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Vendrell-Navarro G, Rúa F, Bujons J, Brockmeyer A, Janning P, Ziegler S, Messeguer A, Waldmann H. Positional Scanning Synthesis of a Peptoid Library Yields New Inducers of Apoptosis that Target Karyopherins and Tubulin. Chembiochem 2015; 16:1580-7. [DOI: 10.1002/cbic.201500169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/05/2022]
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2
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Firempong CK, Cao X, Tong S, Yu J, Xu X. Prospects for multitarget lipid-raft-coated silica beads: a remarkable online biomaterial for discovering multitarget antitumor lead compounds. RSC Adv 2015. [DOI: 10.1039/c5ra08322b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Application of lipid raft biomaterial with multiple cancer-related receptors for screening novel multitarget antitumour lead compounds.
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Affiliation(s)
- Caleb Kesse Firempong
- Department of Pharmaceutics
- School of Pharmacy
- Centre for Nano Drug/Gene Delivery and Tissue Engineering
- Jiangsu University
- Zhenjiang
| | - Xia Cao
- Department of Pharmaceutics
- School of Pharmacy
- Centre for Nano Drug/Gene Delivery and Tissue Engineering
- Jiangsu University
- Zhenjiang
| | - Shanshan Tong
- Department of Pharmaceutics
- School of Pharmacy
- Centre for Nano Drug/Gene Delivery and Tissue Engineering
- Jiangsu University
- Zhenjiang
| | - Jiangnan Yu
- Department of Pharmaceutics
- School of Pharmacy
- Centre for Nano Drug/Gene Delivery and Tissue Engineering
- Jiangsu University
- Zhenjiang
| | - Ximing Xu
- Department of Pharmaceutics
- School of Pharmacy
- Centre for Nano Drug/Gene Delivery and Tissue Engineering
- Jiangsu University
- Zhenjiang
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3
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Wassermann AM, Camargo LM, Auld DS. Composition and applications of focus libraries to phenotypic assays. Front Pharmacol 2014; 5:164. [PMID: 25104937 PMCID: PMC4109565 DOI: 10.3389/fphar.2014.00164] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/21/2014] [Indexed: 11/16/2022] Open
Abstract
The wealth of bioactivity information now available on low-molecular weight compounds has enabled a paradigm shift in chemical biology and early phase drug discovery efforts. Traditionally chemical libraries have been most commonly employed in screening approaches where a bioassay is used to characterize a chemical library in a random search for active samples. However, robust curating of bioassay data, establishment of ontologies enabling mining of large chemical biology datasets, and a wealth of public chemical biology information has made possible the establishment of highly annotated compound collections. Such annotated chemical libraries can now be used to build a pathway/target hypothesis and have led to a new view where chemical libraries are used to characterize a bioassay. In this article we discuss the types of compounds in these annotated libraries composed of tools, probes, and drugs. As well, we provide rationale and a few examples for how such libraries can enable phenotypic/forward chemical genomic approaches. As with any approach, there are several pitfalls that need to be considered and we also outline some strategies to avoid these.
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Affiliation(s)
- Anne Mai Wassermann
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
| | - Luiz M Camargo
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
| | - Douglas S Auld
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research Cambridge, MA, USA
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4
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Byler KG, Li Y, Houghten RA, Martinez-Mayorga K. The role of imidazole in peptide cyclization by transesterification: parallels to the catalytic triads of serine proteases. Org Biomol Chem 2013; 11:2979-87. [PMID: 23529282 DOI: 10.1039/c3ob27464k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The improved bioavailability, stability and selectivity of cyclic peptides over their linear counterparts make them attractive structures in the design and discovery of novel therapeutics. In our previous work, we developed an imidazole-promoted preparation of cyclic depsipeptides in which we observed that increasing the concentration of imidazole resulted in the concomitant increase in the yield of cyclic product and reduction in dimerization, but also resulted in the generation of an acyl-substituted side product. In this work, we used transition state analysis to explore the mechanism of the imidazole-catalyzed esterification of one such peptide, Ac-SAFYG-SCH2φ, and determined the acyl substitution product to be an intermediate in a competing reaction pathway involving acyl substitution of the thioester by imidazole. Our findings indicate that imidazole plays an essential role in this side-chain to C-terminal coupling, and by extension, in transesterifications in general, through a concerted mechanism wherein imidazole deprotonates the nucleophile as the nucleophile attacks the carbonyl. The system under study is identical to the histidine-serine portion of the catalytic triads in serine proteases and it is likely that these enzymes employ the same concerted mechanism in the first step of peptide cleavage. Additionally, relatively high concentrations of imidazole must be used to effectively catalyze reactions in aprotic solvents since the overall reaction involves imidazole acting both as an acid and as a base, existing in solution as an equilibrium distribution between the neutral form and its conjugate acid.
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Affiliation(s)
- Kendall G Byler
- Torrey Pines Institute for Molecular Studies, 11350 Southwest Village Parkway, Port St. Lucie, FL 34987, USA
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5
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Medina-Franco JL, Giulianotti MA, Welmaker GS, Houghten RA. Shifting from the single to the multitarget paradigm in drug discovery. Drug Discov Today 2013; 18:495-501. [PMID: 23340113 PMCID: PMC3642214 DOI: 10.1016/j.drudis.2013.01.008] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/03/2012] [Accepted: 01/14/2013] [Indexed: 01/30/2023]
Abstract
Increasing evidence that several drug compounds exert their effects through interactions with multiple targets is boosting the development of research fields that challenge the data reductionism approach. In this article, we review and discuss the concepts of drug repurposing, polypharmacology, chemogenomics, phenotypic screening and high-throughput in vivo testing of mixture-based libraries in an integrated manner. These research fields offer alternatives to the current paradigm of drug discovery, from a one target-one drug model to a multiple-target approach. Furthermore, the goals of lead identification are being expanded accordingly to identify not only 'key' compounds that fit with a single-target 'lock', but also 'master key' compounds that favorably interact with multiple targets (i.e. operate a set of desired locks to gain access to the expected clinical effects).
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Affiliation(s)
- José L Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, D.F. 04510, Mexico.
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6
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Armishaw CJ, Banerjee J, Ganno ML, Reilley KJ, Eans SO, Mizrachi E, Gyanda R, Hoot MR, Houghten RA, McLaughlin JP. Discovery of novel antinociceptive α-conotoxin analogues from the direct in vivo screening of a synthetic mixture-based combinatorial library. ACS COMBINATORIAL SCIENCE 2013; 15:153-61. [PMID: 23414173 DOI: 10.1021/co300152x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Marine cone snail venoms consist of large, naturally occurring combinatorial libraries of disulfide-constrained peptide neurotoxins known as conotoxins, which have profound potential in the development of analgesics. In this study, we report a synthetic combinatorial strategy that probes the hypervariable regions of conotoxin frameworks to discover novel analgesic agents by utilizing high diversity mixture-based positional-scanning synthetic combinatorial libraries (PS-SCLs). We hypothesized that the direct in vivo testing of these mixture-based combinatorial library samples during the discovery phase would facilitate the identification of novel individual compounds with desirable antinociceptive profiles while simultaneously eliminating many compounds with poor activity or liabilities of locomotion and respiration. A PS-SCL was designed based on the α-conotoxin RgIA-ΔR n-loop region and consisted of 10,648 compounds systematically arranged into 66 mixture samples. Mixtures were directly screened in vivo using the mouse 55 °C warm-water tail-withdrawal assay, which allowed deconvolution of amino acid residues at each position that confer antinociceptive activity. A second generation library of 36 individual α-conotoxin analogues was synthesized using systematic combinations of amino acids identified from PS-SCL deconvolution and further screened for antinociceptive activity. Six individual analogues exhibited comparable antinociceptive activity to that of the recognized analgesic α-conotoxin RgIA-ΔR, and were selected for further examination of antinociceptive, respiratory, and locomotor effects. Three lead compounds were identified that produced dose-dependent antinociception without significant respiratory depression or decreased locomotor activity. Our results represent a unique approach for rapidly developing novel lead α-conotoxin analogues as low-liability analgesics with promising therapeutic potential.
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Affiliation(s)
- Christopher J. Armishaw
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Jayati Banerjee
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Michelle L. Ganno
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Kate J. Reilley
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Shainnel O. Eans
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Elisa Mizrachi
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Reena Gyanda
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Michelle R. Hoot
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
| | - Jay P. McLaughlin
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Pkwy, Port St. Lucie, Florida
34987, United States
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7
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Bojnik E, Boynik E, Corbani M, Babos F, Magyar A, Borsodi A, Benyhe S. Phylogenetic diversity and functional efficacy of the C-terminally expressed heptapeptide unit in the opioid precursor polypeptide proenkephalin A. Neuroscience 2011; 178:56-67. [DOI: 10.1016/j.neuroscience.2011.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 01/04/2011] [Accepted: 01/05/2011] [Indexed: 01/28/2023]
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8
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Yongye AB, Pinilla C, Medina-Franco JL, Giulianotti MA, Dooley CT, Appel JR, Nefzi A, Scior T, Houghten RA, Martínez-Mayorga K. Integrating computational and mixture-based screening of combinatorial libraries. J Mol Model 2010; 17:1473-82. [DOI: 10.1007/s00894-010-0850-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 09/06/2010] [Indexed: 11/29/2022]
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9
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Yamaotsu N, Hirono S. 3D-Pharmacophore Identification for κ-Opioid Agonists Using Ligand-Based Drug-Design Techniques. Top Curr Chem (Cham) 2010; 299:277-307. [DOI: 10.1007/128_2010_84] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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10
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Yongye AB, Li Y, Giulianotti MA, Yu Y, Houghten RA, Martínez-Mayorga K. Modeling of peptides containing D-amino acids: implications on cyclization. J Comput Aided Mol Des 2009; 23:677-89. [PMID: 19593648 DOI: 10.1007/s10822-009-9295-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 06/25/2009] [Indexed: 11/25/2022]
Abstract
Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclizes in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated alpha(L) rotamers even when simulations were performed at a higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L: -amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods.
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Affiliation(s)
- Austin B Yongye
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, FL 34987, USA
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11
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Carroll FI, Houghten RA. From rapid in vitro screening to rapid in vivo screening in the drug discovery process. Neuropsychopharmacology 2009; 34:251-2. [PMID: 19079076 DOI: 10.1038/npp.2008.160] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- F Ivy Carroll
- Center for Organic and Medicinal Chemistry, Research Triangle Institute, Research Triangle Park, NC, USA.
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12
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Sasaki Y, Tsujii T, Takeda S, Obinata H, Izumi T, Yamada K, Katakai R. Identification of novel peptide agonists from a random peptide library for a 5-oxo-ETE receptor, a receptor for bioactive lipids. J Pept Sci 2008; 14:1251-8. [DOI: 10.1002/psc.1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Martínez-Mayorga K, Medina-Franco JL, Giulianotti MA, Pinilla C, Dooley CT, Appel JR, Houghten RA. Conformation-opioid activity relationships of bicyclic guanidines from 3D similarity analysis. Bioorg Med Chem 2008; 16:5932-8. [PMID: 18468907 PMCID: PMC2533277 DOI: 10.1016/j.bmc.2008.04.061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 04/19/2008] [Accepted: 04/23/2008] [Indexed: 11/19/2022]
Abstract
Conformation of bicyclic guanidines with kappa-opioid receptor activity derived in our laboratory from a positional scanning synthetic combinatorial library is presented in this work. We propose a common bioactive conformation and putative pharmacophoric features by means of 3D similarity methods. Our 'Y' shape molecular binding model explains structure-activity relationships and suggests that the guanidine functionality and a 4-methoxybenzyl group may be involved in key interactions with the receptor. Comparison of our model with known opiates suggest a similar binding mode showing that the bicyclic guanidines presented in this work are suitable scaffolds for further development of new opioid receptors ligands.
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MESH Headings
- Binding Sites
- Bridged Bicyclo Compounds, Heterocyclic/chemistry
- Bridged Bicyclo Compounds, Heterocyclic/metabolism
- Combinatorial Chemistry Techniques
- Computational Biology
- Guanidine/analogs & derivatives
- Guanidine/chemistry
- Guanidine/metabolism
- Nucleic Acid Conformation
- Receptors, Opioid/chemistry
- Receptors, Opioid/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/metabolism
- Thermodynamics
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Affiliation(s)
- Karina Martínez-Mayorga
- Torrey Pines Institute for Molecular Studies, 5775 Old Dixie Highway, Fort Pierce, FL 34946, USA.
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Johnson SL, Chen LH, Pellecchia M. A high-throughput screening approach to anthrax lethal factor inhibition. Bioorg Chem 2007; 35:306-12. [PMID: 17320146 PMCID: PMC2020844 DOI: 10.1016/j.bioorg.2006.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2006] [Revised: 12/27/2006] [Accepted: 12/29/2006] [Indexed: 11/22/2022]
Abstract
A high-throughput screening approach was used to identify new inhibitors of the metallo-protease lethal factor from Bacillus anthracis. A library of approximately 14,000 compounds was screened using a fluorescence-based in vitro assay and hits were further characterized enzymatically via measurements of IC50 and Ki values against a small panel of metallo-proteases. This study led to the identification of new scaffolds that inhibit LF and the Botulinum Neurotoxin Type A in the low micromolar range, while sparing the human metallo-proteases MMP-2 and MMP-9. Therefore, these scaffolds could be further exploited for the development of potent and selective anti-toxin agents.
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Affiliation(s)
| | | | - Maurizio Pellecchia
- * To whom correspondence should be addressed: Tel. 858.646.3159 Fax. 858.795.5225
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