201
|
Zhang C, Dai P, Spokoyny AM, Pentelute BL. Enzyme-catalyzed macrocyclization of long unprotected peptides. Org Lett 2014; 16:3652-5. [PMID: 25002256 PMCID: PMC4372082 DOI: 10.1021/ol501609y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
A glutathione S-transferase (GST) catalyzed macrocyclization
reaction for peptides up to 40 amino acids in length is reported.
GST catalyzes the selective SNAr reaction between an N-terminal glutathione (GSH, γ-Glu-Cys-Gly) tag and
a C-terminal perfluoroaryl-modified cysteine on the
same polypeptide chain. Cyclic peptides ranging from 9 to 24 residues
were quantitatively produced within 2 h in aqueous pH = 8 buffer at
room temperature. The reaction was highly selective for cyclization
at the GSH tag, enabling the combination of GST-catalyzed ligation
with native chemical ligation to generate a large 40-residue peptide
macrocycle.
Collapse
Affiliation(s)
- Chi Zhang
- Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | | | | | | |
Collapse
|
202
|
Lau YH, de Andrade P, Sköld N, McKenzie GJ, Venkitaraman AR, Verma C, Lane DP, Spring DR. Investigating peptide sequence variations for 'double-click' stapled p53 peptides. Org Biomol Chem 2014; 12:4074-7. [PMID: 24817343 DOI: 10.1039/c4ob00742e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Stapling peptides for inhibiting the p53/MDM2 interaction is a promising strategy for developing anti-cancer therapeutic leads. We evaluate double-click stapled peptides formed from p53-based diazidopeptides with different staple positions and azido amino acid side-chain lengths, determining the impact of these variations on MDM2 binding and cellular activity. We also demonstrate a K24R mutation, necessary for cellular activity in hydrocarbon-stapled p53 peptides, is not required for analogous 'double-click' peptides.
Collapse
Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
| | | | | | | | | | | | | | | |
Collapse
|
203
|
Affiliation(s)
| | - Matthew Bogyo
- Departments of 1Chemical and Systems Biology,
- Microbiology and Immunology, and
- Pathology, Stanford University School of Medicine, Stanford, California 94305-5324;
| |
Collapse
|
204
|
de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014; 53:6965-9. [DOI: 10.1002/anie.201310245] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/10/2014] [Indexed: 11/09/2022]
|
205
|
de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310245] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
206
|
Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| |
Collapse
|
207
|
Smith JM, Frost JR, Fasan R. Designer macrocyclic organo-peptide hybrids inhibit the interaction between p53 and HDM2/X by accommodating a functional α-helix. Chem Commun (Camb) 2014; 50:5027-30. [PMID: 24710524 DOI: 10.1039/c4cc01199f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the design of side-chain-to-tail linked organo-peptide hybrids incorporating an α-helical protein-binding motif. Using this strategy, macrocyclic inhibitors of the p53:HDM2 interaction displaying dual specificity against the HDMX homolog as well as increased proteolytic stability could be obtained.
Collapse
Affiliation(s)
- Jessica M Smith
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
| | | | | |
Collapse
|
208
|
Cross-talk between malarial cysteine proteases and falstatin: the BC loop as a hot-spot target. PLoS One 2014; 9:e93008. [PMID: 24699522 PMCID: PMC3974720 DOI: 10.1371/journal.pone.0093008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/27/2014] [Indexed: 02/05/2023] Open
Abstract
Cysteine proteases play a crucial role in the development of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Our earlier studies demonstrated that these enzymes are equipped with specific domains for defined functions and further suggested the mechanism of activation of cysteine proteases. The activities of these proteases are regulated by a new class of endogenous inhibitors of cysteine proteases (ICPs). Structural studies of the ICPs of Trypanosoma cruzi (chagasin) and Plasmodium berghei (PbICP) indicated that three loops (termed BC, DE, and FG) are crucial for binding to target proteases. Falstatin, an ICP of P. falciparum, appears to play a crucial role in invasion of erythrocytes and hepatocytes. However, the mechanism of inhibition of cysteine proteases by falstatin has not been established. Our study suggests that falstatin is the first known ICP to function as a multimeric protein. Using site-directed mutagenesis, hemoglobin hydrolysis assays and peptide inhibition studies, we demonstrate that the BC loop, but not the DE or FG loops, inhibits cysteine proteases of P. falciparum and P. vivax via hydrogen bonds. These results suggest that the BC loop of falstatin acts as a hot-spot target for inhibiting malarial cysteine proteases. This finding suggests new strategies for the development of anti-malarial agents based on protease-inhibitor interactions.
Collapse
|
209
|
Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
Collapse
Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | | | | | | | | |
Collapse
|
210
|
Goldberg JM, Chen X, Meinhardt N, Greenbaum DC, Petersson EJ. Thioamide-based fluorescent protease sensors. J Am Chem Soc 2014; 136:2086-93. [PMID: 24472041 PMCID: PMC3985465 DOI: 10.1021/ja412297x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Thioamide
quenchers can be paired with compact fluorophores to
design “turn-on” fluorescent protease substrates. We
have used this method to study a variety of serine-, cysteine-, carboxyl-,
and metallo-proteases, including trypsin, chymotrypsin, pepsin, thermolysin,
papain, and calpain. Since thioamides quench some fluorophores red-shifted
from those naturally occurring in proteins, this technique can be
used for real time monitoring of protease activity in crude preparations
of virtually any protease. We demonstrate the value of this method
in three model applications: (1) characterization of papain enzyme
kinetics using rapid-mixing experiments, (2) selective monitoring
of cleavage at a single site in a peptide with multiple proteolytic
sites, and (3) analysis of the specificity of an inhibitor of calpain
in cell lysates.
Collapse
Affiliation(s)
- Jacob M Goldberg
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | | | | | | | | |
Collapse
|
211
|
Zou Y, Spokoyny AM, Zhang C, Simon MD, Yu H, Lin YS, Pentelute BL. Convergent diversity-oriented side-chain macrocyclization scan for unprotected polypeptides. Org Biomol Chem 2014; 12:566-73. [PMID: 24310320 PMCID: PMC3935340 DOI: 10.1039/c3ob42168f] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we describe a general synthetic platform for side-chain macrocyclization of an unprotected peptide library based on the SNAr reaction between cysteine thiolates and a new generation of highly reactive perfluoroaromatic small molecule linkers. This strategy enabled us to simultaneously "scan" two cysteine residues positioned from i, i + 1 to i, i + 14 sites in a polypeptide, producing 98 macrocyclic products from reactions of 14 peptides with 7 linkers. A complementary reverse strategy was developed; cysteine residues within the polypeptide were first modified with non-bridging perfluoroaryl moieties and then commercially available dithiol linkers were used for macrocyclization. The highly convergent, site-independent, and modular nature of these two strategies coupled with the unique chemoselectivity of a SNAr transformation allows for the rapid diversity-oriented synthesis of hybrid macrocyclic peptide libraries with varied chemical and structural complexities.
Collapse
Affiliation(s)
- Yekui Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | | | | | | | | | | | | |
Collapse
|
212
|
Haney CM, Horne WS. Dynamic covalent side-chain cross-links via intermolecular oxime or hydrazone formation from bifunctional peptides and simple organic linkers. J Pept Sci 2014; 20:108-14. [PMID: 24402694 DOI: 10.1002/psc.2596] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 01/08/2023]
Abstract
Peptide cyclization via chemoselective reactions between side chains has proven a useful strategy to control folded structure. We report here a method for the synthesis of side-chain to side-chain cyclic peptides based on the intermolecular reaction between a linear peptide functionalized with two aminooxy or hydrazide side chains and an organic dialdehyde linker. A family of oxime-based and hydrazone-based cyclic products is prepared in a modular and convergent fashion by combination of unprotected linear peptide precursors and various small molecule linkers in neutral aqueous buffer. The side-chain to side-chain linkages that result can alter peptide folding behavior. The dynamic covalent nature of the Schiff bases in the cyclic products can be utilized to create mixtures where product composition changes in response to experimental conditions. Thus, a linear peptide precursor can select one organic linker from a mixture, and a cyclic product can dynamically exchange the small molecule component of the macrocycle.
Collapse
Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
213
|
Lau YH, de Andrade P, Quah ST, Rossmann M, Laraia L, Sköld N, Sum TJ, Rowling PJE, Joseph TL, Verma C, Hyvönen M, Itzhaki LS, Venkitaraman AR, Brown CJ, Lane DP, Spring DR. Functionalised staple linkages for modulating the cellular activity of stapled peptides. Chem Sci 2014. [DOI: 10.1039/c4sc00045e] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A divergent synthetic strategy for generating helical p53 peptides bearing functionalised staple linkages, allowing for efficient optimisation of cellular activity.
Collapse
Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | | | | | - Maxim Rossmann
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA, UK
| | - Luca Laraia
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
- MRC Cancer Unit
- Hutchison/MRC Research Centre
| | - Niklas Sköld
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | - Tze Jing Sum
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| | | | | | - Chandra Verma
- Bioinformatics Institute (A*STAR)
- , Singapore 138671
- Department of Biological Sciences
- National University of Singapore (NUS)
- Singapore 117543
| | - Marko Hyvönen
- Department of Biochemistry
- University of Cambridge
- Cambridge CB2 1GA, UK
| | - Laura S. Itzhaki
- Department of Pharmacology
- University of Cambridge
- Cambridge CB2 1PD, UK
| | | | | | | | - David R. Spring
- University Chemical Laboratory
- University of Cambridge
- Cambridge CB2 1EW, UK
| |
Collapse
|
214
|
Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F. Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B 2013; 117:14688-96. [PMID: 24205975 DOI: 10.1021/jp409334h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal friction arising from local steric hindrance and/or the excluded volume effect plays an important role in controlling not only the dynamics of protein folding but also conformational transitions occurring within the native state potential well. However, experimental assessment of such local friction is difficult because it does not manifest itself as an independent experimental observable. Herein, we demonstrate, using the miniprotein trp-cage as a testbed, that it is possible to selectively increase the local mass density in a protein and hence the magnitude of local friction, thus making its effect directly measurable via folding kinetic studies. Specifically, we show that when a helix cross-linker, m-xylene, is placed near the most congested region of the trp-cage it leads to a significant decrease in both the folding rate (by a factor of 3.8) and unfolding rate (by a factor of 2.5 at 35 °C) but has little effect on protein stability. Thus, these results, in conjunction with those obtained with another cross-linked trp-cage and two uncross-linked variants, demonstrate the feasibility of using a nonperturbing cross-linker to help quantify the effect of internal friction. In addition, we estimate that a m-xylene cross-linker could lead to an increase in the roughness of the folding energy landscape by as much as 0.4-1.0k(B)T.
Collapse
Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and §Department of Biochemistry & Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | | | | | | | | |
Collapse
|
215
|
Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat Chem 2013; 5:161-73. [PMID: 23422557 DOI: 10.1038/nchem.1568] [Citation(s) in RCA: 572] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a significant challenge because it is unclear how they can be effectively and selectively targeted using small molecules. Achieving this goal is critical given the defining role of these interactions in biological processes. A rational approach to inhibitor design based on the secondary structure at the interface is the focus of much research, and different classes of designed ligands have emerged, some of which effectively and selectively disrupt targeted PPIs. This Review discusses the relevance of PPIs and, in particular, the importance of α-helix-mediated PPIs to chemical biology and drug discovery with a focus on designing inhibitors, including constrained peptides, foldamers and proteomimetic-derived ligands. In doing so, key challenges and major advances in developing generic approaches for the elaboration of PPI inhibitors are highlighted. The challenges faced in developing such ligands as drug leads--and how criteria applied to these may differ from conventional small-molecule drugs--are summarized.
Collapse
|
216
|
Spokoyny AM, Zou Y, Ling JJ, Yu H, Lin YS, Pentelute BL. A perfluoroaryl-cysteine S(N)Ar chemistry approach to unprotected peptide stapling. J Am Chem Soc 2013; 135:5946-9. [PMID: 23560559 PMCID: PMC3675880 DOI: 10.1021/ja400119t] [Citation(s) in RCA: 372] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report the discovery of a facile transformation between perfluoroaromatic molecules and a cysteine thiolate, which is arylated at room temperature. This new approach enabled us to selectively modify cysteine residues in unprotected peptides, providing access to variants containing rigid perfluoroaromatic staples. This stapling modification performed on a peptide sequence designed to bind the C-terminal domain of an HIV-1 capsid assembly polyprotein (C-CA) showed enhancement in binding, cell permeability, and proteolytic stability properties, as compared to the unstapled analog. Importantly, chemical stability of the formed staples allowed us to use this motif in the native chemical ligation-mediated synthesis of a small protein affibody that is capable of binding the human epidermal growth factor 2 receptor.
Collapse
Affiliation(s)
- Alexander M. Spokoyny
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Yekui Zou
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jingjing J. Ling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Hongtao Yu
- Department of Chemistry, Tufts University, Medford, MA 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA 02155, United States
| | - Bradley L. Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| |
Collapse
|