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Slater O, Kontoyianni M. A computational study of somatostatin subtype-4 receptor agonist binding. SN APPLIED SCIENCES 2022. [DOI: 10.1007/s42452-022-04968-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
AbstractThe somatostatin subtype-4 receptor (sst4) is highly expressed in neocortical and hippocampal areas, which are affected by amyloid beta accumulation. Sst4 agonists enhance downstream activity of amyloid beta peptide catabolism through neprilysin and may slow the progression of Alzheimer’s disease (AD). Sst4 is a G protein coupled receptor (GPCR), the structure of which has yet to be resolved. A newly constructed sst4 homology model, along with a previously reported model-built sst4 receptor structure, were used in the present study to gain insights into binding requirements of sst4 agonists employing a set of compounds patented by Boehringer Ingelheim. Besides aiming at delineating binding at the macromolecular level of these recently disclosed compounds, our objectives included the generation of a quantitative structure-activity relationship (QSAR) global model to explore the relationship between chemical structure and affinity. Through the implementation of model building, docking, and QSAR, plausible correlations between structural properties and the binding affinity are established. This study sheds light on understanding binding requirements at the sst4 receptor.
Graphical abstract
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Talukdar R. Synthetically Important Ring-Opening Acylations of Alkoxybenzenes. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1707255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractCyclic ketones, anhydrides, lactams and lactones are a particular class of molecules that are often used in synthesis, wherein their electrophilic properties are leveraged to enable facile Friedel–Crafts ring openings through nucleophilic attack at the carbonyl sp2 centre. The use of electron-rich alkoxybenzenes as nucleophiles has also become important since the discovery of the Friedel–Crafts reaction. As a result, various isomeric alkoxybenzenes are used for preparing starting materials in target-oriented syntheses. This review covers the instances of different alkoxybenzenes that are used as nucleophiles in ring-opening acylations with carbonyl-containing cyclic electrophiles, for the construction of important building blocks for multistep transformations. This review summarizes the ring-opening functionalization of three- to seven-membered molecular rings with alkoxybenzenes in a Friedel–Crafts fashion. Sometimes the rings need subtle or considerable activation by the help of Lewis acid(s), followed by nucleophilic attack. This review is aimed to be a summary of the important acylations of electron-rich alkoxybenzenes by nucleophilic ring-opening of cyclic molecules. The works cited employ a wide range of conditions and differently substituted substrates for target-oriented syntheses.1 Introduction and Scope2 Arenes for Acylative Ring Opening2.1 Three-Membered Rings: Ring Opening of Oxirane-2,3-dione2.2 Four-Membered Rings2.2.1 Ring Opening of Cyclobutanones2.2.2 Ring Opening of β-Lactams2.2.3 Ring Opening of β-Lactone2.3 Five-Membered Rings2.3.1 Ring Opening of Phthalimides2.3.2 Ring Opening of γ-Lactones2.3.3 Ring Opening of Anhydrides2.4 Six-Membered Rings2.5 Seven-Membered Rings3 Conclusion
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Affiliation(s)
- Natalie Netz
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Till Opatz
- Institute of Organic Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
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Arya AK, Gupta SK, Kumar M. A domino protocol for the efficient synthesis of structurally diverse benzothiazolylquinoline-2,5-diones and their spiro analogues. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.099] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hu Y, Fu X, Barry BD, Bi X, Dong D. Regiospecific β-lactam ring-opening/recyclization reactions of N-aryl-3-spirocyclic-β-lactams catalyzed by a Lewis–Brønsted acids combined superacid catalyst system: a new entry to 3-spirocyclicquinolin-4(1H)-ones. Chem Commun (Camb) 2012; 48:690-2. [DOI: 10.1039/c1cc15881c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Liu Z, Crider AM, Ansbro D, Hayes C, Kontoyianni M. A structure-based approach to understanding somatostatin receptor-4 agonism (sst4). J Chem Inf Model 2011; 52:171-86. [PMID: 22148589 DOI: 10.1021/ci200375j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
It has been reported that somatostatin receptor subtypes 4 and 5 would be high-impact templates for homology modeling if their 3D structures became available. We have generated a homology model of the somatostatin receptor subtype 4 (sst4), using the newest active state β(2) adrenoreceptor crystal structure, and subsequently docked a variety of agonists into the model-built receptor to elucidate the binding modes of reported agonists. Using experimental restraints, we were able to explain observed activity profiles. We propose two binding modes that can consistently explain findings for high-affinity agonists and reason why certain structures display low affinities for the receptor.
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Affiliation(s)
- Zhaomin Liu
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA
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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.
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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
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Schmidt RG, Bayburt EK, Latshaw SP, Koenig JR, Daanen JF, McDonald HA, Bianchi BR, Zhong C, Joshi S, Honore P, Marsh KC, Lee CH, Faltynek CR, Gomtsyan A. Chroman and tetrahydroquinoline ureas as potent TRPV1 antagonists. Bioorg Med Chem Lett 2011; 21:1338-41. [DOI: 10.1016/j.bmcl.2011.01.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 12/22/2022]
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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.
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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]
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Lee JY, Kim YC. Combinatorial Library Synthesis and Biological Evaluation of Pyrazolo[4,3-e][1,4]diazepine as a Potential Privileged Structure. ChemMedChem 2009; 4:733-7. [DOI: 10.1002/cmdc.200800453] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Haslach EM, Schaub JW, Haskell-Luevano C. Beta-turn secondary structure and melanocortin ligands. Bioorg Med Chem 2009; 17:952-8. [PMID: 18343128 PMCID: PMC2662475 DOI: 10.1016/j.bmc.2008.02.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 02/26/2008] [Accepted: 02/27/2008] [Indexed: 10/22/2022]
Abstract
The melanocortin pathway has emerged during this past decade as an important target area for the discovery and development of therapeutic agents related to obesity and type 2 diabetes. This peptide-G-protein coupled receptor (GPCR) pathway has evolved from peptide-based ligands to small molecules possessing a variety of different molecular scaffolds. Herein, we summarize the originating hypothesis of the importance of the reverse beta-turn secondary structure for agonist ligand potency at the melanocortin receptors and how that information was utilized for the discovery of small molecules based upon this type of turn structure.
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Affiliation(s)
- Erica M. Haslach
- Department of Medicinal Chemistry, University of Florida PO Box 100485, Gainesville, FL 32610
| | - Jay W. Schaub
- Department of Medicinal Chemistry, University of Florida PO Box 100485, Gainesville, FL 32610
| | - Carrie Haskell-Luevano
- Department of Medicinal Chemistry, University of Florida PO Box 100485, Gainesville, FL 32610
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Webb TR, Venegas RE, Wang J, Deschenes A. Generation of New Synthetic Scaffolds Using Framework Libraries Selected and Refined via Medicinal Chemist Synthetic Expertise. J Chem Inf Model 2008; 48:882-8. [DOI: 10.1021/ci7001928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas R. Webb
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Ruben E. Venegas
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Jian Wang
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
| | - Alain Deschenes
- ChemBridge Research Labs., Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, and Chemical Computing Group, Suite 910-1010 Sherbrooke St. W Montreal, Quebec, Canada H3A 2R7
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Feytens D, Cescato R, Reubi JC, Tourwé D. New sst4/5-selective somatostatin peptidomimetics based on a constrained tryptophan scaffold. J Med Chem 2007; 50:3397-401. [PMID: 17559206 DOI: 10.1021/jm070246f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis and biological evaluation of four peptidomimetic analogs of somatostatin based on a constrained Trp residue, 3-amino-indolo[2,3-c]azepin-2-one (Aia), are reported. It is shown that dipeptidomimetics with a D-Aia-Lys sequence, functionalized with N- and C-terminal aromatic substituents, display a good selectivity for both sst4 and sst5. This study allowed us to identify a new highly potent sst5 agonist with good selectivity over the other receptors, except versus sst4.
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Affiliation(s)
- Debby Feytens
- Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium
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Bergmann R, Linusson A, Zamora I. SHOP: scaffold HOPping by GRID-based similarity searches. J Med Chem 2007; 50:2708-17. [PMID: 17489578 DOI: 10.1021/jm061259g] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new GRID-based method for scaffold hopping (SHOP) is presented. In a fully automatic manner, scaffolds were identified in a database based on three types of 3D-descriptors. SHOP's ability to recover scaffolds was assessed and validated by searching a database spiked with fragments of known ligands of three different protein targets relevant for drug discovery using a rational approach based on statistical experimental design. Five out of eight and seven out of eight thrombin scaffolds and all seven HIV protease scaffolds were recovered within the top 10 and 31 out of 31 neuraminidase scaffolds were in the 31 top-ranked scaffolds. SHOP also identified new scaffolds with substantially different chemotypes from the queries. Docking analysis indicated that the new scaffolds would have similar binding modes to those of the respective query scaffolds observed in X-ray structures. The databases contained scaffolds from published combinatorial libraries to ensure that identified scaffolds could be feasibly synthesized.
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Affiliation(s)
- Rikke Bergmann
- Department of Medicinal Chemistry, University of Copenhagen, Faculty of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark.
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Webb TR, Jiang L, Sviridov S, Venegas RE, Vlaskina AV, McGrath D, Tucker J, Wang J, Deschenes A, Li R. Application of a novel design paradigm to generate general nonpeptide combinatorial templates mimicking beta-turns: synthesis of ligands for melanocortin receptors. ACTA ACUST UNITED AC 2007; 9:704-10. [PMID: 17429950 DOI: 10.1021/cc0601581] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the further application of a novel approach to template and ligand design by the synthesis of agonists of the melanocortin receptor. This design method uses the conserved structural data from the three-dimensional conformations of beta-turn peptides to design rigid nonpeptide templates that mimic the orientation of the main chain C-alpha atoms in a peptide beta-turn. We report details on a new synthesis of derivatives of template 1 that are useful for the synthesis of exploratory libraries. The utility of this technique is further exemplified by several iterative rounds of high-throughput synthesis and screening, which result in new partially optimized nonpeptide agonists for several melanocortin receptors.
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Affiliation(s)
- Thomas R Webb
- ChemBridge Research Labs, Inc., ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, USA.
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Khasanov AB, Ramirez-Weinhouse MM, Webb TR, Thiruvazhi M. Novel Asymmetric Approach to Proline-Derived Spiro-β-lactams. J Org Chem 2004; 69:5766-9. [PMID: 15307755 DOI: 10.1021/jo049430o] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a novel asymmetric approach using Staudinger chemistry to proline-derived spiro-beta-lactams. A chiral group at C-4 of the acid chloride of proline directs the stereoselectivity of Staudinger chemistry and later is sacrificed to obtain optically active 5.4-spiro-beta-lactams. The scope, limitations, and mechanistic rationale for the observed results of Staudinger Chemistry of the acid chloride of 4-alkyl(aryl)sulfonyloxy-l-proline with imines are also discussed.
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Affiliation(s)
- Alisher B Khasanov
- Department of Chemistry Research, ChemBridge Research Laboratories and ChemBridge Corporation, 16981 Via Tazon, San Diego, California 92127, USA
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Bleicher KH, Green LG, Martin RE, Rogers-Evans M. Ligand identification for G-protein-coupled receptors: a lead generation perspective. Curr Opin Chem Biol 2004; 8:287-96. [PMID: 15183327 DOI: 10.1016/j.cbpa.2004.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
This review addresses strategies for the generation of ligands for G-protein-coupled receptors outside classical high-throughput screening and literature based approaches. These range from the chemical intuition-based strategies of endogenous ligand elaboration and privileged structure decoration to the in silico approaches of virtual screening and de novo design. Examples are cited where supporting pharmacological data has been presented.
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Affiliation(s)
- Konrad H Bleicher
- F Hoffmann-La Roche Ltd, Pharmaceuticals Division, Lead Generation, PRBD-CI, Bldg 65/410, CH-4070 Basel, Switzerland.
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Im I, Webb TR, Gong YD, Kim JI, Kim YC. Solid-Phase Synthesis of Tetrahydro-1,4-benzodiazepine-2-one Derivatives as a β-Turn Peptidomimetic Library. ACTA ACUST UNITED AC 2004; 6:207-13. [PMID: 15002968 DOI: 10.1021/cc034039m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The beta-turn has been implicated as an important conformation for biological recognition of peptides or proteins. We adapted the concept of general Calpha atom positioning from the cluster analysis and recombination of each ideal beta-turn conformation pattern by Garland and Dean (J. Comput.-Aided Mol. Des. 1999, 13, 469) as one strategy of designing non-peptide beta-turn scaffolds. Herein, the Calpha positions of tetrahydro-1,4-benzodiazepin-2-one scaffold were analyzed after the calculation of the low-energy conformer using a semiempirical protocol. Three points of corresponding Calpha carbons for diverse substitutions in the scaffold were designated, and an efficient solid-phase synthesis of the peptidomimetic library was developed. The scaffold itself was synthesized in solution phase starting from 5-hydroxy-2-nitrobenzaldehyde and loaded to the 4-formyl-3,5-dimethoxyphenoxy (PL-FDMP) resin with high efficiency of reductive amination. Various building blocks for the derivatization of the 7-hydroxyl and N-1 amide nitrogen could be introduced via selective alkylation. Cleavage, parallel column chromatography, and NMR analysis of 62 final compounds confirmed the feasibility of this peptidomimetic library synthesis.
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Affiliation(s)
- Isak Im
- Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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