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Protein Catalyzed Capture (PCC) Agents for Antigen Targeting. Methods Mol Biol 2021. [PMID: 34596849 DOI: 10.1007/978-1-0716-1689-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The protein catalyzed capture agent (PCC) method is a powerful combinatorial screening strategy for discovering synthetic macrocyclic peptide ligands, called PCCs, to designated protein epitopes. The foundational concept of the PCC method is the use of in situ click chemistry to survey large combinatorial libraries of peptides for ligands to designated biological targets. State-of-the-art PCC screens integrate synthetic libraries of constrained macrocyclic peptides with epitope-specific targeting strategies to identify high-affinity (<100 nM) binders de novo. Automated instrumentation can accelerate PCC discovery to a rapid 2-week timeframe. Here, we describe methods to perform combinatorial screens that yield epitope-targeted PCCs.
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2
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Agnew HD, Coppock MB, Idso MN, Lai BT, Liang J, McCarthy-Torrens AM, Warren CM, Heath JR. Protein-Catalyzed Capture Agents. Chem Rev 2019; 119:9950-9970. [PMID: 30838853 DOI: 10.1021/acs.chemrev.8b00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein-catalyzed capture agents (PCCs) are synthetic and modular peptide-based affinity agents that are developed through the use of single-generation in situ click chemistry screens against large peptide libraries. In such screens, the target protein, or a synthetic epitope fragment of that protein, provides a template for selectively promoting the noncopper catalyzed azide-alkyne dipolar cycloaddition click reaction between either a library peptide and a known ligand or a library peptide and the synthetic epitope. The development of epitope-targeted PCCs was motivated by the desire to fully generalize pioneering work from the Sharpless and Finn groups in which in situ click screens were used to develop potent, divalent enzymatic inhibitors. In fact, a large degree of generality has now been achieved. Various PCCs have demonstrated utility for selective protein detection, as allosteric or direct inhibitors, as modulators of protein folding, and as tools for in vivo tumor imaging. We provide a historical context for PCCs and place them within the broader scope of biological and synthetic aptamers. The development of PCCs is presented as (i) Generation I PCCs, which are branched ligands engineered through an iterative, nonepitope-targeted process, and (ii) Generation II PCCs, which are typically developed from macrocyclic peptide libraries and are precisely epitope-targeted. We provide statistical comparisons of Generation II PCCs relative to monoclonal antibodies in which the protein target is the same. Finally, we discuss current challenges and future opportunities of PCCs.
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Affiliation(s)
- Heather D Agnew
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - Matthew B Coppock
- Sensors and Electron Devices Directorate , U.S. Army Research Laboratory , Adelphi , Maryland 20783 , United States
| | - Matthew N Idso
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Bert T Lai
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - JingXin Liang
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Amy M McCarthy-Torrens
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
| | - Carmen M Warren
- Indi Molecular, Inc. , 6162 Bristol Parkway , Culver City , California 90230 , United States
| | - James R Heath
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109-5234 , United States
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3
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Ouyang T, Liu X, Ouyang H, Ren L. Recent trends in click chemistry as a promising technology for virus-related research. Virus Res 2018; 256:21-28. [PMID: 30081058 PMCID: PMC7173221 DOI: 10.1016/j.virusres.2018.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/27/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022]
Abstract
Click chemistry involves reactions that were originally introduced and used in organic chemistry to generate substances by joining small units together with heteroatom linkages (C-X-C). Over the last few decades, click chemistry has been widely used in virus-related research. Using click chemistry, the virus particle as well as viral protein and nucleic acids can be labeled. Subsequently, the labeled virions or molecules can be tracked in real time. Here, we reviewed the recent applications of click reactions in virus-related research, including viral tracking, the design of antiviral agents, the diagnosis of viral infection, and virus-based delivery systems. This review provides an overview of the general principles and applications of click chemistry in virus-related research.
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Affiliation(s)
- Ting Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Xiaohui Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Hongsheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun, 130062, China
| | - Linzhu Ren
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, 5333 Xi'an Road, Changchun, 130062, China.
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4
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Xue A, Szymczak LC, Mrksich M, Bagheri N. Machine Learning on Signal-to-Noise Ratios Improves Peptide Array Design in SAMDI Mass Spectrometry. Anal Chem 2017; 89:9039-9047. [PMID: 28719743 PMCID: PMC5588089 DOI: 10.1021/acs.analchem.7b01728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/18/2017] [Indexed: 12/15/2022]
Abstract
Emerging peptide array technologies are able to profile molecular activities within cell lysates. However, the structural diversity of peptides leads to inherent differences in peptide signal-to-noise ratios (S/N). These complex effects can lead to potentially unrepresentative signal intensities and can bias subsequent analyses. Within mass spectrometry-based peptide technologies, the relation between a peptide's amino acid sequence and S/N remains largely nonquantitative. To address this challenge, we present a method to quantify and analyze mass spectrometry S/N of two peptide arrays, and we use this analysis to portray quality of data and to design future arrays for SAMDI mass spectrometry. Our study demonstrates that S/N varies significantly across peptides within peptide arrays, and variation in S/N is attributable to differences of single amino acids. We apply supervised machine learning to predict peptide S/N based on amino acid sequence, and identify specific physical properties of the amino acids that govern variation of this metric. We find low peptide-S/N concordance between arrays, demonstrating that different arrays require individual characterization and that global peptide-S/N relationships are difficult to identify. However, with proper peptide sampling, this study illustrates how machine learning can accurately predict the S/N of a peptide in an array, allowing for the efficient design of arrays through selection of high S/N peptides.
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Affiliation(s)
- Albert
Y. Xue
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Lindsey C. Szymczak
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Milan Mrksich
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
| | - Neda Bagheri
- Department of Chemical & Biological Engineering, Department of Chemistry, Department of Biomedical
Engineering, Department of Cell & Molecular Biology, and Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208 United States
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5
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Coppock MB, Warner CR, Dorsey B, Orlicki JA, Sarkes DA, Lai BT, Pitram SM, Rohde RD, Malette J, Wilson JA, Kearney P, Fang KC, Law SM, Candelario SL, Farrow B, Finch AS, Agnew HD, Heath JR, Stratis‐Cullum DN. Protein catalyzed capture agents with tailored performance for in vitro and in vivo applications. Biopolymers 2017; 108:e22934. [PMID: 27539157 PMCID: PMC6585716 DOI: 10.1002/bip.22934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/25/2016] [Accepted: 08/17/2016] [Indexed: 12/12/2022]
Abstract
We report on peptide-based ligands matured through the protein catalyzed capture (PCC) agent method to tailor molecular binders for in vitro sensing/diagnostics and in vivo pharmacokinetics parameters. A vascular endothelial growth factor (VEGF) binding peptide and a peptide against the protective antigen (PA) protein of Bacillus anthracis discovered through phage and bacterial display panning technologies, respectively, were modified with click handles and subjected to iterative in situ click chemistry screens using synthetic peptide libraries. Each azide-alkyne cycloaddition iteration, promoted by the respective target proteins, yielded improvements in metrics for the application of interest. The anti-VEGF PCC was explored as a stable in vivo imaging probe. It exhibited excellent stability against proteases and a mean elimination in vivo half-life (T1/2 ) of 36 min. Intraperitoneal injection of the reagent results in slow clearance from the peritoneal cavity and kidney retention at extended times, while intravenous injection translates to rapid renal clearance. The ligand competed with the commercial antibody for binding to VEGF in vivo. The anti-PA ligand was developed for detection assays that perform in demanding physical environments. The matured anti-PA PCC exhibited no solution aggregation, no fragmentation when heated to 100°C, and > 81% binding activity for PA after heating at 90°C for 1 h. We discuss the potential of the PCC agent screening process for the discovery and enrichment of next generation antibody alternatives.
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Affiliation(s)
- Matthew B. Coppock
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | - Candice R. Warner
- Excet, SpringfieldVA 22151 supporting USA Edgewood Chemical Biological CenterAberdeen Proving GroundMD21010
| | - Brandi Dorsey
- Federal Staffing Resources, Annapolis, MD supporting U.S. Army Research LaboratoryAdelphiMD20783
| | - Joshua A. Orlicki
- Weapons and Materials Research DirectorateU.S. Army Research LaboratoryAberdeen Proving GroundMD21005
| | - Deborah A. Sarkes
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | - Bert T. Lai
- Indi Molecular6162 Bristol ParkwayCulver CityCA90230
| | | | | | | | | | | | | | | | | | - Blake Farrow
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 East California BoulevardPasadenaCA91125
| | - Amethist S. Finch
- Sensors and Electron Devices DirectorateU.S. Army Research LaboratoryAdelphiMD20783
| | | | - James R. Heath
- Division of Chemistry and Chemical EngineeringCalifornia Institute of Technology1200 East California BoulevardPasadenaCA91125
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6
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Glassford I, Teijaro CN, Daher SS, Weil A, Small MC, Redhu SK, Colussi DJ, Jacobson MA, Childers WE, Buttaro B, Nicholson AW, MacKerell AD, Cooperman BS, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry. J Am Chem Soc 2016; 138:3136-44. [PMID: 26878192 PMCID: PMC4785600 DOI: 10.1021/jacs.5b13008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over half of all antibiotics target the bacterial ribosome-nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semisynthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a 16-component reaction (i.e., azide 2 and 15 alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd values. Computational analysis using the site-identification by ligand competitive saturation (SILCS) approach indicated that the relative affinity of the ligands was associated with the alteration of macrolactone+desosamine-ribosome interactions caused by the different alkynes. Protein synthesis inhibition experiments confirmed the mechanism of action. Evaluation of the minimal inhibitory concentrations (MIC) quantified the potency of the in situ click products and demonstrated the efficacy of this method in the triaging and prioritization of potent antibiotics that target the bacterial ribosome. Cell viability assays in human fibroblasts confirmed 2 and four analogues with therapeutic indices for bactericidal activity over in vitro mammalian cytotoxicity as essentially identical to solithromycin (1).
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Affiliation(s)
- Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | | | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Amy Weil
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Meagan C. Small
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122
| | - Dennis J. Colussi
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Marlene A. Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Wayne E. Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140
| | | | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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7
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Henning RK, Varghese JO, Das S, Nag A, Tang G, Tang K, Sutherland AM, Heath JR. Degradation of Akt using protein-catalyzed capture agents. J Pept Sci 2016; 22:196-200. [PMID: 26880702 DOI: 10.1002/psc.2858] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 12/22/2022]
Abstract
Abnormal signaling of the protein kinase Akt has been shown to contribute to human diseases such as diabetes and cancer, but Akt has proven to be a challenging target for drugging. Using iterative in situ click chemistry, we recently developed multiple protein-catalyzed capture (PCC) agents that allosterically modulate Akt enzymatic activity in a protein-based assay. Here, we utilize similar PCCs to exploit endogenous protein degradation pathways. We use the modularity of the anti-Akt PCCs to prepare proteolysis targeting chimeric molecules that are shown to promote the rapid degradation of Akt in live cancer cells. These novel proteolysis targeting chimeric molecules demonstrate that the epitope targeting selectivity of PCCs can be coupled with non-traditional drugging moieties to inhibit challenging targets.
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Affiliation(s)
- Ryan K Henning
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Joseph O Varghese
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Samir Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Grace Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Kevin Tang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - Alexander M Sutherland
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 127-72, Pasadena, CA 91125
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8
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Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez‐Rivera FP, McCarthy A, Alvarez‐Villalonga B, Chen A, Heath J, Stratis‐Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N. Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B. Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A. Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S. Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D. Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A. Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M. Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P. Rodriguez‐Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez‐Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N. Stratis‐Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R. Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
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9
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Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez-Rivera FP, McCarthy A, Alvarez-Villalonga B, Chen A, Heath J, Stratis-Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015; 54:13219-24. [PMID: 26377818 DOI: 10.1002/anie.201505243] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/12/2015] [Indexed: 12/20/2022]
Abstract
We describe a general synthetic strategy for developing high-affinity peptide binders against specific epitopes of challenging protein biomarkers. The epitope of interest is synthesized as a polypeptide, with a detection biotin tag and a strategically placed azide (or alkyne) presenting amino acid. This synthetic epitope (SynEp) is incubated with a library of complementary alkyne or azide presenting peptides. Library elements that bind the SynEp in the correct orientation undergo the Huisgen cycloaddition, and are covalently linked to the SynEp. Hit peptides are tested against the full-length protein to identify the best binder. We describe development of epitope-targeted linear or macrocycle peptide ligands against 12 different diagnostic or therapeutic analytes. The general epitope targeting capability for these low molecular weight synthetic ligands enables a range of therapeutic and diagnostic applications, similar to those of monoclonal antibodies.
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Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P Rodriguez-Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez-Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
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10
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Deyle KM, Farrow B, Hee YQ, Work J, Wong M, Lai B, Umeda A, Millward SW, Nag A, Das S, Heath JR. A protein-targeting strategy used to develop a selective inhibitor of the E17K point mutation in the PH domain of Akt1. Nat Chem 2015; 7:455-62. [PMID: 25901825 PMCID: PMC4408887 DOI: 10.1038/nchem.2223] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/27/2015] [Indexed: 11/08/2022]
Abstract
Ligands that can bind selectively to proteins with single amino-acid point mutations offer the potential to detect or treat an abnormal protein in the presence of the wild type (WT). However, it is difficult to develop a selective ligand if the point mutation is not associated with an addressable location, such as a binding pocket. Here we report an all-chemical synthetic epitope-targeting strategy that we used to discover a 5-mer peptide with selectivity for the E17K-transforming point mutation in the pleckstrin homology domain of the Akt1 oncoprotein. A fragment of Akt1 that contained the E17K mutation and an I19[propargylglycine] substitution was synthesized to form an addressable synthetic epitope. Azide-presenting peptides that clicked covalently onto this alkyne-presenting epitope were selected from a library using in situ screening. One peptide exhibits a 10:1 in vitro selectivity for the oncoprotein relative to the WT, with a similar selectivity in cells. This 5-mer peptide was expanded into a larger ligand that selectively blocks the E17K Akt1 interaction with its PIP3 (phosphatidylinositol (3,4,5)-trisphosphate) substrate.
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Affiliation(s)
- Kaycie M. Deyle
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Blake Farrow
- Department of Applied Physics and Materials Science, California Institute of Technology, Pasadena, CA, USA 91125
| | - Ying Qiao Hee
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Jeremy Work
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Michelle Wong
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Bert Lai
- InDi Molecular, Culver City, CA, USA 90230
| | - Aiko Umeda
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Steven W. Millward
- Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, USA 77054
| | - Arundhati Nag
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - Samir Das
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
| | - James R. Heath
- Department of Chemistry, California Institute of Technology, Pasadena, CA, USA 91125
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Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope Targeting of Tertiary Protein Structure Enables Target-Guided Synthesis of a Potent In-Cell Inhibitor of Botulinum Neurotoxin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope targeting of tertiary protein structure enables target-guided synthesis of a potent in-cell inhibitor of botulinum neurotoxin. Angew Chem Int Ed Engl 2015; 54:7114-9. [PMID: 25925721 DOI: 10.1002/anie.201502451] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/09/2015] [Indexed: 12/14/2022]
Abstract
Botulinum neurotoxin (BoNT) serotype A is the most lethal known toxin and has an occluded structure, which prevents direct inhibition of its active site before it enters the cytosol. Target-guided synthesis by in situ click chemistry is combined with synthetic epitope targeting to exploit the tertiary structure of the BoNT protein as a landscape for assembling a competitive inhibitor. A substrate-mimicking peptide macrocycle is used as a direct inhibitor of BoNT. An epitope-targeting in situ click screen is utilized to identify a second peptide macrocycle ligand that binds to an epitope that, in the folded BoNT structure, is active-site-adjacent. A second in situ click screen identifies a molecular bridge between the two macrocycles. The resulting divalent inhibitor exhibits an in vitro inhibition constant of 165 pM against the BoNT/A catalytic chain. The inhibitor is carried into cells by the intact holotoxin, and demonstrates protection and rescue of BoNT intoxication in a human neuron model.
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Affiliation(s)
- Blake Farrow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).,Department of Applied Physics and Materials Science, California Institute of Technology (USA)
| | - Michelle Wong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Jacquie Malette
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Kaycie M Deyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Samir Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
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Nag A, Das S, Yu MB, Deyle KM, Millward SW, Heath JR. A chemical epitope-targeting strategy for protein capture agents: the serine 474 epitope of the kinase Akt2. Angew Chem Int Ed Engl 2013; 52:13975-9. [PMID: 24254999 PMCID: PMC4059071 DOI: 10.1002/anie.201305882] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 09/23/2013] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M. Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | | | - James R. Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
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Nag A, Das S, Yu MB, Deyle KM, Millward SW, Heath JR. A Chemical Epitope-Targeting Strategy for Protein Capture Agents: The Serine 474 Epitope of the Kinase Akt2. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305882] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Farrow B, Hong SA, Romero EC, Lai B, Coppock MB, Deyle KM, Finch AS, Stratis-Cullum DN, Agnew HD, Yang S, Heath JR. A chemically synthesized capture agent enables the selective, sensitive, and robust electrochemical detection of anthrax protective antigen. ACS NANO 2013; 7:9452-9460. [PMID: 24063758 DOI: 10.1021/nn404296k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We report on a robust and sensitive approach for detecting protective antigen (PA) exotoxin from Bacillus anthracis in complex media. A peptide-based capture agent against PA was developed by improving a bacteria display-developed peptide into a highly selective biligand through in situ click screening against a large, chemically synthesized peptide library. This biligand was coupled with an electrochemical enzyme-linked immunosorbent assay utilizing nanostructured gold electrodes. The resultant assay yielded a limit of detection of PA of 170 pg/mL (2.1 pM) in buffer, with minimal sensitivity reduction in 1% serum. The powdered capture agent could be stably stored for several days at 65 °C, and the full electrochemical biosensor showed no loss of performance after extended storage at 40 °C. The engineered stability and specificity of this assay should be extendable to other cases in which biomolecular detection in demanding environments is required.
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Affiliation(s)
- Blake Farrow
- Department of Applied Physics and Materials Science, and ‡Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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