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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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2
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Li J, Zhao S, Yang G, Liu R, Xiao W, Disano P, Lam KS, Pan T. Combinatorial Peptide Microarray Synthesis Based on Microfluidic Impact Printing. ACS COMBINATORIAL SCIENCE 2019; 21:6-10. [PMID: 30521316 PMCID: PMC6335607 DOI: 10.1021/acscombsci.8b00125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
In this Research
Article, a novel inkjet printing technique, micro
impact printing (MI printing), is applied for the first time to combinatorial
peptide microarray synthesis on amine functionalized microdisc arrays
through standard Fmoc chemistry. MI printing shows great advantages
in combinatorial peptide microarray synthesis compared with other
printing techniques, including (1) a disposable cartridge; (2) a small
spot size (80 μm) increases array density; (3) minimal loading
volume (0.6 μL) and dead volume (<0.1 μL), reduce chemical
waste; and (4) multiplexibility of 5 channels/cartridge and capacity
of multiple cartridges. Using this synthesis platform, a tetrapeptide
library with 625 permutations was constructed and then applied for
the screening of ligands targeting α4β1 integrin on Jurkat cells.
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Affiliation(s)
- Jiannan Li
- Department of Biomedical Engineering, University of California, Davis, California 95616-5270, United States
| | - Siwei Zhao
- Department of Biomedical Engineering, Tufts University, Boston, Massachusetts 02155, United States
| | - Gaomai Yang
- Department of Biomedical Engineering, University of California, Davis, California 95616-5270, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95817, United States
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95817, United States
| | - Paolo Disano
- Department of Biomedical Engineering, University of California, Davis, California 95616-5270, United States
| | - Kit S. Lam
- Department of Biochemistry and Molecular Medicine, University of California, Davis, California 95817, United States
| | - Tingrui Pan
- Department of Biomedical Engineering, University of California, Davis, California 95616-5270, United States
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3
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Liang X, Vézina-Dawod S, Bédard F, Porte K, Biron E. One-Pot Photochemical Ring-Opening/Cleavage Approach for the Synthesis and Decoding of Cyclic Peptide Libraries. Org Lett 2016; 18:1174-7. [PMID: 26914725 DOI: 10.1021/acs.orglett.6b00296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A novel dual ring-opening/cleavage strategy to determine the sequence of cyclic peptides from one bead, one compound libraries is described. The approach uses a photolabile residue within the macrocycle and as a linker to allow a simultaneous ring opening and cleavage from the beads upon UV irradiation and provide linearized molecules. Cyclic peptides of five to nine residues were synthesized and the generated linear peptides successfully sequenced by tandem mass spectrometry.
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Affiliation(s)
- Xinxia Liang
- Faculty of Pharmacy, Université Laval , Québec, Québec G1V 0A6, Canada.,Laboratory of Medicinal Chemistry, Centre de recherche du Centre Hospitalier Universitaire de Québec , 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Simon Vézina-Dawod
- Faculty of Pharmacy, Université Laval , Québec, Québec G1V 0A6, Canada.,Laboratory of Medicinal Chemistry, Centre de recherche du Centre Hospitalier Universitaire de Québec , 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | | | - Karine Porte
- Faculty of Pharmacy, Université Laval , Québec, Québec G1V 0A6, Canada.,Laboratory of Medicinal Chemistry, Centre de recherche du Centre Hospitalier Universitaire de Québec , 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy, Université Laval , Québec, Québec G1V 0A6, Canada.,Laboratory of Medicinal Chemistry, Centre de recherche du Centre Hospitalier Universitaire de Québec , 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
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4
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Wang Y, Xiao W, Zhang Y, Meza L, Tseng H, Takada Y, Ames JB, Lam KS. Optimization of RGD-Containing Cyclic Peptides against αvβ3 Integrin. Mol Cancer Ther 2015; 15:232-40. [PMID: 26719578 DOI: 10.1158/1535-7163.mct-15-0544] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
We have previously reported the use of one-bead-one-compound (OBOC) combinatorial technology to develop a disulfide cyclic, Arg-Gly-Asp-containing octapeptide LXW7 (cGRGDdvc), that targets αvβ3 integrin with high affinity and specificity. αvβ3 integrin is known to be overexpressed in many cancers and in tumor vasculature, and it has been established as a cancer therapeutic target. To further optimize LXW7, we have performed systematic structure-activity relationship studies. On the basis of the results, two highly focused OBOC peptide libraries were designed, synthesized, and screened against αvβ3 integrin-transfected K562 cells. One of the best ligands, LXW64, was found to have 6.6-fold higher binding affinity than LXW7, and showed preferential binding to cells expressing αvβ3 integrin. In addition to binding strongly to U-87MG glioblastoma cells in vitro, LXW64 also targets U-87MG xenografts implanted in nude mice, indicating that it is an excellent vehicle for the delivery of cytotoxic payload to tumors and tumor blood vessels that overexpress αvβ3 integrin. Mol Cancer Ther; 15(2); 232-40. ©2015 AACR.
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Affiliation(s)
- Yan Wang
- Department of Biochemistry and Molecular Medicine, University of California Davis Cancer Center, Sacramento, California
| | - Wenwu Xiao
- Department of Biochemistry and Molecular Medicine, University of California Davis Cancer Center, Sacramento, California
| | - Yonghong Zhang
- Department of Chemistry, University of Texas-Pan American, Edinburg, Texas
| | - Leah Meza
- Department of Biochemistry and Molecular Medicine, University of California Davis Cancer Center, Sacramento, California
| | - Harry Tseng
- Department of Biochemistry and Molecular Medicine, University of California Davis Cancer Center, Sacramento, California
| | - Yoshikazu Takada
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, California
| | - James B Ames
- Department of Chemistry, University of California Davis, Davis, California
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California Davis Cancer Center, Sacramento, California.
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5
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Doran TM, Kodadek T. A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions. ACS Chem Biol 2014; 9:339-46. [PMID: 24245981 PMCID: PMC3944025 DOI: 10.1021/cb400806r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic molecule microarrays, consisting of many different compounds spotted onto a planar surface such as modified glass or cellulose, have proven to be useful tools for the multiplexed analysis of small molecule- and peptide-protein interactions. However, these arrays are technically difficult to manufacture and use with high reproducibility and require specialized equipment. Here we report a more convenient alternative composed of color-encoded beads that display a small molecule protein ligand on the surface. Quantitative, multiplexed assay of protein binding to up to 24 different ligands can be achieved using a common flow cytometer for the readout. This technology should be useful for evaluating hits from library screening efforts, the determination of structure activity relationships, and certain types of serological analyses.
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Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida , 130 Scripps Way, Jupiter , Florida 33458, United States
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6
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Liang X, Girard A, Biron E. Practical ring-opening strategy for the sequence determination of cyclic peptides from one-bead-one-compound libraries. ACS COMBINATORIAL SCIENCE 2013; 15:535-40. [PMID: 24016186 DOI: 10.1021/co4000979] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of cyclic peptides in one-bead-one-compound libraries is limited by difficulties in sequencing hit compounds. Lacking a free N-terminal amine, such peptides cannot be sequenced by the Edman degradation approach, and complex fragmentation patterns are obtained by tandem mass spectrometry. To overcome this problem, we designed an alternative approach introducing a methionine residue within the macrocycle and as a linker to allow simultaneous ring-opening and release from the resin upon treatment with cyanogen bromide. The methionine linker was inverted relative to the peptide chain to allow the synthesis of cyclic peptides anchored by a lysine side chain and to avoid the presence of two C-terminal homoserine lactones on the released linear peptides. After MALDI-TOF MS/MS analysis, the peptides released from a single bead were sequenced manually and with a de novo sequencing software. The strategy described herein is compatible with commonly used amino acids and allows sequencing of cyclic peptides in one-bead-one-compound libraries, thus reducing the need for encoding.
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Affiliation(s)
- Xinxia Liang
- Faculty of Pharmacy, Université Laval, Pavillon Ferdinand-Vandry, Québec, Québec, G1 V 0A6, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Center (CHUL Section), 2705 Boulevard Laurier, Québec, Québec, G1V 4G2, Canada
| | - Anick Girard
- Faculty of Pharmacy, Université Laval, Pavillon Ferdinand-Vandry, Québec, Québec, G1 V 0A6, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Center (CHUL Section), 2705 Boulevard Laurier, Québec, Québec, G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy, Université Laval, Pavillon Ferdinand-Vandry, Québec, Québec, G1 V 0A6, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Center (CHUL Section), 2705 Boulevard Laurier, Québec, Québec, G1V 4G2, Canada
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7
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Bédard F, Girard A, Biron É. A Convenient Approach to Prepare Topologically Segregated Bilayer Beads for One-Bead Two-Compound Combinatorial Peptide Libraries. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9316-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Kumaresan PR, Wang Y, Saunders M, Maeda Y, Liu R, Wang X, Lam KS. Rapid discovery of death ligands with one-bead-two-compound combinatorial library methods. ACS COMBINATORIAL SCIENCE 2011; 13:259-64. [PMID: 21302937 DOI: 10.1021/co100069t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The one-bead-one-compound (OBOC) technology enables one to generate thousands to millions of chemical molecules on resin beads (90 μm diameter) such that each bead displays 10(13) copies of the same chemical entity. Whole-cell binding assays have been developed to screen OBOC combinatorial libraries for ligands that bind to specific cell surface receptors. While very powerful, this screening method does not address the downstream cell signaling properties of the binding ligand. We have modified the OBOC technology by introducing a fixed known cell adhesion ligand to the outer layer of each bead. This one-bead-two-compound (OB2C) library configuration allows the bound cells to interact with the random immobilized chemical molecules on each bead. The bound cells can then be probed for specific cellular responses such as apoptosis and activation or inhibition of a specific cell signaling pathway. To validate this concept, an OB2C combinatorial library was created such that a random hexapeptide plus a high affinity lymphoma targeting ligand LLP2A were displayed on each bead. This LLP2A-X(6) OB2C library was then screened with human T-cell leukemia cells (Molt-4) for cell death responses. After 5 days of incubation, propidium iodide was added to the bead library to stain dead cells. Beads coated by red fluorescent cells were isolated for sequence analysis. Two ligands identified by this method, when added to the lymphoid cancer cells, were able to induce cell death.
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Affiliation(s)
- Pappanaicken R. Kumaresan
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Yan Wang
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Mary Saunders
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Yoshiko Maeda
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Xiaobing Wang
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
| | - Kit Sang Lam
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, and Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, 2700 Stockton Boulevard, Sacramento, California 95817, United States
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9
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Townsend JB, Shaheen F, Liu R, Lam KS. Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries. ACTA ACUST UNITED AC 2010; 12:700-12. [PMID: 20593859 DOI: 10.1021/cc100083f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds were resynthesized and found to be cytotoxic (IC(50) 50-150 μM) against two T-lymphoma cell lines and less so against the MDA-MB 231 breast cancer cell line. This novel ultrahigh-throughput OBOC releasable method can potentially be adapted to many existing 96- or 384-well solution-phase cell-based or biochemical assays.
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Affiliation(s)
- Jared B Townsend
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, University of California Davis Cancer Center, University of California Davis, 4501 X Street, Sacramento, California 95817, USA
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Baek HG, Liu R, Lam KS. Development of hydrogel TentaGel shell-core beads for ultrahigh throughput solution-phase screening of encoded OBOC combinatorial small molecule libraries. ACTA ACUST UNITED AC 2009; 11:91-102. [PMID: 19061339 DOI: 10.1021/cc800092y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The one-bead one-compound (OBOC) combinatorial library method enables the rapid generation and screening of millions of discrete chemical compounds on beads. Most of the OBOC screening methods require the library compounds to remain tethered to the bead during screening process. Methods have also been developed to release library compounds from immobilized beads for in situ solution phase or "lawn" assays. However, this latter approach, while extremely powerful, is severely limited by the lack of suitable solid supports for such assays. Here, we report on the development of a novel hydrogel TentaGel shell-core (HTSC) bead in which hydrogel is grafted onto the polystyrene-based TentaGel (TG) bead as an outer shell (5-80 mum thick) via free radical surface-initiated polymerization. This novel shell-core bilayer resin enables the preparation of encoded OBOC combinatorial small molecule libraries, such that the library compounds reside on the highly hydrophilic outer layer and the coding tags reside in the polystyrene-based TG core. Using fluorescein as a model small molecule compound, we have demonstrated that fluorescein molecules that have been linked covalently to the hydrogel shell via a disulfide bond could readily diffuse out of the hydrogel layer into the bead surrounding after reduction with dithiothreitol. In contrast, under identical condition, the released fluorescein molecules remained bound to unmodified TG bead. We have prepared an encoded OBOC small molecule library on the novel shell-core beads and demonstrated that the beads can be readily decoded.
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Affiliation(s)
- Hyoung Gee Baek
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, Sacramento, California 95817, USA
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11
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Yao N, Xiao W, Wang X, Marik J, Park SH, Takada Y, Lam KS. Discovery of targeting ligands for breast cancer cells using the one-bead one-compound combinatorial method. J Med Chem 2009; 52:126-33. [PMID: 19055415 DOI: 10.1021/jm801062d] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four "one-bead one-compound" (OBOC) combinatorial libraries were designed, synthesized, and screened against MDA-MB-231 breast cancer cells. A novel cyclic peptide 1 (LXY1) with high binding specificity to alpha3 integrin was identified. Molecular interactions between alpha3 integrin and 1 were characterized by using a series of K562 cells transfected with various mutant alpha3 integrins. Using analytic flow cytometry, the binding affinity (K(d)) of 1 to alpha3 integrin on MDA-MB-231 breast cancer cells was determined to be approximately 0.4 microM. Based on the established structure-activity relationship (SAR) study, two highly focused cyclic peptide libraries were further designed, synthesized, and screened against MDA-MB-231 breast cancer cells under stringent conditions. A novel cyclic peptide 2 (LXY3) with a high binding affinity (IC(50) = 57 nM) was identified. Moreover, the targeting efficiency and specificity of 2 to the breast adenocarcinoma tumors in mouse xenografts were further confirmed by in vivo and ex vivo near-infrared fluorescence optical imaging.
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Affiliation(s)
- Nianhuan Yao
- Department of Internal Medicine, Division of Hematology and Oncology, UC Davis Cancer Center, University of California, Davis, Sacramento, California 95817, USA
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12
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Application of the “Libraries from Libraries” Concept to “One-bead One-compound” Combinatorial Chemistry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009. [DOI: 10.1007/978-0-387-73657-0_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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13
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Luo J, Zhang H, Xiao W, Kumaresan PR, Shi C, Pan CX, Aina OH, Lam KS. Rainbow beads: a color coding method to facilitate high-throughput screening and optimization of one-bead one-compound combinatorial libraries. ACTA ACUST UNITED AC 2008; 10:599-604. [PMID: 18558750 DOI: 10.1021/cc8000663] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new color-encoding method that facilitates high-throughput screening of one-bead one-compound (OBOC) combinatorial libraries. Polymer beads displaying chemical compounds or families of compounds are stained with oil-based organic dyes that are used as coding tags. The color dyes do not affect cell binding to the compounds displayed on the surface of the beads. We have applied such rainbow beads in a multiplex manner to discover and profile ligands against cell surface receptors. In the first application, a series of OBOC libraries with different scaffolds or motifs are each color-coded; small samples of each library are then combined and screened concurrently against live cells for cell attachment. Preferred libraries can be rapidly identified and selected for subsequent large-scale screenings for cell surface binding ligands. In a second application, beads with a series of peptide analogues (e.g., alanine scan) are color-coded, combined, and tested for binding against a specific cell line in a single-tissue culture well; the critical residues required for binding can be easily determined. In a third application, ligands reacting against a series of integrins are color-coded and used as a readily applied research tool to determine the integrin profile of any cell type. One major advantage of this straightforward and yet powerful method is that only an ordinary inverted microscope is needed for the analysis, instead of sophisticated (and expensive) fluorescent microscopes or flow cytometers.
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Affiliation(s)
- Juntao Luo
- Division of Hematology & Oncology, Department of Internal Medicine, UC Davis Cancer Center, University of California Davis, Sacramento, California 95817, USA
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14
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Galliford CV, Scheidt KA. Pyrrolidinyl-spirooxindole natural products as inspirations for the development of potential therapeutic agents. Angew Chem Int Ed Engl 2008; 46:8748-58. [PMID: 17943924 DOI: 10.1002/anie.200701342] [Citation(s) in RCA: 2033] [Impact Index Per Article: 127.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 3,3'-pyrrolidinyl-spirooxindole unit is a privileged heterocyclic motif that forms the core of a large family of alkaloid natural products with strong bioactivity profiles and interesting structural properties. Significant recent advances in the synthesis of this fused heterocyclic system have led to intense interest in the development of related compounds as potential medicinal agents or biological probes.
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Affiliation(s)
- Chris V Galliford
- Chemistry Department, Northwestern University, 2145 Sheridan Road, Evanston IL 60201, USA
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15
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Kappel JC, Fan YC, Lam KS. Global Transformation of OBOC Combinatorial Peptide Libraries into OBOC Polyamine and Small Molecule Libraries. ACTA ACUST UNITED AC 2008; 10:333-42. [DOI: 10.1021/cc700165s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joseph C. Kappel
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
| | - Yi C. Fan
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
| | - Kit S. Lam
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, 4501 X Street, Sacramento, California 95817
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Galliford C, Scheidt K. Natürliche Pyrrolidinylspirooxindole als Vorlagen für die Entwicklung medizinischer Wirkstoffe. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701342] [Citation(s) in RCA: 497] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Miyamoto S, Liu R, Hung S, Wang X, Lam KS. Screening of a one bead-one compound combinatorial library for beta-actin identifies molecules active toward Ramos B-lymphoma cells. Anal Biochem 2007; 374:112-20. [PMID: 18023409 DOI: 10.1016/j.ab.2007.10.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 10/11/2007] [Accepted: 10/15/2007] [Indexed: 11/25/2022]
Abstract
The search for small molecules that specifically recognize protein targets is a laborious process if conducted in a one protein-one compound manner. A high-throughput antibody-based screening of one bead-one compound (OBOC) combinatorial small molecule libraries is described here, whereby libraries containing thousands of different small molecule ligands are synthesized on individual TentaGel beads and simultaneously screened for protein binding to individual beads, each with a different compound. The use of OBOC libraries greatly facilitates this simultaneous screening of thousands of compounds. Now, through the use of monoclonal or affinity-purified antibodies, small molecules that bind a particular protein contained in a complex mixture of biological molecules have been identified. This method identified small molecule ligands that bound beta-actin present in cytoplasmic cell extracts of Ramos B-lymphoma cells. These small molecule ligands were resynthesized in immobilized and soluble forms and tested for binding of beta-actin present in Ramos B-cell extracts and for activity against Ramos lymphoma cells. This high-throughput screening immunoassay method has great promise for improving our ability to find relevant, bioactive small molecules that target a specific native protein in a complex protein mixture without purification of the protein.
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Affiliation(s)
- Suzanne Miyamoto
- Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Cancer Center, University of California Davis, Sacramento, CA 95817, USA.
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