1
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Molakaseema V, Selvaraj A, Chen HT, Chen YW, Liu YC, Kao CL. Simple and Rapid Synthesis of Branched Peptides through Microwave-Assisted On-Bead Ligation. J Org Chem 2021; 87:1-9. [PMID: 34677067 DOI: 10.1021/acs.joc.1c01455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A rapid on-bead convergent method for preparing branched peptides was reported. Linear peptides were prepared on Dbz resin and ligated various branched cores, including lysine dendrons and other dendritic compounds. Alongside microwave irradiation, <1.5 equiv of peptides is sufficient to afford 50-65% yields of pure branched peptides without chromatographic purification. Remarkably, the desired compounds were prepared within hours.
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Affiliation(s)
- Vijayasimha Molakaseema
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Anand Selvaraj
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hui-Ting Chen
- Department of Fragrance and Cosmetic Science, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yen-Wei Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Chang Liu
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Division of Hematology-Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chai-Lin Kao
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.,Department of Chemistry, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.,College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
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2
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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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3
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Chan KH, Lim J, Jee JE, Aw JH, Lee SS. Peptide-Peptide Co-Assembly: A Design Strategy for Functional Detection of C-peptide, A Biomarker of Diabetic Neuropathy. Int J Mol Sci 2020; 21:ijms21249671. [PMID: 33352955 PMCID: PMC7766332 DOI: 10.3390/ijms21249671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/29/2022] Open
Abstract
Diabetes-related neuropathy is a debilitating condition that may be averted if it can be detected early. One possible way this can be achieved at low cost is to utilise peptides to detect C-peptide, a biomarker of diabetic neuropathy. This depends on peptide-peptide co-assembly, which is currently in a nascent stage of intense study. Instead, we propose a bead-based triple-overlay combinatorial strategy that can preserve inter-residue information during the screening process for a suitable complementary peptide to co-assemble with C-peptide. The screening process commenced with a pentapeptide general library, which revealed histidine to be an essential residue. Further screening with seven tetrapeptide focused libraries led to a table of self-consistent peptide sequences that included tryptophan and lysine at high frequencies. Three complementary nonapeptides (9mer com-peptides), wpkkhfwgq (Trp-D), kwkkhfwgq (Lys-D), and KWKKHFWGQ (Lys-L) (as a negative control) were picked from this table for co-assembly studies with C-peptide. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) and circular dichroism (CD) spectroscopies were utilized to study inter-peptide interactions and changes in secondary structures respectively. ATR-FTIR studies showed that there is indeed inter-peptide interaction between C-peptide and the tryptophan residues of the 9mer com-peptides. CD studies of unaggregated and colloidal C-peptide with the 9mer com-peptides suggest that the extent of co-assembly of C-peptide with Trp-D is greatest, followed by Lys-D and Lys-L. These results are promising and indicate that the presented strategy is viable for designing and evaluating longer complementary peptides, as well as complementary peptides for co-assembly with other polypeptides of interest and importance. We discuss the possibility of designing complementary peptides to inhibit toxic amyloidosis with this approach.
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Affiliation(s)
- Kiat Hwa Chan
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
- Correspondence: (K.H.C.); (S.S.L.)
| | - Jaehong Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Joo Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
| | - Jia Hui Aw
- Division of Science, Yale-NUS College, 16 College Avenue West, Singapore 138527, Singapore;
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore; (J.L.); (J.E.J.)
- Correspondence: (K.H.C.); (S.S.L.)
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4
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Li Y, Cao X, Tian C, Zheng JS. Chemical protein synthesis-assisted high-throughput screening strategies for d-peptides in drug discovery. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2020.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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5
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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6
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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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7
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Pícha J, Buděšínský M, Macháčková K, Collinsová M, Jiráček J. Optimized syntheses of Fmoc azido amino acids for the preparation of azidopeptides. J Pept Sci 2017; 23:202-214. [PMID: 28120383 PMCID: PMC5347871 DOI: 10.1002/psc.2968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 12/17/2022]
Abstract
The rise of CuI‐catalyzed click chemistry has initiated an increased demand for azido and alkyne derivatives of amino acid as precursors for the synthesis of clicked peptides. However, the use of azido and alkyne amino acids in peptide chemistry is complicated by their high cost. For this reason, we investigated the possibility of the in‐house preparation of a set of five Fmoc azido amino acids: β‐azido l‐alanine and d‐alanine, γ‐azido l‐homoalanine, δ‐azido l‐ornithine and ω‐azido l‐lysine. We investigated several reaction pathways described in the literature, suggested several improvements and proposed several alternative routes for the synthesis of these compounds in high purity. Here, we demonstrate that multigram quantities of these Fmoc azido amino acids can be prepared within a week or two and at user‐friendly costs. We also incorporated these azido amino acids into several model tripeptides, and we observed the formation of a new elimination product of the azido moiety upon conditions of prolonged couplings with 2‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyluronium hexafluorophosphate/DIPEA. We hope that our detailed synthetic protocols will inspire some peptide chemists to prepare these Fmoc azido acids in their laboratories and will assist them in avoiding the too extensive costs of azidopeptide syntheses. Experimental procedures and/or analytical data for compounds 3–5, 20, 25, 26, 30 and 43–47 are provided in the supporting information. © 2017 The Authors Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.
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Affiliation(s)
- Jan Pícha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Kateřina Macháčková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Michaela Collinsová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 166 10, Prague 6, Czech Republic
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8
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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 2016; 108. [PMID: 27539157 PMCID: PMC6585716 DOI: 10.1002/bip.22934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [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 Directorate, U.S. Army Research Laboratory, Adelphi, MD, 20783
| | - Candice R Warner
- Excet, Springfield, VA 22151 supporting USA Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, 21010
| | - Brandi Dorsey
- Federal Staffing Resources, Annapolis, MD supporting U.S. Army Research Laboratory, Adelphi, MD, 20783
| | - Joshua A Orlicki
- Weapons and Materials Research Directorate, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD, 21005
| | - Deborah A Sarkes
- Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, Adelphi, MD, 20783
| | - Bert T Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA, 90230
| | - Suresh M Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA, 90230
| | | | - Jacquie Malette
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA, 90230
| | - Jeré A Wilson
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA, 90230
| | | | | | | | | | - Blake Farrow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125
| | - Amethist S Finch
- Sensors and Electron Devices Directorate, U.S. Army Research Laboratory, Adelphi, MD, 20783
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA, 90230
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125
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9
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Pape S, Wessig P, Brunner H. Iron Trichloride and Air Mediated Guanylation of Acylthioureas. An Ecological Route to Acylguanidines: Scope and Mechanistic Insights. J Org Chem 2016; 81:4701-12. [DOI: 10.1021/acs.joc.6b00600] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Simon Pape
- Atotech Deutschland GmbH, Erasmusstrasse
20, D-10553 Berlin, Germany
| | - Pablo Wessig
- Universität Potsdam, Institut für Chemie, Karl-Liebknecht-Straße 24-25,
Haus 25, D-14476 Potsdam, Germany
| | - Heiko Brunner
- Atotech Deutschland GmbH, Erasmusstrasse
20, D-10553 Berlin, Germany
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10
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Crittenden CM, Parker WR, Jenner ZB, Bruns KA, Akin LD, McGee WM, Ciccimaro E, Brodbelt JS. Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:856-863. [PMID: 26864791 DOI: 10.1007/s13361-016-1355-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/13/2016] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.
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Affiliation(s)
| | - W Ryan Parker
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - Zachary B Jenner
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Kerry A Bruns
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Lucas D Akin
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
| | - William M McGee
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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11
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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: 44] [Impact Index Per Article: 5.5] [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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12
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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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13
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Toguchi S, Hirose T, Yorita K, Fukui K, Sharpless KB, Ōmura S, Sunazuka T. In Situ Click Chemistry for the Identification of a Potent D-Amino Acid Oxidase Inhibitor. Chem Pharm Bull (Tokyo) 2016; 64:695-703. [DOI: 10.1248/cpb.c15-00867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shohei Toguchi
- Graduate School of Infection Control Sciences, Kitasato University
| | - Tomoyasu Hirose
- Graduate School of Infection Control Sciences, Kitasato University
- The Kitasato Institute for Life Sciences, Kitasato University
| | | | | | | | - Satoshi Ōmura
- The Kitasato Institute for Life Sciences, Kitasato University
| | - Toshiaki Sunazuka
- Graduate School of Infection Control Sciences, Kitasato University
- The Kitasato Institute for Life Sciences, Kitasato University
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14
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Hirose T, Sunazuka T, Ōmura S. Rapid Identification via <i>In Situ</i> Click Chemistry of a Novel Chitinase Inhibitor. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.1090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomoyasu Hirose
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Toshiaki Sunazuka
- Kitasato Institute for Life Sciences, Kitasato University
- Graduate School of Infection Control Sciences, Kitasato University
| | - Satoshi Ōmura
- Kitasato Institute for Life Sciences, Kitasato University
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15
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Parvatkar P, Kato N, Uesugi M, Sato SI, Ohkanda J. Intracellular Generation of a Diterpene-Peptide Conjugate that Inhibits 14-3-3-Mediated Interactions. J Am Chem Soc 2015; 137:15624-7. [PMID: 26632868 DOI: 10.1021/jacs.5b09817] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic agents that disrupt intracellular protein-protein interactions (PPIs) are highly desirable for elucidating signaling networks and developing new therapeutics. However, designing cell-penetrating large molecules equipped with the many functional groups necessary for binding to large interfaces remains challenging. Here, we describe a rational strategy for the intracellular oxime ligation-mediated generation of an amphipathic bivalent inhibitor composed of a peptide and diterpene natural product, fusicoccin, which binds 14-3-3 protein with submicromolar affinity. Our results demonstrate that co-treatment of cells with small module molecules, the aldehyde-containing fusicoccin 1 and the aminooxy-containing peptide 2, generates the corresponding conjugate 3 in cells, resulting in significant cytotoxicity. In contrast, chemically synthesized 3 is not cytotoxic, likely due to its inability to penetrate cells. Compound 3, but not 1 or 2, disrupts endogenous 14-3-3/cRaf interactions, suggesting that cell death is caused by inhibition of 14-3-3 activity. These results suggest that intracellular generation of large-sized molecules may serve as a new approach for modulating PPIs.
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Affiliation(s)
- Prakash Parvatkar
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nobuo Kato
- Institute of Scientific and Industrial Research, Osaka University , 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Motonari Uesugi
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
| | - Junko Ohkanda
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Gokasho, Uji, Kyoto 611-0011, Japan
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16
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Yoo SM, Lee SY. Optical Biosensors for the Detection of Pathogenic Microorganisms. Trends Biotechnol 2015; 34:7-25. [PMID: 26506111 DOI: 10.1016/j.tibtech.2015.09.012] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/28/2015] [Accepted: 09/17/2015] [Indexed: 12/21/2022]
Abstract
Pathogenic microorganisms are causative agents of various infectious diseases that are becoming increasingly serious worldwide. For the successful treatment of pathogenic infection, the rapid and accurate detection of multiple pathogenic microorganisms is of great importance in all areas related to health and safety. Among various sensor systems, optical biosensors allow easy-to-use, rapid, portable, multiplexed, and cost-effective diagnosis. Here, we review current trends and advances in pathogen-diagnostic optical biosensors. The technological and methodological approaches underlying diverse optical-sensing platforms and methods for detecting pathogenic microorganisms are reviewed, together with the strengths and drawbacks of each technique. Finally, challenges in developing efficient optical biosensor systems and future perspectives are discussed.
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Affiliation(s)
- Seung Min Yoo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus Program), BioProcess Engineering Research Center, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus Program), BioProcess Engineering Research Center, KAIST, Daejeon 34141, Republic of Korea.
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17
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Childs-Disney JL, Disney MD. Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells. Annu Rev Pharmacol Toxicol 2015; 56:123-40. [PMID: 26514201 DOI: 10.1146/annurev-pharmtox-010715-103910] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA has become an increasingly important target for therapeutic interventions and for chemical probes that dissect and manipulate its cellular function. Emerging targets include human RNAs that have been shown to directly cause cancer, metabolic disorders, and genetic disease. In this review, we describe various routes to obtain bioactive compounds that target RNA, with a particular emphasis on the development of small molecules. We use these cases to describe approaches that are being developed for target validation, which include target-directed cleavage, classic pull-down experiments, and covalent cross-linking. Thus, tools are available to design small molecules to target RNA and to identify the cellular RNAs that are their targets.
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Affiliation(s)
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458; ,
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18
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Jee JE, Lim J, Hyun H, Oon J, Ong YS, Massif C, Chang YT, Choi HS, Lee SS. Investigating fluorescent dyes in fluorescence-assisted screenings. Chem Commun (Camb) 2015; 50:15220-3. [PMID: 25340456 DOI: 10.1039/c4cc07008a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Screening of bead-based peptide libraries against fluorescent dye-labeled target proteins was found to be significantly influenced by the dye characteristics. Commercially available red fluorescent dyes with net negative charges adversely showed strong interactions with library beads. The introduction of zwitterionic dyes significantly reduced the unwanted interactions, which sheds light upon using the right fluorescent probe for acquisition of reliable results in various fluorescence-assisted applications.
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Affiliation(s)
- Joo-Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669.
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19
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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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20
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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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21
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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] [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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22
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Biased and unbiased strategies to identify biologically active small molecules. Bioorg Med Chem 2014; 22:4474-89. [DOI: 10.1016/j.bmc.2014.04.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/03/2014] [Accepted: 04/10/2014] [Indexed: 12/20/2022]
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23
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Oueis E, Santoni G, Ronco C, Syzgantseva O, Tognetti V, Joubert L, Romieu A, Weik M, Jean L, Sabot C, Nachon F, Renard PY. Reaction site-driven regioselective synthesis of AChE inhibitors. Org Biomol Chem 2014; 12:156-61. [DOI: 10.1039/c3ob42109k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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24
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Singh G, Mangat SS, Sharma H, Singh J, Arora A, Singh Pannu AP, Singh N. Design and syntheses of novel fluorescent organosilicon-based chemosensors through click silylation: detection of biogenic amines. RSC Adv 2014. [DOI: 10.1039/c4ra02270j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
First report on the use of organosilicon-based chemosensors for the recognition of biogenic amines.
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Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | | | - Hemant Sharma
- Department of Chemistry
- Indian Institute of Technology
- Ropar, India
| | - Jandeep Singh
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | - Aanchal Arora
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | | | - Narinder Singh
- Department of Chemistry
- Indian Institute of Technology
- Ropar, India
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25
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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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26
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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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27
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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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28
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Pfeilsticker JA, Umeda A, Farrow B, Hsueh CL, Deyle KM, Kim JT, Lai BT, Heath JR. A cocktail of thermally stable, chemically synthesized capture agents for the efficient detection of anti-gp41 antibodies from human sera. PLoS One 2013; 8:e76224. [PMID: 24116098 PMCID: PMC3792125 DOI: 10.1371/journal.pone.0076224] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/13/2013] [Indexed: 12/16/2022] Open
Abstract
We report on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60(o)C.
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Affiliation(s)
- Jessica A. Pfeilsticker
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Aiko Umeda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Blake Farrow
- Division of Engineering and Applied Sciences, Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Connie L. Hsueh
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Kaycie M. Deyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jocelyn T. Kim
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Bert T. Lai
- Indi Molecular, Culver City, California, United States of America
| | - James R. Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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29
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Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor. Proc Natl Acad Sci U S A 2013; 110:15892-7. [PMID: 24043811 DOI: 10.1073/pnas.1315049110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Huisgen cycloaddition of azides and alkynes, accelerated by target biomolecules, termed "in situ click chemistry," has been successfully exploited to discover highly potent enzyme inhibitors. We have previously reported a specific Serratia marcescens chitinase B (SmChiB)-templated syn-triazole inhibitor generated in situ from an azide-bearing inhibitor and an alkyne fragment. Several in situ click chemistry studies have been reported. Although some mechanistic evidence has been obtained, such as X-ray analysis of [protein]-["click ligand"] complexes, indicating that proteins act as both mold and template between unique pairs of azide and alkyne fragments, to date, observations have been based solely on "postclick" structural information. Here, we describe crystal structures of SmChiB complexed with an azide ligand and an O-allyl oxime fragment as a mimic of a click partner, revealing a mechanism for accelerating syn-triazole formation, which allows generation of its own distinct inhibitor. We have also performed density functional theory calculations based on the X-ray structure to explore the acceleration of the Huisgen cycloaddition by SmChiB. The density functional theory calculations reasonably support that SmChiB plays a role by the cage effect during the pretranslation and posttranslation states of selective syn-triazole click formation.
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30
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Huo JP, Luo JC, Wu W, Xiong JF, Mo GZ, Wang ZY. Synthesis and Characterization of Fluorescent Brightening Agents with Chiral 2(5H)-Furanone and Bis-1,2,3-triazole Structure. Ind Eng Chem Res 2013. [DOI: 10.1021/ie401149p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jing-Pei Huo
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
| | - Jian-Cheng Luo
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
| | - Wei Wu
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
| | - Jin-Feng Xiong
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
| | - Guang-Zhen Mo
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
| | - Zhao-Yang Wang
- School of Chemistry and Environment,
Key Laboratory
of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People’s
Republic of China
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31
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Androulakis IP, Kamisoglu K, Mattick JS. Topology and Dynamics of Signaling Networks: In Search of Transcriptional Control of the Inflammatory Response. Annu Rev Biomed Eng 2013; 15:1-28. [DOI: 10.1146/annurev-bioeng-071812-152425] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ioannis P. Androulakis
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
- Biomedical Engineering Department, Rutgers University, Piscataway, New Jersey 08854
| | - Kubra Kamisoglu
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
| | - John S. Mattick
- Chemical & Biochemical Engineering Department, Rutgers University, Piscataway, New Jersey 08854;
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32
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Millward SW, Agnew HD, Lai B, Lee SS, Lim J, Nag A, Pitram S, Rohde R, Heath JR. In situ click chemistry: from small molecule discovery to synthetic antibodies. Integr Biol (Camb) 2013; 5:87-95. [PMID: 22836343 DOI: 10.1039/c2ib20110k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Advances in the fields of proteomics, molecular imaging, and therapeutics are closely linked to the availability of affinity reagents that selectively recognize their biological targets. Here we present a review of Iterative Peptide In Situ Click Chemistry (IPISC), a novel screening technology for designing peptide multiligands with high affinity and specificity. This technology builds upon in situ click chemistry, a kinetic target-guided synthesis approach where the protein target catalyzes the conjugation of two small molecules, typically through the azide-alkyne Huisgen cycloaddition. Integrating this methodology with solid phase peptide libraries enables the assembly of linear and branched peptide multiligands we refer to as Protein Catalyzed Capture Agents (PCC Agents). The resulting structures can be thought of as analogous to the antigen recognition site of antibodies and serve as antibody replacements in biochemical and cell-based applications. In this review, we discuss the recent progress in ligand design through IPISC and related approaches, focusing on the improvements in affinity and specificity as multiligands are assembled by target-catalyzed peptide conjugation. We compare the IPISC process to small molecule in situ click chemistry with particular emphasis on the advantages and technical challenges of constructing antibody-like PCC Agents.
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Affiliation(s)
- Steven W Millward
- Department of Experimental Diagnostic Imaging, University of Texas MD Anderson Cancer Center, Experimental Diagnostic Imaging, Unit 603, P.O. Box 301402, Houston, TX 77230-1402, USA.
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33
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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34
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Peruzzotti C, Borrelli S, Ventura M, Pantano R, Fumagalli G, Christodoulou MS, Monticelli D, Luzzani M, Fallacara AL, Tintori C, Botta M, Passarella D. Probing the binding site of abl tyrosine kinase using in situ click chemistry. ACS Med Chem Lett 2013; 4:274-7. [PMID: 24900659 DOI: 10.1021/ml300394w] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/15/2013] [Indexed: 02/06/2023] Open
Abstract
Modern combinatorial chemistry is used to discover compounds with desired function by an alternative strategy, in which the biological target is directly involved in the choice of ligands assembled from a pool of smaller fragments. Herein, we present the first experimental result where the use of in situ click chemistry has been successfully applied to probe the ligand-binding site of Abl and the ability of this enzyme to form its inhibitor. Docking studies show that Abl is able to allow the in situ click chemistry between specific azide and alkyne fragments by binding to Abl-active sites. This report allows medicinal chemists to use protein-directed in situ click chemistry for exploring the conformational space of a ligand-binding pocket and the ability of the protein to guide its inhibitor. This approach can be a novel, valuable tool to guide drug design synthesis in the field of tyrosine kinases.
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Affiliation(s)
- Cristina Peruzzotti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Stella Borrelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Micol Ventura
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Rebecca Pantano
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | - Gaia Fumagalli
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
| | | | - Damiano Monticelli
- Dipartimento di Scienze Alta
Tecnologia, Università degli Studi dell’Insubria, Via Valleggio 11, 22100 Como, Italy
| | | | - Anna Lucia Fallacara
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Cristina Tintori
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Maurizio Botta
- Dipartimento Farmaco Chimico
Tecnologico, Università degli Studi di Siena, Via Alcide de Gasperi 2, I-53100, Siena, Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi
19, 20133 Milano, Italy
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Sokolova NV, Nenajdenko VG. Recent advances in the Cu(i)-catalyzed azide–alkyne cycloaddition: focus on functionally substituted azides and alkynes. RSC Adv 2013. [DOI: 10.1039/c3ra42482k] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Tieu W, Soares da Costa TP, Yap MY, Keeling KL, Wilce MCJ, Wallace JC, Booker GW, Polyak SW, Abell AD. Optimising in situ click chemistry: the screening and identification of biotin protein ligase inhibitors. Chem Sci 2013. [DOI: 10.1039/c3sc51127h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA versus DNA G-quadruplex targeting by in situ click chemistry. Angew Chem Int Ed Engl 2012; 51:11073-8. [PMID: 23038154 PMCID: PMC3652031 DOI: 10.1002/anie.201206281] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Indexed: 12/22/2022]
Abstract
It all clicks into place: A potent telomere-targeting small molecule has been identified by using the copper-free 1,3-dipolar cycloaddition of a series of alkyne and azide building blocks catalyzed by a non-Watson-Crick DNA secondary structure (see picture). This method rapidly identifies, otherwise unanticipated, potent small-molecule probes to selectively target a given RNA or DNA.
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Affiliation(s)
- Marco Di Antonio
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
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Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S. Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206281] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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39
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Berlinck RGS, Trindade-Silva AE, Santos MFC. The chemistry and biology of organic guanidine derivatives. Nat Prod Rep 2012; 29:1382-406. [PMID: 22991131 DOI: 10.1039/c2np20071f] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The chemistry and biology of organic natural guanidines are reviewed, including the isolation, structure determination, synthesis, biosynthesis and biological activities of alkaloids, non-ribosomal peptides, guanidine-bearing terpenes, polyketides and shikimic acid derivatives from natural sources.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brasil.
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Hood L, Balling R, Auffray C. Revolutionizing medicine in the 21st century through systems approaches. Biotechnol J 2012; 7:992-1001. [PMID: 22815171 DOI: 10.1002/biot.201100306] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/09/2012] [Accepted: 05/16/2012] [Indexed: 11/08/2022]
Abstract
Personalized medicine is a term for a revolution in medicine that envisions the individual patient as the central focus of healthcare in the future. The term "personalized medicine", however, fails to reflect the enormous dimensionality of this new medicine that will be predictive, preventive, personalized, and participatory-a vision of medicine we have termed P4 medicine. This reflects a paradigm change in how medicine will be practiced that is revolutionary rather than evolutionary. P4 medicine arises from the confluence of a systems approach to medicine and from the digitalization of medicine that creates the large data sets necessary to deal with the complexities of disease. We predict that systems approaches will empower the transition from conventional reactive medical practice to a more proactive P4 medicine focused on wellness, and will reverse the escalating costs of drug development an will have enormous social and economic benefits. Our vision for P4 medicine in 10 years is that each patient will be associated with a virtual data cloud of billions of data points and that we will have the information technology for healthcare to reduce this enormous data dimensionality to simple hypotheses about health and/or disease for each individual. These data will be multi-scale across all levels of biological organization and extremely heterogeneous in type - this enormous amount of data represents a striking signal-to-noise (S/N) challenge. The key to dealing with this S/N challenge is to take a "holistic systems approach" to disease as we will discuss in this article.
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Affiliation(s)
- Leroy Hood
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109-5234, USA.
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