1
|
Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 475] [Impact Index Per Article: 237.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
Collapse
|
2
|
Draper SRE, Ashton DS, Conover BM, Carter AJ, Stern KL, Xiao Q, Price JL. PEGylation near a Patch of Nonpolar Surface Residues Increases the Conformational Stability of the WW Domain. J Org Chem 2020; 85:1725-1730. [PMID: 31749365 DOI: 10.1021/acs.joc.9b02615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many proteins have one or more surface-exposed patches of nonpolar residues; our observations here suggest that PEGylation near such locations might be a useful strategy for increasing protein conformational stability. Specifically, we show that conjugating a PEG-azide to a propargyloxyphenylalanine via the copper(I)-catalyzed azide-alkyne cycloaddition can increase the conformational stability of the WW domain due to a favorable synergistic effect that depends on the hydrophobicity of a nearby patch of nonpolar surface residues.
Collapse
Affiliation(s)
- Steven R E Draper
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Dallin S Ashton
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Benjamin M Conover
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Anthony J Carter
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Kimberlee L Stern
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Qiang Xiao
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Joshua L Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| |
Collapse
|
3
|
Xiao Q, Draper SRE, Smith MS, Brown N, Pugmire NAB, Ashton DS, Carter AJ, Lawrence EEK, Price JL. Influence of PEGylation on the Strength of Protein Surface Salt Bridges. ACS Chem Biol 2019; 14:1652-1659. [PMID: 31188563 DOI: 10.1021/acschembio.9b00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Conjugation of polyethylene glycol (PEGylation) is a well-known strategy for extending the serum half-life of protein drugs and for increasing their resistance to proteolysis and aggregation. We previously showed that PEGylation can increase protein conformational stability; the extent of PEG-based stabilization depends on the PEGylation site, the structure of the PEG-protein linker, and the ability of PEG to release water molecules from the surrounding protein surface to the bulk solvent. The strength of a noncovalent interaction within a protein depends strongly on its microenvironment, with salt-bridge and hydrogen-bond strength increasing in nonpolar versus aqueous environments. Accordingly, we wondered whether partial desolvation by PEG of the surrounding protein surface might result in measurable increases in the strength of a salt bridge near a PEGylation site. Here we explore this possibility using triple-mutant box analysis to assess the impact of PEGylation on the strength of nearby salt bridges at specific locations within three peptide model systems. The results indicate that PEG can increase the nearby salt-bridge strength, though this effect is not universal, and its precise structural prerequisites are not a simple function of secondary structural context, of the orientation and distance between the PEGylation site and salt bridge, or of salt-bridge residue identity. We obtained high-resolution X-ray diffraction data for a PEGylated peptide in which PEG enhances the strength of a nearby salt bridge. Comparing the electron density map of this PEGylated peptide versus that of its non-PEGylated counterpart provides evidence of localized protein surface desolvation as a mechanism for PEG-based salt-bridge stabilization.
Collapse
Affiliation(s)
- Qiang Xiao
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Steven R. E. Draper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mason S. Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Nathaniel Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Natalie A. B. Pugmire
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dallin S. Ashton
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Anthony J. Carter
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Eliza E. K. Lawrence
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
4
|
Lawrence PB, Price JL. How PEGylation influences protein conformational stability. Curr Opin Chem Biol 2016; 34:88-94. [PMID: 27580482 DOI: 10.1016/j.cbpa.2016.08.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 08/08/2016] [Accepted: 08/10/2016] [Indexed: 12/18/2022]
Abstract
PEGylation is an important strategy for enhancing the pharmacokinetic properties of protein therapeutics. The development of chemoselective side-chain modification reactions has enabled researchers to PEGylate proteins with high selectivity at defined locations. However, aside from avoiding active sites and binding interfaces, there are few guidelines for the selection of optimal PEGylation sites. Because conformational stability is intimately related to the ability of a protein to avoid proteolysis, aggregation, and immune responses, it is possible that PEGylating a protein at sites where PEG enhances conformational stability will result in PEG-protein conjugates with enhanced pharmacokinetic properties. However, the impact of PEGylation on protein conformational stability is incompletely understood. This review describes recent advances toward understanding the impact of PEGylation on protein conformational stability, along with the development of structure-based guidelines for selecting stabilizing PEGylation sites.
Collapse
Affiliation(s)
- Paul B Lawrence
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| | - Joshua L Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| |
Collapse
|
5
|
Zang Q, Tada S, Uzawa T, Kiga D, Yamamura M, Ito Y. Two site genetic incorporation of varying length polyethylene glycol into the backbone of one peptide. Chem Commun (Camb) 2015; 51:14385-8. [PMID: 26273708 DOI: 10.1039/c5cc04486c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Polyethylene glycol (PEG) of different lengths was genetically incorporated into the backbone of a polypeptide using stop-anticodon and frameshift anticodon-containing tRNAs, which were acylated with PEG-containing amino acids.
Collapse
Affiliation(s)
- Qingmin Zang
- Nano Medical Engineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | | | | | | | | | | |
Collapse
|
6
|
Soye BJD, Patel JR, Isaacs FJ, Jewett MC. Repurposing the translation apparatus for synthetic biology. Curr Opin Chem Biol 2015; 28:83-90. [PMID: 26186264 DOI: 10.1016/j.cbpa.2015.06.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
The translation system (the ribosome and associated factors) is the cell's factory for protein synthesis. The extraordinary catalytic capacity of the protein synthesis machinery has driven extensive efforts to harness it for novel functions. For example, pioneering efforts have demonstrated that it is possible to genetically encode more than the 20 natural amino acids and that this encoding can be a powerful tool to expand the chemical diversity of proteins. Here, we discuss recent advances in efforts to expand the chemistry of living systems, highlighting improvements to the molecular machinery and genomically recoded organisms, applications of cell-free systems, and extensions of these efforts to include eukaryotic systems. The transformative potential of repurposing the translation apparatus has emerged as one of the defining opportunities at the interface of chemical and synthetic biology.
Collapse
Affiliation(s)
- Benjamin J Des Soye
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jaymin R Patel
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510, USA
| | - Michael C Jewett
- Interdisciplinary Biological Sciences Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Northwestern Institute on Complex Systems, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Simpson Querrey Institute, Northwestern University, 303 East Superior Street, Suite 11-131, Chicago, IL 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.,Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| |
Collapse
|
7
|
Lawrence PB, Gavrilov Y, Matthews SS, Langlois MI, Shental-Bechor D, Greenblatt HM, Pandey BK, Smith MS, Paxman R, Torgerson CD, Merrell JP, Ritz CC, Prigozhin MB, Levy Y, Price JL. Criteria for Selecting PEGylation Sites on Proteins for Higher Thermodynamic and Proteolytic Stability. J Am Chem Soc 2014; 136:17547-60. [DOI: 10.1021/ja5095183] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Paul B. Lawrence
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yulian Gavrilov
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sam S. Matthews
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Minnie I. Langlois
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dalit Shental-Bechor
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M. Greenblatt
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Brijesh K. Pandey
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mason S. Smith
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan Paxman
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Chad D. Torgerson
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jacob P. Merrell
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Cameron C. Ritz
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Maxim B. Prigozhin
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yaakov Levy
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joshua L. Price
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
8
|
Tuckey C, Asahara H, Zhou Y, Chong S. Protein synthesis using a reconstituted cell-free system. ACTA ACUST UNITED AC 2014; 108:16.31.1-16.31.22. [PMID: 25271715 DOI: 10.1002/0471142727.mb1631s108] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Most cell-free protein-synthesis systems are based on cell extracts, which often contain undesirable activities. Reconstituted systems, by contrast, are composed of a defined number of purified and recombinant components with minimal nuclease and protease activities. This unit describes the use of a particular commercial reconstituted system, PURExpress. This system allows in vitro synthesis of proteins from mRNA and circular and linear DNA templates, as well as co-translational labeling of proteins. Unique to this system, all recombinant protein components of the system are His-tagged, allowing purification of the synthesized untagged protein by removing the rest of the system's components. Newly synthesized proteins can often be visible on an SDS-PAGE gel and directly assayed for their functions without labeling and purification. Certain components of the system, such as ribosomes or release factors, can be omitted for specific applications. Such "delta" versions of the system are well suited for studies of bacterial translation, assays of ribosome function, incorporation of unnatural amino acids, and ribosome display of protein libraries.
Collapse
|
9
|
Smith MT, Wilding KM, Hunt JM, Bennett AM, Bundy BC. The emerging age of cell-free synthetic biology. FEBS Lett 2014; 588:2755-61. [PMID: 24931378 DOI: 10.1016/j.febslet.2014.05.062] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 01/16/2023]
Abstract
The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology.
Collapse
Affiliation(s)
- Mark Thomas Smith
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Kristen M Wilding
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Jeremy M Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Anthony M Bennett
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
| |
Collapse
|
10
|
Wang W, Hirano Y, Uzawa T, Liu M, Taiji M, Ito Y. In vitro selection of a peptide aptamer that potentiates inhibition of cyclin-dependent kinase 2 by purvalanol. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00142g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To increase the inhibitory activity of purvalanol against cyclin-dependent kinase 2, we increased the extent of interaction between the inhibitor and the target by coupling a peptide aptamer to purvalanol.
Collapse
Affiliation(s)
- Wei Wang
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
| | - Yoshinori Hirano
- Laboratory for Computational Molecular Design
- Computational Biology Research Core
- RIKEN Quantitative Biology Center
- Chuo-ku, Japan
| | - Takanori Uzawa
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
| | - Mingzhe Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery (Shenyang Pharmaceutical University) of Ministry of Education
- School of Pharmaceutical Engineering
- Shenyang Pharmaceutical University
- , China
| | - Makoto Taiji
- Laboratory for Computational Molecular Design
- Computational Biology Research Core
- RIKEN Quantitative Biology Center
- Chuo-ku, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory
- RIKEN 2-1 Hirosawa
- Wako, Japan
- Emergent Bioengineering Materials Research Team
- RIKEN Center for Emergent Matter Science
| |
Collapse
|
11
|
Bio-orthogonal and combinatorial approaches for the design of binding growth factors. Biomaterials 2013; 34:7565-74. [PMID: 23859658 DOI: 10.1016/j.biomaterials.2013.06.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 06/23/2013] [Indexed: 11/22/2022]
Abstract
Merrifield chemistry enables the convenient synthesis of oligonucleotides and peptides, while recombinant DNA technology has facilitated protein engineering. Recently, protein engineering has been extended into bio-orthogonal protein engineering by the development of specific chemical or enzymatic modification technologies. The combinatorial approach of molecular evolutionary engineering (or in vitro selection) has also provided a new design tool for functional peptides. These methodologies have enabled the development of various new proteinaceous materials for biological and medical applications. Here, we will discuss recent progress in the molecular design of proteins with respect to the preparation of binding growth factors, which are of increasing importance in the biomaterials field.
Collapse
|
12
|
TADA S, WANG W, LI Z, UZAWA T, ITO Y. Creation of Novel Functional Peptides by Mimicking Darwinian Evolution. KOBUNSHI RONBUNSHU 2013. [DOI: 10.1295/koron.70.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|