddy T, Rainey JK. Structural Insight into G-Protein Coupled Receptor Binding by Apelin. Biochemistry 2009; 48:537-48. [DOI: 10.1021/bi801864b] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- David N. Langelaan
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - E. Meghan Bebbington
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - Tyler Reddy
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| | - Jan K. Rainey
- Departments of Biochemistry & Molecular Biology and Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 1X5 Canada
| |
Collapse
|
145
|
Abstract
During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorganization of the competing ligand enhances the binding affinity and potential selectivity of the inhibitor. In this chapter, current progress in these efforts is reviewed.
Collapse
|
146
|
Tomita K, Popiel HA, Nagai Y, Toda T, Yoshimitsu Y, Ohno H, Oishi S, Fujii N. Structure-activity relationship study on polyglutamine binding peptide QBP1. Bioorg Med Chem 2008; 17:1259-63. [PMID: 19121945 DOI: 10.1016/j.bmc.2008.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 12/06/2008] [Accepted: 12/09/2008] [Indexed: 01/21/2023]
Abstract
Aggregation and deposition of expanded polyglutamine proteins in the brain cause neurodegenerative diseases including Huntington disease. This pathogenic process is suppressed and delayed in the presence of polyglutamine binding peptide 1 (QBP1), which we previously identified as an undecapeptide binding to pathogenic polyglutamine proteins from phage display peptide libraries. In this paper, a structure-activity relationship study on QBP1 was conducted to determine the pharmacophores for inhibition of polyglutamine aggregation. Furthermore, a truncation study identified an octapeptide as the minimum structure for suppressing aggregation of polyglutamine proteins, which is equipotent to the parent undecapeptide QBP1.
Collapse
Affiliation(s)
- Kenji Tomita
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | | | | | | | | | | | | | | |
Collapse
|
147
|
Abstract
For more than a decade now, a search for answers to the following two questions has taken us on a new and exciting journey into the world of beta- and gamma-peptides: What happens if the oxygen atoms in a 3i-helix of a polymeric chain composed of (R)-3-hydroxybutanoic acid are replaced by NH units? What happens if one or two CH2 groups are introduced into each amino acid building block in the chain of a peptide or protein, thereby providing homologues of the proteinogenic alpha-amino acids? Our journey has repeatedly thrown up surprises, continually expanding the potential of these classes of compound and deepening our understanding of the structures, properties, and multifaceted functions of the natural "models" to which they are related. Beta-peptides differ from their natural counterparts, the alpha-peptides, by having CH2 groups inserted into every amino acid residue, either between the C=O groups and the alpha-carbon atoms (beta(3)) or between the alpha-carbon and nitrogen atoms (beta(2)). The synthesis of these homologated proteinogenic amino acids and their assembly into beta-peptides can be performed using known methods. Despite the increased number of possible conformers, the beta-peptides form secondary structures (helices, turns, sheets) even when the chain lengths are as short as four residues. Furthermore, they are stable toward degrading and metabolizing enzymes in living organisms. Linear, helical, and hairpin-type structures of beta-peptides can now be designed in such a way that they resemble the characteristic and activity-related structural features ("epitopes") of corresponding natural peptides or protein sections. This Account presents examples of beta-peptidic compounds binding, as agonists or antagonists (inhibitors), to (i) major histocompatibility complex (MHC) proteins (immune response), (ii) the lipid-transport protein SR-B1 (cholesterol uptake from the small intestine), (iii) the core (1-60) of interleukin-8 (inflammation), (iv) the oncoprotein RDM2, (v) the HIVgp41 fusion protein, (vi) G-protein-coupled somatostatin hsst receptors, (vii) the TNF immune response receptor CD40 (apoptosis), and (viii) DNA. Short-chain beta-peptides may be orally bioavailable and excreted from the body of mammals; long-chain beta-peptides may require intravenous administration but will have longer half-lives of clearance. It has been said that an interesting field of research distinguishes itself in that the results always throw up new questions; in this sense, the structural and biological investigation of beta-peptides has been a gold mine. We expect that these peptidic peptidomimetics will play an increasing role in biomedical research and drug development in the near future.
Collapse
Affiliation(s)
- Dieter Seebach
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - James Gardiner
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| |
Collapse
|
148
|
A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. J Comput Aided Mol Des 2008; 23:87-95. [PMID: 18797997 DOI: 10.1007/s10822-008-9241-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 09/02/2008] [Indexed: 10/21/2022]
Abstract
Reverse turns are often recognition sites for protein/protein interactions and, therefore, valuable potential targets for determining recognition motifs in development of potential therapeutics. A virtual combinatorial library of cyclic tetrapeptides (CTPs) was generated and the bonds in the low-energy structures were overlapped with canonical reverse-turn Calpha-Cbeta bonds (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005) to determine the utility of CTPs as reverse-turn peptidomimetics. All reverse turns in the Protein Data Bank (PDB) with a crystal structures resolution < or = 3.0 A were classified into the same known canonical reverse-turn Calpha-Cbeta bond clusters (Tran et al., J Comput Aided Mol Des 19(8):551-566, 2005). CTP reverse-turn mimics were compiled that mimicked both the relative orientations of three of the four as well as all four Calpha-Cbeta bonds in the reverse turns of the PDB. 54% of reverse turns represented in the PDB had eight or more CTPs structures that mimicked the orientation of all four of the Calpha-Cbeta bonds in the reverse turn.
Collapse
|
149
|
Seebach D, Dubost E, Mathad R, Jaun B, Limbach M, Löweneck M, Flögel O, Gardiner J, Capone S, Beck A, Widmer H, Langenegger D, Monna D, Hoyer D. New Open-Chain and Cyclic Tetrapeptides, Consisting ofα-,β2-, andβ3-Amino-Acid Residues, as Somatostatin Mimics - A Survey. Helv Chim Acta 2008. [DOI: 10.1002/hlca.200890190] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
150
|
Lescot E, Bureau R, Rault S. Nonpeptide Urotensin-II receptor agonists and antagonists: review and structure-activity relationships. Peptides 2008; 29:680-90. [PMID: 18022732 DOI: 10.1016/j.peptides.2007.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 09/19/2007] [Accepted: 09/26/2007] [Indexed: 02/07/2023]
Abstract
Human Urotensin-II (hU-II) is a cyclic 11-amino acid peptide that plays a role in cardiovascular homeostasis. Its receptor is a member of the class A of G-protein-coupled receptors, called GPR14. In recent years, several nonpeptide ligands have been reported in the literature. Most were identified by high-throughput screening and optimized by medicinal chemistry methods. Other nonpeptide ligands were discovered starting from the 3D structure of hU-II or other ligands. They were identified by a virtual screening approach based on a 3D pharmacophore or by structural similarity with others cyclic peptides. In this review, nonpeptide agonists and antagonists are presented in relation to structure-activity relationships.
Collapse
Affiliation(s)
- Elodie Lescot
- Université de Caen, U.F.R. des Sciences Pharmaceutiques, Centre d'Etudes et de Recherche sur le Médicament de Normandie, 5 rue Vaubénard, 14032 Caen Cedex, France
| | | | | |
Collapse
|