51
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Tang J, He Y, Chen H, Sheng W, Wang H. Synthesis of bioactive and stabilized cyclic peptides by macrocyclization using C(sp 3)-H activation. Chem Sci 2017; 8:4565-4570. [PMID: 28936334 PMCID: PMC5590095 DOI: 10.1039/c6sc05530c] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/11/2017] [Indexed: 12/22/2022] Open
Abstract
Synthesis of cyclic peptides with novel Cβ–Ar crosslinks has been achieved by C(sp3)–H activation, and their biological properties have been evaluated for the first time.
Cyclic peptides have attracted increasing attention in recent years due to their ability to inhibit protein–protein interactions. Current strategies to prepare cyclic peptides often rely on functional amino acid side chains or the incorporation of unnatural amino acids, thus limiting their structural diversity. Here, we describe the development of a highly versatile peptide macrocyclization strategy through a palladium-catalyzed C(sp3)–H activation and the synthesis of cyclic peptides featuring unique hydrocarbon linkages between the β-carbon of amino acids and the aromatic side chains of Phe and Trp. We demonstrate that such peptides exhibit improved biological properties compared to their acyclic counterparts. Finally, we applied this method in the synthesis of the natural product celogentin C.
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Affiliation(s)
- Jian Tang
- State Key Laboratory of Coordination Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , China .
| | - Yadong He
- State Key Laboratory of Coordination Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , China .
| | - Hongfei Chen
- State Key Laboratory of Coordination Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , China .
| | - Wangjian Sheng
- State Key Laboratory of Coordination Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , China .
| | - Huan Wang
- State Key Laboratory of Coordination Chemistry , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , China .
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52
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Vastl J, Wang T, Trinh TB, Spiegel DA. Encoded Silicon-Chip-Based Platform for Combinatorial Synthesis and Screening. ACS COMBINATORIAL SCIENCE 2017; 19:255-261. [PMID: 28263558 DOI: 10.1021/acscombsci.6b00181] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Solid-supported chemical libraries have proven useful for the rapid and cost-effective discovery of bioactive compounds. However, traditional on-bead screening involves time-intensive chemical characterization of hit compounds and high false positive rates. Herein, we report a new platform for encoded chemical synthesis and solid-supported screening using p-Chips, microsized silicon microtransponders capable of storing and emitting unique numerical identifiers (IDs). By encoding the structures of library members using p-Chip IDs, we can track compound identities throughout both split-and-pool synthesis and protein binding assays without destructive cleavage. Thanks to the numerical IDs, our p-Chip platform can provide binding constants for library members simply by stripping and reprobing with different protein concentrations, unlike traditional on-bead assays. To showcase these features, we synthesized a library of 108 hemagglutinin (HA) peptide variants using split-and-pool approach, and measured EC50s for each variant directly on p-Chips. On-chip EC50s obtained from these studies showed excellent correlation (80%) with those obtained using traditional ELISA methods. Our screen also yielded a false positive rate of 14%, markedly superior to that reported for conventional bead-based binding studies (66-96%).1-9 On the basis of these results, we believe the p-Chip platform has the potential to improve the effectiveness of solid-supported high-throughput screening by a significant margin.
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Affiliation(s)
- Julian Vastl
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - Tina Wang
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - Thi B. Trinh
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
| | - David A. Spiegel
- Department of Chemistry, Yale University, 225
Prospect Street, New Haven, Connecticut 06511, United States
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53
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Macrocycles as protein-protein interaction inhibitors. Biochem J 2017; 474:1109-1125. [PMID: 28298556 DOI: 10.1042/bcj20160619] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
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54
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MacConnell AB, Price AK, Paegel BM. An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening. ACS COMBINATORIAL SCIENCE 2017; 19:181-192. [PMID: 28199790 PMCID: PMC5350604 DOI: 10.1021/acscombsci.6b00192] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
DNA-encoded synthesis
is rekindling interest in combinatorial compound
libraries for drug discovery and in technology for automated and quantitative
library screening. Here, we disclose a microfluidic circuit that enables
functional screens of DNA-encoded compound beads. The device carries
out library bead distribution into picoliter-scale assay reagent droplets,
photochemical cleavage of
compound from the bead, assay incubation, laser-induced fluorescence-based
assay detection, and fluorescence-activated droplet sorting to isolate
hits. DNA-encoded compound beads (10-μm diameter) displaying
a photocleavable positive control inhibitor pepstatin A were mixed
(1920 beads, 729 encoding sequences) with negative control beads (58 000
beads, 1728 encoding sequences) and screened for cathepsin D inhibition
using a biochemical enzyme activity assay. The circuit sorted 1518
hit droplets for collection following 18 min incubation over a 240
min analysis. Visual inspection of a subset of droplets (1188 droplets)
yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative
control beads). Using template barcoding strategies, it was possible
to count hit collection beads (1863) using next-generation sequencing
data. Bead-specific barcodes enabled replicate counting, and the false
discovery rate was reduced to 2.6% by only considering hit-encoding
sequences that were observed on >2 beads. This work represents
a complete
distributable small molecule discovery platform, from microfluidic
miniaturized automation to ultrahigh-throughput hit deconvolution
by sequencing.
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Affiliation(s)
- Andrew B. MacConnell
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alexander K. Price
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department
of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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55
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van de Langemheen H, Korotkovs V, Bijl J, Wilson C, Kale SS, Heinis C, Liskamp RMJ. Polar Hinges as Functionalized Conformational Constraints in (Bi)cyclic Peptides. Chembiochem 2017; 18:387-395. [DOI: 10.1002/cbic.201600612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Helmus van de Langemheen
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Valerijs Korotkovs
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Joachim Bijl
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Claire Wilson
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
| | - Sangram S. Kale
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Rob M. J. Liskamp
- School of Chemistry; University of Glasgow; Joseph Black Building University Avenue Glasgow G12 8QQ UK
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56
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He J, Gui S, Huang Y, Hu F, Jin Y, Yu Y, Zhang G, Zhang D, Zhao R. Rapid, sensitive, and in-solution screening of peptide probes for targeted imaging of live cancer cells based on peptide recognition-induced emission. Chem Commun (Camb) 2017; 53:11091-11094. [DOI: 10.1039/c7cc06485c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A generally applicable method was developed for screening cancer cell-specific peptides with one-residue resolution based on a ligand binding-induced emission phenomenon.
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Affiliation(s)
- Jiayuan He
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Shilang Gui
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Yanyan Huang
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Fang Hu
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Yulong Jin
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Yang Yu
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Guanxin Zhang
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Deqing Zhang
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
| | - Rui Zhao
- CAS Key Laboratories of Analytical Chemistry for Living Biosystems and Organic Solids
- CAS Research/Education Center for Excellence in Molecular Sciences
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing
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57
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Maini R, Umemoto S, Suga H. Ribosome-mediated synthesis of natural product-like peptides via cell-free translation. Curr Opin Chem Biol 2016; 34:44-52. [DOI: 10.1016/j.cbpa.2016.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/06/2016] [Indexed: 11/29/2022]
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58
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Kanasty RL, Vegas AJ, Ceo LM, Maier M, Charisse K, Nair JK, Langer R, Anderson DG. Sequence-Defined Oligomers from Hydroxyproline Building Blocks for Parallel Synthesis Applications. Angew Chem Int Ed Engl 2016; 55:9529-33. [PMID: 27365192 PMCID: PMC5245870 DOI: 10.1002/anie.201602748] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/04/2016] [Indexed: 01/01/2023]
Abstract
The functionality of natural biopolymers has inspired significant effort to develop sequence-defined synthetic polymers for applications including molecular recognition, self-assembly, and catalysis. Conjugation of synthetic materials to biomacromolecules has played an increasingly important role in drug delivery and biomaterials. We developed a controlled synthesis of novel oligomers from hydroxyproline-based building blocks and conjugated these materials to siRNA. Hydroxyproline-based monomers enable the incorporation of broad structural diversity into defined polymer chains. Using a perfluorocarbon purification handle, we were able to purify diverse oligomers through a single solid-phase extraction method. The efficiency of synthesis was demonstrated by building 14 unique trimers and 4 hexamers from 6 diverse building blocks. We then adapted this method to the parallel synthesis of hundreds of materials in 96-well plates. This strategy provides a platform for the screening of libraries of modified biomolecules.
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Affiliation(s)
- Rosemary L Kanasty
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
| | - Arturo J Vegas
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Luke M Ceo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Martin Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Division of Health Science Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA.
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA.
- Division of Health Science Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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59
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Gao M, Cheng K, Yin H. Targeting protein-protein interfaces using macrocyclic peptides. Biopolymers 2016; 104:310-6. [PMID: 25664609 DOI: 10.1002/bip.22625] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 01/10/2023]
Abstract
Protein-protein interactions (PPIs) are critical in numerous biological processes including signaling transduction, function regulations, and disease development. To regulate PPIs has been thought to be challenging due to their highly dynamic and expansive interfacial areas. Nonetheless, successful examples have been reported of targeting PPIs using small molecules, peptides, and proteins. Peptides, especially macrocyclic peptides have proven to be a particularly useful tool to inhibit PPIs for their exquisite potency, stability and selectivity. Herein we review the recent developments of this area of research, focusing on the macrocyclic peptides isolated from natural products, identified from library screening, and rationally designed based on structures, as PPI regulators.
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Affiliation(s)
- Meng Gao
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Kui Cheng
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082
| | - Hang Yin
- Department of Chemistry, Center of Basic Molecular Science, Tsinghua University, Beijing, China , 100082.,Department of Chemistry and Biochemistry, the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309-0596
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60
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Kanasty RL, Vegas AJ, Ceo LM, Maier M, Charisse K, Nair JK, Langer R, Anderson DG. Sequence-Defined Oligomers from Hydroxyproline Building Blocks for Parallel Synthesis Applications. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rosemary L. Kanasty
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
| | - Arturo J. Vegas
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Boston MA 02215 USA
| | - Luke M. Ceo
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Boston MA 02215 USA
| | - Martin Maier
- Alnylam Pharmaceuticals; 300 Third Street Cambridge MA 02142 USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals; 300 Third Street Cambridge MA 02142 USA
| | | | - Robert Langer
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Division of Health Science Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- Institute for Medical Engineering and Science; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA. Harvard-MIT Division of Health Science and Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Daniel G. Anderson
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Division of Health Science Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- Institute for Medical Engineering and Science; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA. Harvard-MIT Division of Health Science and Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
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61
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Morimoto J, Kodadek T. Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues. MOLECULAR BIOSYSTEMS 2016; 11:2770-9. [PMID: 26067000 DOI: 10.1039/c5mb00308c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Large combinatorial libraries of macrocyclic peptides are a useful source of bioactive compounds. However, peptides are not generally cell permeable, so there is great interest in the development of methods to create large libraries of modified peptides. In particular, N-alkylation of peptides is known to improve their bioavailability significantly. Incorporation of some level of N-methylated amino acids into peptide libraries has been accomplished with ribosome display or related methods, but the modest efficiency and the inability to employ more diverse N-alkylated amino acids in this type of system argue for the development of synthetic libraries. Here we present optimized procedures for synthesizing macrocyclic peptides containing multiple N-alkylated units and show that this chemistry is efficient enough for the creation of high quality combinatorial libraries by split and pool solid-phase synthesis.
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Affiliation(s)
- Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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62
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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63
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Doran TM, Sarkar M, Kodadek T. Chemical Tools To Monitor and Manipulate Adaptive Immune Responses. J Am Chem Soc 2016; 138:6076-94. [PMID: 27115249 PMCID: PMC5332222 DOI: 10.1021/jacs.6b02954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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64
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Doran TM, Morimoto J, Simanski S, Koesema EJ, Clark LF, Pels K, Stoops SL, Pugliese A, Skyler JS, Kodadek T. Discovery of Phosphorylated Peripherin as a Major Humoral Autoantigen in Type 1 Diabetes Mellitus. Cell Chem Biol 2016; 23:618-628. [PMID: 27185639 DOI: 10.1016/j.chembiol.2016.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/03/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
Abstract
A major goal in understanding autoimmune diseases is to define the antigens that elicit a self-destructive immune response, but this is a difficult endeavor. In an effort to discover autoantigens associated with type 1 diabetes (T1D), we used epitope surrogate technology that screens combinatorial libraries of synthetic molecules for compounds that could recognize disease-linked autoantibodies and enrich them from serum. Autoantibodies from one patient revealed a highly phosphorylated form of peripherin, a neuroendocrine filament protein, as a candidate T1D antigen. Peripherin antibodies were detected in 72% of donor patient sera. Further analysis revealed that the T1D-associated antibodies only recognized a dimeric conformation of peripherin. These data explain why peripherin was dismissed as an important T1D antigen previously. The discovery of this novel autoantigen would not have been possible using standard methods, such as hybridizing serum antibodies to recombinant protein arrays, highlighting the power of epitope surrogate technology for probing the mechanism of autoimmune diseases.
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Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eric J Koesema
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Lorraine F Clark
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kevin Pels
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sydney L Stoops
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Jay S Skyler
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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65
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Kodadek T, McEnaney PJ. Towards vast libraries of scaffold-diverse, conformationally constrained oligomers. Chem Commun (Camb) 2016; 52:6038-59. [PMID: 26996593 PMCID: PMC4846527 DOI: 10.1039/c6cc00617e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is great interest in the development of probe molecules and drug leads that would bind tightly and selectively to protein surfaces that are difficult to target with traditional molecules, such as those involved in protein-protein interactions. The currently available evidence suggests that this will require molecules that are larger and have quite different chemical properties than typical Lipinski-compliant molecules that target enzyme active sites. We describe here efforts to develop vast libraries of conformationally constrained oligomers as a potentially rich source of these molecules.
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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66
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Sarma BK, Liu X, Kodadek T. Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. Bioorg Med Chem 2016; 24:3953-3963. [PMID: 27160052 DOI: 10.1016/j.bmc.2016.04.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022]
Abstract
A potent and selective inhibitor of platelet-activating factor acetylhydrolase 1B2 (PAFAH1B2) is described. The compound was derived by improvement of a modest affinity primary hit isolated from the screening of a bead-displayed peptoid-azapeptoid hybrid library tethered to an oxadiazolone 'warhead'. The oxadiazolone moiety of the inhibitors was found to react covalently with the active site serine residue of PAFAH1B2. This screening strategy may be useful for the identification of many selective, covalent inhibitors of serine hydrolases.
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Affiliation(s)
- Bani Kanta Sarma
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh-201314, India
| | - Xiaodan Liu
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
| | - Thomas Kodadek
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
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67
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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68
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016; 55:4472-5. [DOI: 10.1002/anie.201511308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/02/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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69
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Bandyopadhyay A, Gao J. Iminoboronate-Based Peptide Cyclization That Responds to pH, Oxidation, and Small Molecule Modulators. J Am Chem Soc 2016; 138:2098-101. [PMID: 26859098 DOI: 10.1021/jacs.5b12301] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a rich source of therapeutic agents, peptide natural products usually adopt a cyclic or multicyclic scaffold that minimizes structural flexibility to favor target binding. Inspired by nature, chemists have been interested in developing synthetic cyclic and multicyclic peptides that serve as biological probes and potential therapeutics. Herein we describe a novel strategy for peptide cyclization in which intramolecular iminoboronate formation allows spontaneous cyclization under physiologic conditions to yield monocyclic and bicyclic peptides. Importantly the iminoboronate-based cyclization can be rapidly reversed in response to multiple stimuli, including pH, oxidation, and small molecules. This highly versatile strategy for peptide cyclization should find applications in many areas of chemical biology.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Merkert Chemistry Center, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College , 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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70
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Sarkar M, Liu Y, Qi J, Peng H, Morimoto J, Rader C, Chiorazzi N, Kodadek T. Targeting Stereotyped B Cell Receptors from Chronic Lymphocytic Leukemia Patients with Synthetic Antigen Surrogates. J Biol Chem 2016; 291:7558-70. [PMID: 26851280 DOI: 10.1074/jbc.m115.701656] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 12/17/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a disease in which a single B-cell clone proliferates relentlessly in peripheral lymphoid organs, bone marrow, and blood. DNA sequencing experiments have shown that about 30% of CLL patients have stereotyped antigen-specific B-cell receptors (BCRs) with a high level of sequence homology in the variable domains of the heavy and light chains. These include many of the most aggressive cases that haveIGHV-unmutated BCRs whose sequences have not diverged significantly from the germ line. This suggests a personalized therapy strategy in which a toxin or immune effector function is delivered selectively to the pathogenic B-cells but not to healthy B-cells. To execute this strategy, serum-stable, drug-like compounds able to target the antigen-binding sites of most or all patients in a stereotyped subset are required. We demonstrate here the feasibility of this approach with the discovery of selective, high affinity ligands for CLL BCRs of the aggressive, stereotyped subset 7P that cross-react with the BCRs of several CLL patients in subset 7p, but not with BCRs from patients outside this subset.
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Affiliation(s)
| | - Yun Liu
- The Karches Center for Chronic Lymphocytic Leukemia Research, Hofstra North Shore-LIJ School of Medicine, The Feinstein Institute for Medical Research, Manhasset, New York 11030
| | | | | | | | - Christoph Rader
- Cancer Biology, and Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458 and
| | - Nicholas Chiorazzi
- The Karches Center for Chronic Lymphocytic Leukemia Research, Hofstra North Shore-LIJ School of Medicine, The Feinstein Institute for Medical Research, Manhasset, New York 11030
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71
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Trinh TB, Upadhyaya P, Qian Z, Pei D. Discovery of a Direct Ras Inhibitor by Screening a Combinatorial Library of Cell-Permeable Bicyclic Peptides. ACS COMBINATORIAL SCIENCE 2016; 18:75-85. [PMID: 26645887 PMCID: PMC4710893 DOI: 10.1021/acscombsci.5b00164] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Cyclic
peptides have great potential as therapeutic agents and research tools.
However, their applications against intracellular targets have been
limited, because cyclic peptides are generally impermeable to the
cell membrane. It was previously shown that fusion of cyclic peptides
with a cyclic cell-penetrating peptide resulted in cell-permeable
bicyclic peptides that are proteolytically stable and biologically
active in cellular assays. In this work, we tested the generality
of the bicyclic approach by synthesizing a combinatorial library of
5.7 × 106 bicyclic peptides featuring a degenerate
sequence in the first ring and an invariant cell-penetrating peptide
in the second ring. Screening of the library against oncoprotein K-Ras
G12V followed by hit optimization produced a moderately potent and
cell-permeable K-Ras inhibitor, which physically blocks the Ras-effector
interactions in vitro, inhibits the signaling events downstream of
Ras in cancer cells, and induces apoptosis of the cancer cells. Our
approach should be generally applicable to developing cell-permeable
bicyclic peptide inhibitors against other intracellular proteins.
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Affiliation(s)
- Thi B. Trinh
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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72
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Nevola L, Giralt E. Modulating protein-protein interactions: the potential of peptides. Chem Commun (Camb) 2015; 51:3302-15. [PMID: 25578807 DOI: 10.1039/c4cc08565e] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important and challenging targets in chemical biology and medicinal chemistry. The main difficulty encountered in the discovery of small molecule modulators derives from the large contact surfaces involved in PPIs when compared with those that participate in protein-small molecule interactions. Because of their intrinsic features, peptides can explore larger surfaces and therefore represent a useful alternative to modulate PPIs. The use of peptides as therapeutics has been held back by their instability in vivo and poor cell internalization. However, more than 200 peptide drugs and homologous compounds (proteins or antibodies) containing peptide bonds are (or have been) on the market, and many alternatives are now available to tackle these limitations. This review will focus on the latest progress in the field, spanning from "lead" identification methods to binding evaluation techniques, through an update of the most successful examples described in the literature.
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Affiliation(s)
- Laura Nevola
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, 08028 Barcelona, Spain.
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73
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Oh M, Lee JH, Moon H, Hyun YJ, Lim HS. A Chemical Inhibitor of the Skp2/p300 Interaction that Promotes p53-Mediated Apoptosis. Angew Chem Int Ed Engl 2015; 55:602-6. [PMID: 26593157 DOI: 10.1002/anie.201508716] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/22/2015] [Indexed: 12/16/2022]
Abstract
Skp2 is thought to have two critical roles in tumorigenesis. As part of the SCF(Skp2) ubiquitin ligase, Skp2 drives the cell cycle by mediating the degradation of cell cycle proteins. Besides the proteolytic activity, Skp2 also blocks p53-mediated apoptosis by outcompeting p53 for binding p300. Herein, we exploit the Skp2/p300 interaction as a new target for Skp2 inhibition. An affinity-based high-throughput screen of a combinatorial cyclic peptoid library identified an inhibitor that binds to Skp2 and interferes with the Skp2/p300 interaction. We show that antagonism of the Skp2/p300 interaction by the inhibitor leads to p300-mediated p53 acetylation, resulting in p53-mediated apoptosis in cancer cells, without affecting Skp2 proteolytic activity. Our results suggest that inhibition of the Skp2/p300 interaction has a great potential as a new anticancer strategy, and our Skp2 inhibitor can be developed as a chemical probe to delineate Skp2 non-proteolytic function in tumorigenesis.
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Affiliation(s)
- Misook Oh
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673 (Republic of Korea).,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 (USA)
| | - Ji Hoon Lee
- New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, Daegu 41061 (Republic of Korea)
| | - Heejo Moon
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673 (Republic of Korea)
| | - Yu-Jung Hyun
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673 (Republic of Korea)
| | - Hyun-Suk Lim
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673 (Republic of Korea). .,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202 (USA).
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74
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Oh M, Lee JH, Moon H, Hyun YJ, Lim HS. A Chemical Inhibitor of the Skp2/p300 Interaction that Promotes p53-Mediated Apoptosis. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508716] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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75
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Cardote TAF, Ciulli A. Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions. ChemMedChem 2015; 11:787-94. [PMID: 26563831 PMCID: PMC4848765 DOI: 10.1002/cmdc.201500450] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 01/25/2023]
Abstract
Targeting protein surfaces and protein-protein interactions (PPIs) with small molecules is a frontier goal of chemical biology and provides attractive therapeutic opportunities in drug discovery. The molecular properties of protein surfaces, including their shallow features and lack of deep binding pockets, pose significant challenges, and as a result have proved difficult to target. Peptides are ideal candidates for this mission due to their ability to closely mimic many structural features of protein interfaces. However, their inherently low intracellular stability and permeability and high in vivo clearance have thus far limited their biological applications. One way to improve these properties is to constrain the secondary structure of linear peptides by cyclisation. Herein we review various classes of cyclic and macrocyclic peptides as chemical probes of protein surfaces and modulators of PPIs. The growing interest in this area and recent advances provide evidence of the potential of developing peptide-like molecules that specifically target these interactions.
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Affiliation(s)
- Teresa A F Cardote
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK.
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76
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Doran TM, Gao Y, Simanski S, McEnaney P, Kodadek T. High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies. Bioorg Med Chem Lett 2015; 25:4910-4917. [PMID: 26067174 PMCID: PMC4607566 DOI: 10.1016/j.bmcl.2015.05.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
'Antigen surrogates' are synthetic, non-natural molecules that recognize the antigen-binding sites of antibodies. These molecules are of interest as replacements for native antigens as antibody 'capture agents' in ELISA-like assays of potential diagnostic utility, for example when the antibody is indicative of a disease state. Antigen surrogates for disease-related antibodies can be mined from one-bead one-compound (OBOC) libraries by first denuding the library of ligands for antibodies present in the serum of control patients or animals, followed by screening the remainder of the library against serum from individuals with a particular disease of interest. Most of the work in this area has been done with peptoids (oligomers of N-alkylated glycine), which provide antibody ligands with only modest affinity and selectivity. Here, we explore the hypothesis that this is due to the 'floppiness' of the peptoid backbone by creating libraries of peptoid-like molecules that have conformation-restricting structural elements inserted into their backbones. Indeed, we show here that these libraries can provide high affinity and selectivity antigen surrogates and that this much-improved binding is completely dependent on conformational restriction of the oligomer chain.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yu Gao
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Scott Simanski
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Patrick McEnaney
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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77
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Rational, computer-enabled peptide drug design: principles, methods, applications and future directions. Future Med Chem 2015; 7:2173-93. [PMID: 26510691 DOI: 10.4155/fmc.15.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Peptides provide promising templates for developing drugs to occupy a middle space between small molecules and antibodies and for targeting 'undruggable' intracellular protein-protein interactions. Importantly, rational or in cerebro design, especially when coupled with validated in silico tools, can be used to efficiently explore chemical space and identify islands of 'drug-like' peptides to satisfy diverse drug discovery program objectives. Here, we consider the underlying principles of and recent advances in rational, computer-enabled peptide drug design. In particular, we consider the impact of basic physicochemical properties, potency and ADME/Tox opportunities and challenges, and recently developed computational tools for enabling rational peptide drug design. Key principles and practices are spotlighted by recent case studies. We close with a hypothetical future case study.
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78
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Vasconcelos SNS, Shamim A, Ali B, de Oliveira IM, Stefani HA. Functionalization of protected tyrosine via Sonogashira reaction: synthesis of 3-(1,2,3-triazolyl)-tyrosine. Mol Divers 2015; 20:469-81. [DOI: 10.1007/s11030-015-9642-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/15/2015] [Indexed: 12/01/2022]
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79
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Mendes K, Ndungu JM, Clark LF, Kodadek T. Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens. ACS COMBINATORIAL SCIENCE 2015. [PMID: 26221913 DOI: 10.1021/acscombsci.5b00090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries is a useful procedure for the identification of protein ligands. An important aspect of this experiment is the method by which beads that bind the target protein are separated from those that do not. Ideally, such a method would be rapid and convenient and result in the isolation of 100% of the "hits" with no false positives (beads that display compounds that are not good ligands for the target). We introduced a technique in which beads that have bound a labeled target protein can be magnetized, thus allowing their convenient isolation ( Astle et al. Chem. Biol. 2010 , 17 , 38 - 45 ). However, recent work in our laboratory and others has shown that magnetic hit recovery can result in the isolation of large numbers of false positives and has also suggested that many true hit beads are missed. In this study, we employ a well-defined model system to examine the efficiency of various magnetic hit isolation protocols. We show that the choice of reagents and the particular operations employed are critical for optimal results.
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Affiliation(s)
- Kimberly Mendes
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - J. M. Ndungu
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - Lorraine F. Clark
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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80
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Jiang B, Pei D. A Selective, Cell-Permeable Nonphosphorylated Bicyclic Peptidyl Inhibitor against Peptidyl-Prolyl Isomerase Pin1. J Med Chem 2015; 58:6306-12. [PMID: 26196061 PMCID: PMC4594195 DOI: 10.1021/acs.jmedchem.5b00411] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Pin1 regulates the levels and functions of phosphoproteins by catalyzing phosphorylation-dependent cis/trans isomerization of peptidyl-prolyl bonds. Previous Pin1 inhibitors contained phosphoamino acids, which are metabolically unstable and have poor membrane permeability. In this work, we report a cell-permeable and metabolically stable nonphosphorylated bicyclic peptide as a potent and selective Pin1 inhibitor, which inhibited the intracellular Pin1 activity in cultured mammalian cells but had little effect on other isomerases such as Pin4, FKBP12, or cyclophilin A.
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Affiliation(s)
- Bisheng Jiang
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43220
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43220
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81
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Wang Z, Wang W, Bu X, Wei Z, Geng L, Wu Y, Dong C, Li L, Zhang D, Yang S, Wang F, Lausted C, Hood L, Hu Z. Microarray based screening of peptide nano probes for HER2 positive tumor. Anal Chem 2015. [PMID: 26218790 DOI: 10.1021/acs.analchem.5b01588] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Peptides are excellent biointerface molecules and diagnostic probes with many advantages such as good penetration, short turnover time, and low cost. We report here an efficient peptide screening strategy based on in situ single bead sequencing on a microarray. Two novel peptides YLFFVFER (H6) and KLRLEWNR (H10) specifically binding to the tumor biomarker human epidermal growth factor receptor 2 (HER2) with aKD of 10(-8) M were obtained from a 10(5) library. Conjugated to nanoparticles, both the H6 and H10 probes showed specific accumulation in HER2-positive tumor tissues in xenografted mice by in vivo imaging.
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Affiliation(s)
| | | | | | | | | | - Yue Wu
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Chengyan Dong
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Liqiang Li
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | | | | | - Fan Wang
- ‡Medical Isotopes Research Center, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing China, 100191
| | - Christopher Lausted
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Leroy Hood
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Zhiyuan Hu
- §Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States.,∥Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing China, 102206
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82
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Sarma BK, Liu X, Wu H, Gao Y, Kodadek T. Solid phase synthesis of 1,3,4-oxadiazin-5 (6R)-one and 1,3,4-oxadiazol-2-one scaffolds from acyl hydrazides. Org Biomol Chem 2015; 13:59-63. [PMID: 25354697 DOI: 10.1039/c4ob01883d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Solid phase synthesis of 1,3,4-oxadiazin-5(6R)-one and 1,3,4-oxadiazol-2-one scaffolds from resin-bound acyl hydrazides is described. We demonstrate here that the reactions of resin-bound aryl or hetero-aromatic acyl hydrazides with 2-substituted-2-bromoacetic acids and 4-nitrophenyl chloroformate and subsequent treatment with DIEA lead to intramolecular cyclization reactions to produce six-membered 1,3,4-oxadiazin-5(6R)-ones and five-membered 1,3,4-oxadiazol-2-ones, respectively. We also show that acyl hydrazide-derived 1,3,4-oxadiazol-2-ones may be useful serine hydrolase inhibitors.
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Affiliation(s)
- Bani Kanta Sarma
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh-201314, India
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83
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Trader DJ, Simanski S, Kodadek T. A reversible and highly selective inhibitor of the proteasomal ubiquitin receptor rpn13 is toxic to multiple myeloma cells. J Am Chem Soc 2015; 137:6312-9. [PMID: 25914958 PMCID: PMC4455945 DOI: 10.1021/jacs.5b02069] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The proteasome is a multisubunit complex responsible for most nonlysosomal turnover of proteins in eukaryotic cells. Proteasome inhibitors are of great interest clinically, particularly for the treatment of multiple myeloma (MM). Unfortunately, resistance arises almost inevitably to these active site-targeted drugs. One strategy to overcome this resistance is to inhibit other steps in the protein turnover cascade mediated by the proteasome. Previously, Anchoori et al. identified Rpn13 as the target of an electrophilic compound (RA-190) that was selectively toxic to MM cells (Cancer Cell 2013, 24, 791-805), suggesting that this subunit of the proteasome is also a viable cancer drug target. Here we describe the discovery of the first highly selective, reversible Rpn13 ligands and show that they are also selectively toxic to MM cells. These data strongly support the hypothesis that Rpn13 is a viable target for the development of drugs to treat MM and other cancers.
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Affiliation(s)
- Darci J. Trader
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Scott Simanski
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
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84
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Antitumor and antimicrobial activity of some cyclic tetrapeptides and tripeptides derived from marine bacteria. Mar Drugs 2015; 13:3029-45. [PMID: 25988520 PMCID: PMC4446616 DOI: 10.3390/md13053029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 04/22/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
Abstract
Marine derived cyclo(Gly-l-Ser-l-Pro-l-Glu) was selected as a lead to evaluate antitumor-antibiotic activity. Histidine was chosen to replace the serine residue to form cyclo(Gly-l-His-l-Pro-l-Glu). Cyclic tetrapeptides (CtetPs) were then synthesized using a solution phase method, and subjected to antitumor and antibiotic assays. The benzyl group protected CtetPs derivatives, showed better activity against antibiotic-resistant Staphylococcus aureus in the range of 60–120 μM. Benzyl group protected CtetPs 3 and 4, exhibited antitumor activity against several cell lines at a concentration of 80–108 μM. However, shortening the size of the ring to the cyclic tripeptide (CtriP) scaffold, cyclo(Gly-l-Ser-l-Pro), cyclo(Ser-l-Pro-l-Glu) and their analogues showed no antibiotic or antitumor activity. This phenomenon can be explained from their backbone structures.
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85
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Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem 2015; 94:459-70. [DOI: 10.1016/j.ejmech.2015.01.014] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
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86
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Gao Y, Kodadek T. Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands. ACS COMBINATORIAL SCIENCE 2015; 17:190-5. [PMID: 25623285 PMCID: PMC4356041 DOI: 10.1021/co500161c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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There has been much discussion of
the potential desirability of
macrocyclic molecules for the development of tool compounds and drug
leads. But there is little experimental data comparing otherwise equivalent
macrocyclic and linear compound libraries as a source of protein ligands.
In this Letter, we probe this point in the context of peptoid libraries.
Bead-displayed libraries of macrocyclic and linear peptoids containing
four variable positions and 0–2 fixed residues, to vary the
ring size, were screened against streptavidin and the affinity of
every hit for the target was measured. The data show that macrocyclization
is advantageous, but only when the ring contains 17 atoms, not 20
or 23 atoms. This technology will be useful for conducting direct
comparisons between many different types of chemical libraries to
determine their relative utility as a source of protein ligands.
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Affiliation(s)
- Yu Gao
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
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87
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Foster AD, Ingram JD, Leitch EK, Lennard KR, Osher EL, Tavassoli A. Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery. ACTA ACUST UNITED AC 2015; 20:563-76. [DOI: 10.1177/1087057114566803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/11/2014] [Indexed: 12/23/2022]
Abstract
The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.
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Affiliation(s)
| | | | | | | | | | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, UK
- Cancer Sciences, University of Southampton, Southampton, UK
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88
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Gao Y, Amar S, Pahwa S, Fields G, Kodadek T. Rapid lead discovery through iterative screening of one bead one compound libraries. ACS COMBINATORIAL SCIENCE 2015; 17:49-59. [PMID: 25434974 PMCID: PMC4294594 DOI: 10.1021/co500154e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Primary hits that arise from screening one bead one compound (OBOC) libraries against a target of interest rarely have high potency. However, there has been little work focused on the development of an efficient workflow for primary hit improvement. In this study, we show that by characterizing the binding constants for all of the hits that arise from a screen, structure-activity relationship (SAR) data can be obtained to inform the design of "derivative libraries" of a primary hit that can then be screened under more demanding conditions to obtain improved compounds. Here, we demonstrate the rapid improvement of a primary hit against matrix metalloproteinase-14 using this approach.
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Affiliation(s)
- Yu Gao
- Departments
of Chemistry and Cancer Biology The Scripps Research Institutem 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Sabrina Amar
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Sonia Pahwa
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Gregg Fields
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology The Scripps Research Institutem 130
Scripps Way, Jupiter, Florida 33458, United States
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89
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Stability of structured Kaposi's sarcoma-associated herpesvirus ORF57 protein is regulated by protein phosphorylation and homodimerization. J Virol 2015; 89:3256-74. [PMID: 25568207 DOI: 10.1128/jvi.03721-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 plays an essential role in KSHV lytic infection by promoting viral gene expression at the posttranscriptional level. Using bioinformatic and biochemical approaches, we determined that ORF57 contains two structurally and functionally distinct domains: a disordered nonstructural N-terminal domain (amino acids [aa] 1 to 152) and a structured α-helix-rich C-terminal domain (aa 153 to 455). The N-terminal domain mediates ORF57 interaction with several RNA-protein complexes essential for ORF57 to function. The N-terminal phosphorylation by cellular casein kinase II (CKII) at S21, T32, and S43, and other cellular kinases at S95 and S97 residues in proximity of the caspase-7 cleavage site, 30-DETD-33, inhibits caspase-7 digestion of ORF57. The structured C-terminal domain mediates homodimerization of ORF57, and the critical region for this function was mapped carefully to α-helices 7 to 9. Introduction of point mutations into α-helix 7 at ORF57 aa 280 to 299, a region highly conserved among ORF57 homologues from other herpesviruses, inhibited ORF57 homodimerization and led to proteasome-mediated degradation of ORF57 protein. Thus, homodimerization of ORF57 via its C terminus prevents ORF57 from degrading and allows two structure-free N termini of the dimerized ORF57 to work coordinately for host factor interactions, leading to productive KSHV lytic infection and pathogenesis. IMPORTANCE KSHV is a human oncogenic virus linked to the development of several malignancies. KSHV-mediated oncogenesis requires both latent and lytic infection. The KSHV ORF57 protein is essential for KSHV lytic replication, as it regulates the expression of viral lytic genes at the posttranscriptional level. This report provides evidence that the structural conformation of the ORF57 protein plays a critical role in regulation of ORF57 stability. Phosphorylation by CKII on the identified serine/threonine residues at the N-terminal unstructured domain of ORF57 prevents its digestion by caspase-7. The C-terminal domain of ORF57, which is rich in α-helices, contributes to homodimerization of ORF57 to prevent proteasome-mediated protein degradation. Elucidation of the ORF57 structure not only enables us to better understand ORF57 stability and functions but also provides an important tool for us to modulate ORF57's activity with the aim to inhibit KSHV lytic replication.
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90
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Upadhyaya P, Qian Z, Habir NAA, Pei D. Direct Ras Inhibitors Identified from a Structurally Rigidified Bicyclic Peptide Library. Tetrahedron 2014; 70:7714-7720. [PMID: 25284901 PMCID: PMC4180945 DOI: 10.1016/j.tet.2014.05.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A one-bead-two-compound (OBTC) library of structurally rigidified bicyclic peptides was chemically synthesized on TentaGel microbeads (90 μm), with each bead displaying a unique bicyclic peptide on its surface and a linear encoding peptide of the same sequence in its interior. Screening of the library against oncogenic K-Ras G12V mutant identified two classes of Ras ligands. The class I ligands apparently bind to the effector-binding site and inhibit the Ras-Raf interaction, whereas the class II ligand appears to bind to a yet unidentified site different from the effector-binding site. These Ras ligands provide useful research tools and may be further developed into therapeutic agents.
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Affiliation(s)
- Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Nurlaila A. A. Habir
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18 Avenue, Columbus, Ohio 43210, USA
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91
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Smith JM, Hill NC, Krasniak PJ, Fasan R. Synthesis of bicyclic organo-peptide hybrids via oxime/intein-mediated macrocyclization followed by disulfide bond formation. Org Biomol Chem 2014; 12:1135-42. [PMID: 24395107 DOI: 10.1039/c3ob42222d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A new strategy is described to generate bicyclic peptides that incorporate non-peptidic backbone elements starting from recombinant polypeptide precursors. These compounds are produced via a one-pot, two-step sequence, in which peptide macrocyclization by means of a bifunctional oxyamine/1,3-amino-thiol synthetic precursor is followed by intramolecular disulfide formation between the synthetic precursor-borne thiol and a cysteine embedded in the peptide sequence. This approach was found to be compatible with the cysteine residue occupying different positions within 8mer and 10mer target peptide sequences and across different synthetic precursor scaffolds, thereby enabling the formation of a variety of diverse bicyclic scaffolds.
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Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA.
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92
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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93
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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94
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Kodadek T. Chemical tools to monitor and manipulate the adaptive immune system. CHEMISTRY & BIOLOGY 2014; 21:1066-74. [PMID: 25237855 PMCID: PMC4171709 DOI: 10.1016/j.chembiol.2014.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 12/20/2022]
Abstract
The ability to monitor and manipulate antigen-specific immune responses would have a major impact on several areas of biology and medicine. In this perspective, I consider pharmacological methods to do this, with a focus on the development of abiological "antigen surrogates" capable of binding to the antigen-binding sites of antibodies and B cell receptors with high affinity and selectivity. I describe the application of combinatorial library screening to identify antigen surrogates for monoclonal antibodies of therapeutic interest using chronic lymphocytic leukemia as an example. Furthermore, I discuss the use of multiplexed assays for the quantification of antigen surrogate-antibody complexes as diagnostic tools and antigen surrogate discovery via serum screening. Although antigen surrogates are a fairly new concept, I argue that they will open new avenues for both basic and clinical research and that major advances can be expected over the next few years.
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MESH Headings
- Adaptive Immunity
- Antibodies/immunology
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antigen-Antibody Complex/chemistry
- Antigens/chemistry
- Antigens/immunology
- Antigens/metabolism
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Quantum Dots/chemistry
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/therapeutic use
- Small Molecule Libraries/chemistry
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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95
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Chen S, Gopalakrishnan R, Schaer T, Marger F, Hovius R, Bertrand D, Pojer F, Heinis C. Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides. Nat Chem 2014; 6:1009-16. [PMID: 25343607 DOI: 10.1038/nchem.2043] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/24/2014] [Indexed: 12/13/2022]
Abstract
The disulfide bonds that form between two cysteine residues are important in defining and rigidifying the structures of proteins and peptides. In polypeptides containing multiple cysteine residues, disulfide isomerization can lead to multiple products with different biological activities. Here, we describe the development of a dithiol amino acid (Dtaa) that can form two disulfide bridges at a single amino acid site. Application of Dtaas to a serine protease inhibitor and a nicotinic acetylcholine receptor inhibitor that contain disulfide constraints enhanced their inhibitory activities 40- and 7.6-fold, respectively. X-ray crystallographic and NMR structure analysis show that the peptide ligands containing Dtaas have retained their native tertiary structures. We furthermore show that replacement of two cysteines by Dtaas can avoid the formation of disulfide bond isomers. With these properties, Dtaas are likely to have broad application in the rational design or directed evolution of peptides and proteins with high activity and stability.
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Affiliation(s)
- Shiyu Chen
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ranganath Gopalakrishnan
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | | | - Ruud Hovius
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Florence Pojer
- Protein Crystallography Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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96
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Takahashi T, Saito A. Interaction-dependent Native Chemical Ligation and Enzyme Reconstitution for Detection of Peptide–Peptide Interaction. CHEM LETT 2014. [DOI: 10.1246/cl.140437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tsuyoshi Takahashi
- Advanced Scientific Research Leaders Development (ASRLD) Unit, Gunma University
| | - Akinori Saito
- Division of Molecular Science, Faculty of Science and Technology, Gunma University
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97
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Lian W, Jiang B, Qian Z, Pei D. Cell-permeable bicyclic peptide inhibitors against intracellular proteins. J Am Chem Soc 2014; 136:9830-3. [PMID: 24972263 PMCID: PMC4227718 DOI: 10.1021/ja503710n] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cyclic peptides have great potential as therapeutic agents and research tools but are generally impermeable to the cell membrane. Fusion of cyclic peptides with a cyclic cell-penetrating peptide produces bicyclic peptides that are cell-permeable and retain the ability to recognize specific intracellular targets. Application of this strategy to protein tyrosine phosphatase 1B and a peptidyl-prolyl cis-trans isomerase (Pin1) isomerase resulted in potent, selective, proteolytically stable, and biologically active inhibitors against the enzymes.
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Affiliation(s)
- Wenlong Lian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Bisheng Jiang
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department
of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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98
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Mukherjee S, van der Donk WA. Mechanistic studies on the substrate-tolerant lanthipeptide synthetase ProcM. J Am Chem Soc 2014; 136:10450-9. [PMID: 24972336 PMCID: PMC4111213 DOI: 10.1021/ja504692v] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Lanthipeptides
are a class of post-translationally modified peptide
natural products. They contain lanthionine (Lan) and methyllanthionine
(MeLan) residues, which generate cross-links and endow the peptides
with various biological activities. The mechanism of a highly substrate-tolerant
lanthipeptide synthetase, ProcM, was investigated herein. We
report a hybrid ligation strategy to prepare a series of substrate
analogues designed to address a number of mechanistic questions regarding
catalysis by ProcM. The method utilizes expressed protein ligation
to generate a C-terminal thioester of the leader peptide of ProcA,
the substrate of ProcM. This thioester was ligated with a cysteine
derivative that resulted in an alkyne at the C-terminus of the leader
peptide. This alkyne in turn was used to conjugate the leader peptides
to a variety of synthetic peptides by copper-catalyzed azide–alkyne
cycloaddition. Using deuterium-labeled Ser and Thr in the substrate
analogues thus prepared, dehydration by ProcM was established to occur
from C-to-N-terminus for two different substrates. Cyclization also
occurred with a specific order, which depended on the sequence of
the substrate peptides. Furthermore, using orthogonal cysteine side-chain
protection in the two semisynthetic peptide substrates, we were
able to rule out spontaneous non-enzymatic cyclization events to explain
the very high substrate tolerance of ProcM. Finally, the enzyme was
capable of exchanging protons at the α-carbon of MeLan, suggesting
that ring formation could be reversible. These findings are discussed
in the context of the mechanism of the substrate-tolerant ProcM, which
may aid future efforts in lanthipeptide engineering.
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Affiliation(s)
- Subha Mukherjee
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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99
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Qian Z, LaRochelle J, Jiang B, Lian W, Hard RL, Selner NG, Luechapanichkul R, Barrios AM, Pei D. Early endosomal escape of a cyclic cell-penetrating peptide allows effective cytosolic cargo delivery. Biochemistry 2014; 53:4034-46. [PMID: 24896852 PMCID: PMC4075989 DOI: 10.1021/bi5004102] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 05/27/2014] [Indexed: 12/29/2022]
Abstract
Cyclic heptapeptide cyclo(FΦRRRRQ) (cFΦR4, where Φ is l-2-naphthylalanine) was recently found to be efficiently internalized by mammalian cells. In this study, its mechanism of internalization was investigated by perturbing various endocytic events through the introduction of pharmacologic agents and genetic mutations. The results show that cFΦR4 binds directly to membrane phospholipids, is internalized into human cancer cells through endocytosis, and escapes from early endosomes into the cytoplasm. Its cargo capacity was examined with a wide variety of molecules, including small-molecule dyes, linear and cyclic peptides of various charged states, and proteins. Depending on the nature of the cargos, they may be delivered by endocyclic (insertion of cargo into the cFΦR4 ring), exocyclic (attachment of cargo to the Gln side chain), or bicyclic approaches (fusion of cFΦR4 and cyclic cargo rings). The overall delivery efficiency (i.e., delivery of cargo into the cytoplasm and nucleus) of cFΦR4 was 4-12-fold higher than those of nonaarginine, HIV Tat-derived peptide, or penetratin. The higher delivery efficiency, coupled with superior serum stability, minimal toxicity, and synthetic accessibility, renders cFΦR4 a useful transporter for intracellular cargo delivery and a suitable system for investigating the mechanism of endosomal escape.
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Affiliation(s)
- Ziqing Qian
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Jonathan
R. LaRochelle
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, United States
| | - Bisheng Jiang
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Wenlong Lian
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Ryan L. Hard
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Nicholas G. Selner
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Rinrada Luechapanichkul
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
| | - Amy M. Barrios
- Department
of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Dehua Pei
- Department
of Chemistry and Biochemistry, The Ohio
State University, 100
West 18th Avenue, Columbus, Ohio 43210, United
States
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100
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Doran TM, Gao Y, Mendes K, Dean S, Simanski S, Kodadek T. Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS COMBINATORIAL SCIENCE 2014; 16:259-70. [PMID: 24749624 PMCID: PMC4053090 DOI: 10.1021/co500030f] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Large
one-bead one-compound (OBOC) combinatorial libraries can
be constructed relatively easily by solid-phase split and pool synthesis.
The use of resins with hydrophilic surfaces, such as TentaGel, allows
the beads to be used directly in screens for compounds that bind selectively
to labeled proteins, nucleic acids, or other biomolecules. However,
we have found that this method, while useful, has a high false positive
rate. In other words, beads that are scored as hits often display
compounds that prove to be poor ligands for the target of interest
when they are resynthesized and carried through validation trials.
This results in a significant waste of time and resources in cases
where putative hits cannot be validated without resynthesis. Here,
we report that this problem can be largely eliminated through the
use of redundant OBOC libraries, where more than one bead displaying
the same compound is present in the screen. We show that compounds
isolated more than once are likely to be high quality ligands for
the target of interest, whereas compounds isolated only once have
a much higher likelihood of being poor ligands. While the use of redundant
libraries does limit the number of unique compounds that can be screened
at one time in this format, the overall savings in time, effort, and
materials makes this a more efficient route to the isolation of useful
ligands for biomolecules.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Yu Gao
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Kimberly Mendes
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Sonja Dean
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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