51
|
Furman JL, Chiu M, Hunter MJ. Early engineering approaches to improve peptide developability and manufacturability. AAPS JOURNAL 2014; 17:111-20. [PMID: 25338742 DOI: 10.1208/s12248-014-9681-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/02/2014] [Indexed: 02/08/2023]
Abstract
Downstream success in Pharmaceutical Development requires thoughtful molecule design early in the lifetime of any potential therapeutic. Most therapeutic monoclonal antibodies are quite similar with respect to their developability properties. However, the properties of therapeutic peptides tend to be as diverse as the molecules themselves. Analysis of the primary sequence reveals sites of potential adverse posttranslational modifications including asparagine deamidation, aspartic acid isomerization, methionine, tryptophan, and cysteine oxidation and, potentially, chemical and proteolytic degradation liabilities that can impact the developability and manufacturability of a potential therapeutic peptide. Assessing these liabilities, both biophysically and functionally, early in a molecule's lifetime can drive a more effective path forward in the drug discovery process. In addition to these potential liabilities, more complex peptides that contain multiple disulfide bonds can pose particular challenges with respect to production and manufacturability. Approaches to reducing the disulfide bond complexity of these peptides are often explored with mixed success. Proteolytic degradation is a major contributor to decreased half-life and efficacy. Addressing this aspect of peptide stability early in the discovery process increases downstream success. We will address aspects of peptide sequence analysis, molecule complexity, developability analysis, and manufacturing routes that drive the decision making processes during peptide therapeutic development.
Collapse
Affiliation(s)
- Jennifer L Furman
- Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California, 92121, USA
| | | | | |
Collapse
|
52
|
Sawyer TK, Guerlavais V, Darlak K, Feyfant E. Macrocyclic α-Helical Peptide Drug Discovery. MACROCYCLES IN DRUG DISCOVERY 2014. [DOI: 10.1039/9781782623113-00339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Macrocyclic α-helical peptides have emerged as a promising new drug class and within the scope of hydrocarbon-stapled peptides such molecules have advanced into the clinic. The overarching concept of designing proteomimetics of an α-helical ‘ligand’ which binds its cognate ‘target’ relative to α-helical interfacing protein-protein interactions has been well-validated and expanded through numerous investigations for a plethora of therapeutic targets oftentimes referred to as “undruggable” with respect to other modalities (e.g., small-molecule or proteins). This chapter highlights the evolution of macrocyclic α-helical peptides in terms of target space, biophysical and computational chemistry, structural diversity and synthesis, drug design and chemical biology. It is noteworthy that hydrocarbon-stapled peptides have successfully risen to the summit of such drug discovery campaigns.
Collapse
|
53
|
Mangold S, O’Leary DJ, Grubbs RH. Z-Selective olefin metathesis on peptides: investigation of side-chain influence, preorganization, and guidelines in substrate selection. J Am Chem Soc 2014; 136:12469-78. [PMID: 25102124 PMCID: PMC4156862 DOI: 10.1021/ja507166g] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Indexed: 12/27/2022]
Abstract
Olefin metathesis has emerged as a promising strategy for modulating the stability and activity of biologically relevant compounds; however, the ability to control olefin geometry in the product remains a challenge. Recent advances in the design of cyclometalated ruthenium catalysts has led to new strategies for achieving such control with high fidelity and Z selectivity, but the scope and limitations of these catalysts on substrates bearing multiple functionalities, including peptides, remained unexplored. Herein, we report an assessment of various factors that contribute to both productive and nonproductive Z-selective metathesis on peptides. The influence of sterics, side-chain identity, and preorganization through peptide secondary structure are explored by homodimerization, cross metathesis, and ring-closing metathesis. Our results indicate that the amino acid side chain and identity of the olefin profoundly influence the activity of cyclometalated ruthenium catalysts in Z-selective metathesis. The criteria set forth for achieving high conversion and Z selectivity are highlighted by cross metathesis and ring-closing metathesis on diverse peptide substrates. The principles outlined in this report are important not only for expanding the scope of Z-selective olefin metathesis to peptides but also for applying stereoselective olefin metathesis in general synthetic endeavors.
Collapse
Affiliation(s)
- Shane
L. Mangold
- Arnold
and Mabel Beckman Laboratories for Chemical Synthesis, Division of
Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Daniel J. O’Leary
- Department
of Chemistry, Pomona College, Claremont, California 91711, United States
| | - Robert H. Grubbs
- Arnold
and Mabel Beckman Laboratories for Chemical Synthesis, Division of
Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| |
Collapse
|
54
|
Bonache MÁ, Balsera B, López-Méndez B, Millet O, Brancaccio D, Gómez-Monterrey I, Carotenuto A, Pavone LM, Reille-Seroussi M, Gagey-Eilstein N, Vidal M, de la Torre-Martı́nez R, Fernández-Carvajal A, Ferrer-Montiel A, García-López MT, Martín-Martínez M, de Vega MJP, González-Muñiz R. De novo designed library of linear helical peptides: an exploratory tool in the discovery of protein-protein interaction modulators. ACS COMBINATORIAL SCIENCE 2014; 16:250-8. [PMID: 24725184 DOI: 10.1021/co500005x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) have emerged as important targets for pharmaceutical intervention because of their essential role in numerous physiological and pathological processes, but screening efforts using small-molecules have led to very low hit rates. Linear peptides could represent a quick and effective approach to discover initial PPI hits, particularly if they have inherent ability to adopt specific peptide secondary structures. Here, we address this hypothesis through a linear helical peptide library, composed of four sublibraries, which was designed by theoretical predictions of helicity (Agadir software). The 13-mer peptides of this collection fixes either a combination of three aromatic or two aromatic and one aliphatic residues on one face of the helix (Ac-SSEEX(5)ARNX(9)AAX(12)N-NH2), since these are structural features quite common at PPIs interfaces. The 81 designed peptides were conveniently synthesized by parallel solid-phase methodologies, and the tendency of some representative library components to adopt the intended secondary structure was corroborated through CD and NMR experiments. As proof of concept in the search for PPI modulators, the usefulness of this library was verified on the widely studied p53-MDM2 interaction and on the communication between VEGF and its receptor Flt-1, two PPIs for which a hydrophobic α-helix is essential for the interaction. We have demonstrated here that, in both cases, selected peptides from the library, containing the right hydrophobic sequence of the hot-spot in one of the protein partners, are able to interact with the complementary protein. Moreover, we have discover some new, quite potent inhibitors of the VEGF-Flt-1 interaction, just by replacing one of the aromatic residues of the initial F(5)Y(9)Y(12) peptide by W, in agreement with previous results on related antiangiogenic peptides. Finally, the HTS evaluation of the full collection on thermoTRPs has led to a few antagonists of TRPV1 and TRPA1 channels, which open new avenues on the way to innovative modulators of these channels.
Collapse
Affiliation(s)
- M. Ángeles Bonache
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Beatriz Balsera
- Instituto de Química-Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Oscar Millet
- CICbioGUNE, Structural Biology Unit, 48160 Bilbao, Spain
| | - Diego Brancaccio
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Isabel Gómez-Monterrey
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Alfonso Carotenuto
- Department
of Pharmacy, University of Naples “Federico II”, Via D. Montesano
49, 80131 Naples, Italy
| | - Luigi M. Pavone
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples “Federico II”, Via S. Pansini 5, 80131, Naples, Italy
| | - Marie Reille-Seroussi
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Nathalie Gagey-Eilstein
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
| | - Michel Vidal
- UMR
8638
CNRS, UFR de Pharmacie, Université Paris Descartes, PRES
Sorbonne Paris Cité, 4 avenue de l’Observatoire, 75006 Paris, France
- UF
“Pharmacocinétique et pharmacochimie”, Hôpital Cochin, , AP-HP, 27 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Roberto de la Torre-Martı́nez
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Asia Fernández-Carvajal
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | - Antonio Ferrer-Montiel
- Instituto
de Biología Molecular y Celular, Universidad Miguel Hernández, Avenida de la Universidad s/n, 03202 Elche (Alicante), Spain
| | | | | | | | | |
Collapse
|
55
|
Sim AYL, Joseph T, Lane DP, Verma C. Mechanism of Stapled Peptide Binding to MDM2: Possible Consequences for Peptide Design. J Chem Theory Comput 2014; 10:1753-61. [DOI: 10.1021/ct4009238] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Adelene Y. L. Sim
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - Thomas Joseph
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
| | - David P. Lane
- p53
Laboratory (p53Lab, A*STAR), 8A Biomedical Grove, #06-06, Immunos, Singapore 138648
| | - Chandra Verma
- Bioinformatics
Institute (A*STAR), 30
Biopolis Street #07-01, Matrix, Singapore 138671
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551
- Department
of Biological Sciences, National University of Singapore, 14 Science
Drive 4, Singapore 117543
| |
Collapse
|
56
|
Lama D, Quah ST, Verma CS, Lakshminarayanan R, Beuerman RW, Lane DP, Brown CJ. Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces. Sci Rep 2013; 3:3451. [PMID: 24336354 PMCID: PMC6506440 DOI: 10.1038/srep03451] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/20/2013] [Indexed: 12/26/2022] Open
Abstract
eIF4E is frequently over-expressed in different cancers and causes increased translation of oncogenic proteins via deregulated cap-dependent translation. Inhibitors of the eIF4E:eIF4G interactions represent an approach that would normalize cap-dependent translation. Stapled peptides represent an emerging class of therapeutics that can target protein: protein interactions. We present here molecular dynamics simulations for a set of rationally designed stapled peptides in solution and in complex with eIF4E, supported with biophysical and crystallographic data. Clustering of the simulated structures revealed the favoured conformational states of the stapled peptides in their bound or free forms in solution. Identifying these populations has allowed us to design peptides with improved affinities by introducing mutations into the peptide sequence to alter their conformational distributions. These studies emphasise the effects that engineered mutations have on the conformations of free and bound peptides, and illustrate that both states must be considered in efforts to attain high affinity binding.
Collapse
Affiliation(s)
- Dilraj Lama
- 1] Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671 [2]
| | - Soo T Quah
- 1] p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648 [2]
| | - Chandra S Verma
- 1] Bioinformatics Institute, A*STAR (Agency for Science, Technology and Research), 30 Biopolis Street, #07-01 Matrix, Singapore 138671 [2] Department of Biological sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543 [3] School of Biological sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551
| | | | - Roger W Beuerman
- Singapore Eye Research Institute, 11 Third Hospital Avenue, Singapore 16875
| | - David P Lane
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| | - Christopher J Brown
- p53 Laboratory, A*STAR (Agency for Science, Technology and Research), 8A Biomedical Grove, #06-04/05, Neuros/Immunos, Singapore 138648
| |
Collapse
|
57
|
Sun TL, Sun Y, Lee CC, Huang HW. Membrane permeability of hydrocarbon-cross-linked peptides. Biophys J 2013; 104:1923-32. [PMID: 23663835 DOI: 10.1016/j.bpj.2013.03.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 03/15/2013] [Accepted: 03/26/2013] [Indexed: 11/24/2022] Open
Abstract
Schafmeister, Po, and Verdine (another study) introduced a method using a hydrocarbon linker (staple) to stabilize a peptide in a helical configuration. One intended goal of this scheme is to facilitate the delivery of peptide drugs into target cells. Here, we investigate whether stapled peptides are intrinsically membrane permeable, by performing a case study on a stapled 12-mer peptide named NYAD-1. We found that the native peptide CAI (an HIV-1 inhibitor) does not bind to lipid bilayers, however NYAD-1 indeed permeates through lipid bilayers even at low solution concentrations. To understand the reason for the membrane permeability, we investigated the physical properties of NYAD-1 as a function of bound peptide/lipid molar ratio P/L. We found that NYAD-1 spontaneously binds to a lipid bilayer. At low P/L, the peptide primarily binds on the polar-apolar interface with its helical axis parallel to the bilayer, which has the effect of stretching the membrane area and thinning the membrane. The membrane thinning reaches its maximum at P/L ∼1/15-1/12 in DOPC bilayers. Additional bound peptides have little thinning effect and their helical axes are normal to the plane of bilayers. Thus, the stapled peptide has a membrane interaction behavior similar to helical antimicrobial peptides, such as magainin and melittin. We emphasize that not all peptides that bind to lipid bilayers in the α-helical form behave this way.
Collapse
Affiliation(s)
- Tzu-Lin Sun
- Department of Physics and Astronomy, Rice University, Houston, Texas, USA
| | | | | | | |
Collapse
|
58
|
All-hydrocarbon stapled peptides as Synthetic Cell-Accessible Mini-Proteins. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 9:e1-e70. [PMID: 24064243 DOI: 10.1016/j.ddtec.2012.01.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
59
|
Hamed E, Xu T, Keten S. Poly(ethylene glycol) Conjugation Stabilizes the Secondary Structure of α-Helices by Reducing Peptide Solvent Accessible Surface Area. Biomacromolecules 2013; 14:4053-60. [DOI: 10.1021/bm401164t] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Elham Hamed
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ting Xu
- Department of Materials
Science and Engineering, University of California, Berkeley, California 94720, United States
| | - Sinan Keten
- Department of Civil
and Environmental Engineering and Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
60
|
Diamante L, Gatti-Lafranconi P, Schaerli Y, Hollfelder F. In vitro affinity screening of protein and peptide binders by megavalent bead surface display. Protein Eng Des Sel 2013; 26:713-24. [PMID: 23980186 PMCID: PMC3785251 DOI: 10.1093/protein/gzt039] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/30/2013] [Accepted: 07/02/2013] [Indexed: 11/12/2022] Open
Abstract
The advent of protein display systems has provided access to tailor-made protein binders by directed evolution. We introduce a new in vitro display system, bead surface display (BeSD), in which a gene is mounted on a bead via strong non-covalent (streptavidin/biotin) interactions and the corresponding protein is displayed via a covalent thioether bond on the DNA. In contrast to previous monovalent or low-copy bead display systems, multiple copies of the DNA and the protein or peptide of interest are displayed in defined quantities (up to 10(6) of each), so that flow cytometry can be used to obtain a measure of binding affinity. The utility of the BeSD in directed evolution is validated by library selections of randomized peptide sequences for binding to the anti-hemagglutinin (HA) antibody that proceed with enrichments in excess of 10(3) and lead to the isolation of high-affinity HA-tags within one round of flow cytometric screening. On-bead K(d) measurements suggest that the selected tags have affinities in the low nanomolar range. In contrast to other display systems (such as ribosome, mRNA and phage display) that are limited to affinity panning selections, BeSD possesses the ability to screen and rank binders by their affinity in vitro, a feature that hitherto has been exclusive to in vivo multivalent cell display systems (such as yeast display).
Collapse
Affiliation(s)
| | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| |
Collapse
|
61
|
Pham TK, Yoo J, Kim YW. Comparison of Oct-2-enyl and Oct-4-enyl Staples for Their Formation and α-Helix Stabilizing Effects. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.9.2640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
62
|
Truncated and helix-constrained peptides with high affinity and specificity for the cFos coiled-coil of AP-1. PLoS One 2013; 8:e59415. [PMID: 23544065 PMCID: PMC3609778 DOI: 10.1371/journal.pone.0059415] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/14/2013] [Indexed: 01/20/2023] Open
Abstract
Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i→i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, α-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable α-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ∼9 kcal/mol, but this was compensated by increased conformational entropy (TΔS ≤7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by α-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases.
Collapse
|
63
|
Hurevich M, Ratner-Hurevich M, Tal-Gan Y, Shalev DE, Ben-Sasson SZ, Gilon C. Backbone cyclic helix mimetic of chemokine (C-C motif) receptor 2: a rational approach for inhibiting dimerization of G protein-coupled receptors. Bioorg Med Chem 2013; 21:3958-66. [PMID: 23706536 DOI: 10.1016/j.bmc.2013.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
Abstract
The transmembrane helical bundle of G protein-coupled receptors (GPCRs) dimerize through helix-helix interactions in response to inflammatory stimulation. A strategy was developed to target the helical dimerization site of GPCRs by peptidomimetics with drug like properties. The concept was demonstrated by selecting a potent backbone cyclic helix mimetic from a library that derived from the dimerization region of chemokine (C-C motif) receptor 2 (CCR2) that is a key player in Multiple Sclerosis. We showed that CCR2 based backbone cyclic peptide having a stable helix structure inhibits specific CCR2-mediated chemotactic migration.
Collapse
Affiliation(s)
- Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | | | | | | | | | | |
Collapse
|
64
|
Bock JE, Gavenonis J, Kritzer JA. Getting in shape: controlling peptide bioactivity and bioavailability using conformational constraints. ACS Chem Biol 2013; 8:488-499. [PMID: 23170954 PMCID: PMC4847942 DOI: 10.1021/cb300515u] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chemical biologists commonly seek out correlations between the physicochemical properties of molecules and their behavior in biological systems. However, a new paradigm is emerging for peptides in which conformation is recognized as the primary determinant of bioactivity and bioavailability. This review highlights an emerging body of work that directly addresses how a peptide's conformation controls its biological effects, cell penetration, and intestinal absorption. Based on this work, the dream of mimicking the potency and bioavailability of natural product peptides is getting closer to reality.
Collapse
Affiliation(s)
- Jonathan E. Bock
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jason Gavenonis
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| |
Collapse
|
65
|
Nakamura Y, Nakazawa K, Hamasaki K. Host–Guest-bridge Induces Irreversible Helix Folding in a Short Peptide. CHEM LETT 2012. [DOI: 10.1246/cl.2012.908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuki Nakamura
- Department of Applied Chemistry, Shibaura Institute of Technology
| | - Kazuya Nakazawa
- Department of Applied Chemistry, Shibaura Institute of Technology
| | - Keita Hamasaki
- Department of Applied Chemistry, Shibaura Institute of Technology
| |
Collapse
|
66
|
Beharry AA, Chen T, Al-Abdul-Wahid MS, Samanta S, Davidov K, Sadovski O, Ali AM, Chen SB, Prosser RS, Chan HS, Woolley GA. Quantitative analysis of the effects of photoswitchable distance constraints on the structure of a globular protein. Biochemistry 2012; 51:6421-31. [PMID: 22803618 DOI: 10.1021/bi300685a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoswitchable distance constraints in the form of photoisomerizable chemical cross-links offer a general approach to the design of reversibly photocontrolled proteins. To apply these effectively, however, one must have guidelines for the choice of cross-linker structure and cross-linker attachment sites. Here we investigate the effects of varying cross-linker structure on the photocontrol of folding of the Fyn SH3 domain, a well-studied model protein. We develop a theoretical framework based on an explicit-chain model of protein folding, modified to include detailed model linkers, that allows prediction of the effect of a given linker on the free energy of folding of a protein. Using this framework, we were able to quantitatively explain the experimental result that a longer, but somewhat flexible, cross-linker is less destabilizing to the folded state than a shorter more rigid cross-linker. The models also suggest how misfolded states may be generated by cross-linking, providing a rationale for altered dynamics seen in nuclear magnetic resonance analyses of these proteins. The theoretical framework is readily portable to any protein of known folded state structure and thus can be used to guide the design of photoswitchable proteins generally.
Collapse
Affiliation(s)
- Andrew A Beharry
- Department of Chemistry, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
67
|
Chapuis H, Slaninová J, Bednárová L, Monincová L, Buděšínský M, Čeřovský V. Effect of hydrocarbon stapling on the properties of α-helical antimicrobial peptides isolated from the venom of hymenoptera. Amino Acids 2012; 43:2047-58. [DOI: 10.1007/s00726-012-1283-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
|
68
|
Molecular cloning and characterization of a novel RING zinc-finger protein gene up-regulated under in vitro salt stress in cassava. Mol Biol Rep 2012; 39:6513-9. [PMID: 22307786 DOI: 10.1007/s11033-012-1479-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 01/24/2012] [Indexed: 01/14/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the world's most important food crops. It is cultivated mainly in developing countries of tropics, since its root is a major source of calories for low-income people due to its high productivity and resistance to many abiotic and biotic factors. A previous study has identified a partial cDNA sequence coding for a putative RING zinc finger in cassava storage root. The RING zinc finger protein is a specialized type of zinc finger protein found in many organisms. Here, we isolated the full-length cDNA sequence coding for M. esculenta RZF (MeRZF) protein by a combination of 5' and 3' RACE assays. BLAST analysis showed that its deduced amino acid sequence has a high level of similarity to plant proteins of RZF family. MeRZF protein contains a signature sequence motif for a RING zinc finger at its C-terminal region. In addition, this protein showed a histidine residue at the fifth coordination site, likely belonging to the RING-H2 subgroup, as confirmed by our phylogenetic analysis. There is also a transmembrane domain in its N-terminal region. Finally, semi-quantitative RT-PCR assays showed that MeRZF expression is increased in detached leaves treated with sodium chloride. Here, we report the first evidence of a RING zinc finger gene of cassava showing potential role in response to salt stress.
Collapse
|
69
|
Langlois C, Del Gatto A, Arseneault G, Lafrance-Vanasse J, De Simone M, Morse T, de Paola I, Lussier-Price M, Legault P, Pedone C, Zaccaro L, Omichinski JG. Structure-based design of a potent artificial transactivation domain based on p53. J Am Chem Soc 2012; 134:1715-23. [PMID: 22191432 DOI: 10.1021/ja208999e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Malfunctions in transcriptional regulation are associated with a number of critical human diseases. As a result, there is considerable interest in designing artificial transcription activators (ATAs) that specifically control genes linked to human diseases. Like native transcriptional activator proteins, an ATA must minimally contain a DNA-binding domain (DBD) and a transactivation domain (TAD) and, although there are several reliable methods for designing artificial DBDs, designing artificial TADs has proven difficult. In this manuscript, we present a structure-based strategy for designing short peptides containing natural amino acids that function as artificial TADs. Using a segment of the TAD of p53 as the scaffolding, modifications are introduced to increase the helical propensity of the peptides. The most active artificial TAD, termed E-Cap-(LL), is a 13-mer peptide that contains four key residues from p53, an N-capping motif and a dileucine hydrophobic bridge. In vitro analysis demonstrates that E-Cap-(LL) interacts with several known p53 target proteins, while in vivo studies in a yeast model system show that it is a 20-fold more potent transcriptional activator than the native p53-13 peptide. These results demonstrate that structure-based design represents a promising approach for developing artificial TADs that can be combined with artificial DBDs to create potent and specific ATAs.
Collapse
Affiliation(s)
- Chantal Langlois
- Département de Biochimie, Université de Montréal, C.P. 6128 Succursale, Centre-Ville, Montréal, Quebec H3C 3J7, Canada
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
70
|
Bhattacharya S, Zhang H, Cowburn D, Debnath AK. Novel structures of self-associating stapled peptides. Biopolymers 2011; 97:253-64. [PMID: 22170623 DOI: 10.1002/bip.22015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 11/11/2022]
Abstract
Hydrocarbon stapling of peptides is a powerful technique to transform linear peptides into cell-permeable helical structures that can bind to specific biological targets. In this study, we have used high resolution solution NMR techniques complemented by dynamic light scattering to characterize extensively a family of hydrocarbon stapled peptides with known inhibitory activity against HIV-1 capsid assembly to evaluate the various factors that modulate activity. The helical peptides share a common binding motif but differ in charge, the length, and position of the staple. An important outcome of the study was to show the peptides, share a propensity to self-associate into organized polymeric structures mediated predominantly by hydrophobic interactions between the olefinic chain and the aromatic side-chains from the peptide. We have also investigated in detail the structural significance of the length and position of the staple, and of olefinic bond isomerization in stabilizing the helical conformation of the peptides as potential factors driving polymerization. This study presents the numerous challenges of designing biologically active stapled peptides and the conclusions have broad implications for optimizing a promising new class of compounds in drug discovery.
Collapse
|
71
|
Baek S, Kutchukian PS, Verdine GL, Huber R, Holak TA, Lee KW, Popowicz GM. Structure of the stapled p53 peptide bound to Mdm2. J Am Chem Soc 2011; 134:103-6. [PMID: 22148351 DOI: 10.1021/ja2090367] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Mdm2 is a major negative regulator of the tumor suppressor p53 protein, a protein that plays a crucial role in maintaining genome integrity. Inactivation of p53 is the most prevalent defect in human cancers. Inhibitors of the Mdm2-p53 interaction that restore the functional p53 constitute potential nongenotoxic anticancer agents with a novel mode of action. We present here a 2.0 Å resolution structure of the Mdm2 protein with a bound stapled p53 peptide. Such peptides, which are conformationally and proteolytically stabilized with all-hydrocarbon staples, are an emerging class of biologics that are capable of disrupting protein-protein interactions and thus have broad therapeutic potential. The structure represents the first crystal structure of an i, i + 7 stapled peptide bound to its target and reveals that rather than acting solely as a passive conformational brace, a staple can intimately interact with the surface of a protein and augment the binding interface.
Collapse
Affiliation(s)
- Sohee Baek
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | | | | | | | | | | |
Collapse
|
72
|
Hoang HN, Driver RW, Beyer RL, Malde AK, Le GT, Abbenante G, Mark AE, Fairlie DP. Protein α-Turns Recreated in Structurally Stable Small Molecules. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
73
|
Hoang HN, Driver RW, Beyer RL, Malde AK, Le GT, Abbenante G, Mark AE, Fairlie DP. Protein α-Turns Recreated in Structurally Stable Small Molecules. Angew Chem Int Ed Engl 2011; 50:11107-11. [DOI: 10.1002/anie.201105119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Indexed: 11/08/2022]
|
74
|
Núñez-Villanueva D, Bonache MÁ, Infantes L, García-López MT, Martín-Martínez M, González-Muñiz R. Quaternary α,α-2-Oxoazepane α-Amino Acids: Synthesis from Ornithine-Derived β-Lactams and Incorporation into Model Dipeptides. J Org Chem 2011; 76:6592-603. [DOI: 10.1021/jo200894d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - M. Ángeles Bonache
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
| | | | | | | |
Collapse
|
75
|
Liskamp RMJ, Rijkers DTS, Kruijtzer JAW, Kemmink J. Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics. Chembiochem 2011; 12:1626-53. [PMID: 21751324 DOI: 10.1002/cbic.201000717] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Indexed: 12/17/2022]
Abstract
Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.
Collapse
Affiliation(s)
- Rob M J Liskamp
- Medicinal Chemistry and Chemical Biology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
| | | | | | | |
Collapse
|
76
|
Sviridov DO, Ikpot IZ, Stonik J, Drake SK, Amar M, Osei-Hwedieh DO, Piszczek G, Turner S, Remaley AT. Helix stabilization of amphipathic peptides by hydrocarbon stapling increases cholesterol efflux by the ABCA1 transporter. Biochem Biophys Res Commun 2011; 410:446-51. [PMID: 21672528 DOI: 10.1016/j.bbrc.2011.05.154] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
Abstract
Apolipoprotein mimetic peptides are short amphipathic peptides that efflux cholesterol from cells by the ABCA1 transporter and are being investigated as therapeutic agents for cardiovascular disease. We examined the role of helix stabilization of these peptides in cholesterol efflux. A 23-amino acid long peptide (Ac-VLEDSFKVSFLSALEEYTKKLNTQ-NH2) based on the last helix of apoA-I (A10) was synthesized, as well as two variants, S1A10 and S2A10, in which the third and fourth and third and fifth turn of each peptide, respectively, were covalently joined by hydrocarbon staples. By CD spectroscopy, the stapled variants at 24 °C were more helical in aqueous buffer than A10 (A10 17%, S1A10 62%, S2A10 97%). S1A10 and S2A10 unlike A10 were resistant to proteolysis by pepsin and chymotrypsin. S1A10 and S2A10 showed more than a 10-fold increase in cholesterol efflux by the ABCA1 transporter compared to A10. In summary, hydrocarbon stapling of amphipathic peptides increases their helicity, makes them resistant to proteolysis and enhances their ability to promote cholesterol efflux by the ABCA1 transporter, indicating that this peptide modification may be useful in the development of apolipoprotein mimetic peptides.
Collapse
Affiliation(s)
- D O Sviridov
- Lipoprotein Metabolism Section, Cardiopulmonary Branch, NHLBI, National Institutes of Health, Bethesda, MD 20892-1508, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
77
|
Wender PA, Loy BA, Schrier AJ. Translating Nature's Library: The Bryostatins and Function-Oriented Synthesis. Isr J Chem 2011; 51:453-472. [PMID: 22661768 PMCID: PMC3364006 DOI: 10.1002/ijch.201100020] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We review in part our computational, design, synthesis, and biological studies on a remarkable class of compounds and their designed analogs that have led to preclinical candidates for the treatment of cancer, a first-in-class approach to Alzheimer's disease, and a promising strategy to eradicate HIV/AIDS. Because these leads target, in part, protein kinase C (PKC) isozymes, they have therapeutic potential even beyond this striking set of therapeutic indications. This program has given rise to new synthetic methodology and represents an increasingly important direction of synthesis focused on achieving function through synthesis-informed design (function-oriented synthesis).
Collapse
Affiliation(s)
- Paul A. Wender
- Department of Chemistry Department of Chemical and Systems Biology Stanford University Stanford, CA 94305, USA
| | - Brian A. Loy
- Department of Chemistry Department of Chemical and Systems Biology Stanford University Stanford, CA 94305, USA
| | - Adam J. Schrier
- Department of Chemistry Department of Chemical and Systems Biology Stanford University Stanford, CA 94305, USA
| |
Collapse
|
78
|
Moretto A, Crisma M, Formaggio F, Toniolo C. Building a bridge between peptide chemistry and organic chemistry: intramolecular macrocyclization reactions and supramolecular chemistry with helical peptide substrates. Biopolymers 2011; 94:721-32. [PMID: 20564031 DOI: 10.1002/bip.21445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In our ongoing efforts to build a bridge between peptide chemistry and organic chemistry, we are currently investigating: (1) two types of intramolecular macrocyclization reactions in 3(10)-helical peptides, and (2) a peptido[2]rotaxane molecular machine as a supramolecular tool using a 3(10)-helical peptide as the axle. More specifically, we studied the following two reactions: (a) the intramolecular ring-closing olefin metathesis between two amino acid residues with side chains bearing an allyl group, and (b) the intramolecular Paternò-Yang photoreaction, using a benzophenone-based amino acid as a photoaffinity reagent for a Met residue. Both reactions involve formation of a new C--C bond. As for the supramolecular system examined, we were able to identify the two stations of a new peptido[2]rotaxane characterized by an -(Aib)(6)- axle and to reversibly switch the aromatic tetramide macrocyclic wheel from one station to the next. This article summarizes the information available in the literature from other groups and the published/unpublished data originated from our laboratory on these research areas.
Collapse
Affiliation(s)
- Alessandro Moretto
- Department of Chemistry, Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
| | | | | | | |
Collapse
|
79
|
Xu J, Huang L, Shakhnovich EI. The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins 2011; 79:1704-14. [PMID: 21365688 DOI: 10.1002/prot.22993] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/10/2010] [Accepted: 01/04/2011] [Indexed: 11/10/2022]
Abstract
In this work, we apply a detailed all-atom model with a transferable knowledge-based potential to study the folding kinetics of Formin-Binding protein, FBP28, which is a canonical three-stranded β-sheet WW domain. Replica exchange Monte Carlo simulations starting from random coils find native-like (Cα RMSD of 2.68 Å) lowest energy structure. We also study the folding kinetics of FBP28 WW domain by performing a large number of ab initio Monte Carlo folding simulations. Using these trajectories, we examine the order of formation of two β-hairpins, the folding mechanism of each individual β-hairpin, and transition state ensemble (TSE) of FBP28 WW domain and compare our results with experimental data and previous computational studies. To obtain detailed structural information on the folding dynamics viewed as an ensemble process, we perform a clustering analysis procedure based on graph theory. Further, a rigorous P(fold) analysis is used to obtain representative samples of the TSEs showing good quantitative agreement between experimental and simulated Φ values. Our analysis shows that the turn structure between first and second β strands is a partially stable structural motif that gets formed before entering the TSE in FBP28 WW domain and there exist two major pathways for the folding of FBP28 WW domain, which differ in the order and mechanism of hairpin formation.
Collapse
Affiliation(s)
- Jiabin Xu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | | | | |
Collapse
|
80
|
Abstract
Heart failure is an important cause of morbidity and mortality in individuals of all ages. The many-faceted nature of the clinical heart failure syndrome has historically frustrated attempts to develop an overarching explanative theory. However, much useful information has been gained by basic and clinical investigation, even though a comprehensive understanding of heart failure has been elusive. Heart failure is a growing problem, in both adult and pediatric populations, for which standard medical therapy, as of 2010, can have positive effects, but these are usually limited and progressively diminish with time in most patients. If we want curative or near-curative therapy that will return patients to a normal state of health at a feasible cost, much better diagnostic and therapeutic technologies need to be developed. This review addresses the vexing group of heart failure etiologies that include cardiomyopathies and other ventricular dysfunctions of various types, for which current therapy is only modestly effective. Although there are many unique aspects to heart failure in patients with pediatric and congenital heart disease, many of the innovative approaches that are being developed for the care of adults with heart failure will be applicable to heart failure in childhood.
Collapse
Affiliation(s)
- Daniel J Penny
- Section of Pediatric Cardiology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | | |
Collapse
|
81
|
Liu F, Giubellino A, Simister PC, Qian W, Giano MC, Feller SM, Bottaro DP, Burke TR. Application of ring-closing metathesis to Grb2 SH3 domain-binding peptides. Biopolymers 2011; 96:780-8. [PMID: 21830199 PMCID: PMC3402909 DOI: 10.1002/bip.21692] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular processes depending on protein–protein interactions can use consensus recognition sequences that possess defined secondary structures. Left-handed polyproline II (PPII) helices are a class of secondary structure commonly involved with cellular signal transduction. However, unlike -helices, for which a substantial body of work exists regarding applications of ring-closing metathesis (RCM), there are few reports on the stabilization of PPII helices by RCM methodologies. The current study examined the effects of RCM macrocyclization on left-handed PPII helices involved with the SH3 domain-mediated binding of Sos1–Grb2. Starting with the Sos1-derived peptide “Ac-V1-P2-P3-P4-V5-P6-P7-R8-R9-R10-amide,” RCM macrocyclizations were conducted using alkenyl chains of varying lengths originating from the pyrrolidine rings of the Pro4 and Pro7 residues. The resulting macrocyclic peptides showed increased helicity as indicated by circular dichroism and enhanced abilities to block Grb2–Sos1 interactions in cell lysate pull-down assays. The synthetic approach may be useful in RCM macrocyclizations, where maintenance of proline integrity at both ring junctures is desired.
Collapse
Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Alessio Giubellino
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Philip C. Simister
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Wenjian Qian
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Michael C. Giano
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| | - Stephan M. Feller
- Cell Signalling Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Donald P. Bottaro
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20989
| | - Terrence R. Burke
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702
| |
Collapse
|
82
|
Masica DL, Schrier SB, Specht EA, Gray JJ. De novo design of peptide-calcite biomineralization systems. J Am Chem Soc 2010; 132:12252-62. [PMID: 20712308 DOI: 10.1021/ja1001086] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Many organisms produce complex, hierarchically structured, inorganic materials via protein-influenced crystal growth--a process known as biomineralization. Understanding this process would shed light on hard-tissue formation and guide efforts to develop biomaterials. We created and tested a computational method to design protein-biomineralization systems. The algorithm folds a protein from a fully extended structure and simultaneously optimizes the fold, orientation, and sequence of the protein adsorbed to a crystal surface. We used the algorithm to design peptides (16 residues) to modify calcite (CaCO(3)) crystallization. We chemically synthesized six peptides that were predicted to bind different states of a calcite growth plane. All six peptides dramatically affected calcite crystal growth (as observed by scanning electron microscopy), and the effects were dependent on the targeted state of the {001} growth plane. Additionally, we synthesized and assayed scrambled variants of all six designed peptides to distinguish cases where sequence composition determines the interactions versus cases where sequence order (and presumably structure) plays a role. Scrambled variants of negatively charged peptides also had dramatic effects on calcite crystallization; in contrast, scrambled variants of positively charged peptides had a variable effect on crystallization, ranging from dramatic to mild. Special emphasis is often placed on acidic protein residues in calcified tissue mineralization; the work presented here suggests an important role for basic residues as well. In particular, this work implicates a potential role for basic residues in sequence-order specificity for peptide-mineral interactions.
Collapse
Affiliation(s)
- David L Masica
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | | | | | |
Collapse
|
83
|
Fernández-Reyes M, Díaz D, de la Torre BG, Cabrales-Rico A, Vallès-Miret M, Jiménez-Barbero J, Andreu D, Rivas L. Lysine N(epsilon)-trimethylation, a tool for improving the selectivity of antimicrobial peptides. J Med Chem 2010; 53:5587-96. [PMID: 20617807 DOI: 10.1021/jm100261r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The effects of lysine N(epsilon)-trimethylation at selected positions of the antimicrobial cecropin A-melittin hybrid peptide KWKLFKKIGAVLKVL-amide have been studied. All five monotrimethylated, four bis-trimethylated plus the per-trimethylated analogues have been synthesized and tested for antimicrobial activity on Leishmania parasites and on Gram-positive and -negative bacteria, as well as for hemolysis of sheep erythrocytes as a measure of cytotoxicity. The impact of trimethylation on the solution conformation of selected analogues has been evaluated by NMR, which indicates a slight decrease in the alpha-helical content of the modified peptides, particularly in the N-terminal region. Trimethylation also enhances the proteolytic stability of mono- and bis-trimethylated analogues by 2-3-fold. Although it tends to lower antimicrobial activity in absolute terms, trimethylation causes an even higher decrease in hemolytic activity and therefore results in improved selectivity for several analogues. The monotrimethylated analogue at position 6 shows the overall best selectivity against both the Leishmania donovani protozoan and Acinetobacter baumannii, a Gram-negative bacterium of increasing clinical concern.
Collapse
|
84
|
Hydrocarbon double-stapling remedies the proteolytic instability of a lengthy peptide therapeutic. Proc Natl Acad Sci U S A 2010; 107:14093-8. [PMID: 20660316 DOI: 10.1073/pnas.1002713107] [Citation(s) in RCA: 253] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The pharmacologic utility of lengthy peptides can be hindered by loss of bioactive structure and rapid proteolysis, which limits bioavailability. For example, enfuvirtide (Fuzeon, T20, DP178), a 36-amino acid peptide that inhibits human immunodeficiency virus type 1 (HIV-1) infection by effectively targeting the viral fusion apparatus, has been relegated to a salvage treatment option mostly due to poor in vivo stability and lack of oral bioavailability. To overcome the proteolytic shortcomings of long peptides as therapeutics, we examined the biophysical, biological, and pharmacologic impact of inserting all-hydrocarbon staples into an HIV-1 fusion inhibitor. We find that peptide double-stapling confers striking protease resistance that translates into markedly improved pharmacokinetic properties, including oral absorption. We determined that the hydrocarbon staples create a proteolytic shield by combining reinforcement of overall alpha-helical structure, which slows the kinetics of proteolysis, with complete blockade of peptide cleavage at constrained sites in the immediate vicinity of the staple. Importantly, double-stapling also optimizes the antiviral activity of HIV-1 fusion peptides and the antiproteolytic feature extends to other therapeutic peptide templates, such as the diabetes drug exenatide (Byetta). Thus, hydrocarbon double-stapling may unlock the therapeutic potential of natural bioactive polypeptides by transforming them into structurally fortified agents with enhanced bioavailability.
Collapse
|
85
|
Bautista AD, Appelbaum JS, Craig CJ, Michel J, Schepartz A. Bridged beta(3)-peptide inhibitors of p53-hDM2 complexation: correlation between affinity and cell permeability. J Am Chem Soc 2010; 132:2904-6. [PMID: 20158215 DOI: 10.1021/ja910715u] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Beta-peptides possess several features that are desirable in peptidomimetics; they are easily synthesized, fold into stable secondary structures in physiologic buffers, and resist proteolysis. They can also bind to a diverse array of proteins to inhibit their interactions with alpha-helical ligands. beta-peptides are usually not cell-permeable, however, and this feature limits their utility as research tools and potential therapeutics. Appending an Arg(8) sequence to a beta-peptide improves uptake but adds considerable mass. We previously reported that embedding a small cationic patch within a PPII, alpha-, or beta-peptide helix improves uptake without the addition of significant mass. In another mass-neutral strategy, Verdine, Walensky, and others have reported that insertion of a hydrocarbon bridge between the i and i + 4 positions of an alpha-helix also increases cell uptake. Here we describe a series of beta-peptides containing diether and hydrocarbon bridges and compare them on the basis of cell uptake and localization, affinities for hDM2, and 14-helix structure. Our results highlight the relative merits of the cationic-patch and hydrophobic-bridge strategies for improving beta-peptide uptake and identify a surprising correlation between uptake efficiency and hDM2 affinity.
Collapse
Affiliation(s)
- Arjel D Bautista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
| | | | | | | | | |
Collapse
|
86
|
Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure. Chemistry 2010; 16:6651-9. [DOI: 10.1002/chem.200903092] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
87
|
Guo Z, Mohanty U, Noehre J, Sawyer TK, Sherman W, Krilov G. Probing theα-Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis. Chem Biol Drug Des 2010; 75:348-59. [DOI: 10.1111/j.1747-0285.2010.00951.x] [Citation(s) in RCA: 317] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
88
|
Hyun S, Na J, Lee SJ, Park S, Yu J. RNA Grooves Can Accommodate Disulfide-Bridged Bundles of α-Helical Peptides. Chembiochem 2010; 11:767-70. [DOI: 10.1002/cbic.201000072] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
89
|
Missirlis D, Farine M, Kastantin M, Ananthanarayanan B, Neumann T, Tirrell M. Linker Chemistry Determines Secondary Structure of p5314−29 in Peptide Amphiphile Micelles. Bioconjug Chem 2010; 21:465-75. [DOI: 10.1021/bc900383m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Dimitris Missirlis
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| | - Marc Farine
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| | - Mark Kastantin
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| | - Badriprasad Ananthanarayanan
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| | - Thorsten Neumann
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| | - Matthew Tirrell
- Department of Chemical Engineering and Materials and Materials Research Laboratory, University of California, Santa Barbara, California 93106, and Department of Bioengineering, University of California, Berkeley, California, 94720
| |
Collapse
|
90
|
Mavinahalli JN, Madhumalar A, Beuerman RW, Lane DP, Verma C. Differences in the transactivation domains of p53 family members: a computational study. BMC Genomics 2010; 11 Suppl 1:S5. [PMID: 20158876 PMCID: PMC2822533 DOI: 10.1186/1471-2164-11-s1-s5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The N terminal transactivation domain of p53 is regulated by ligases and coactivator proteins. The functional conformation of this region appears to be an alpha helix which is necessary for its appropriate interactions with several proteins including MDM2 and p300. Folding simulation studies have been carried out to examine the propensity and stability of this region and are used to understand the differences between the family members with the ease of helix formation following the order p53 > p73 > p63. It is clear that hydrophobic clusters control the kinetics of helix formation, while electrostatic interactions control the thermodynamic stability of the helix. Differences in these interactions between the family members may partially account for the differential binding to, and regulation by, MDM2 (and MDMX). Phosphorylations of the peptides further modulate the stability of the helix and control associations with partner proteins.
Collapse
|
91
|
Pérez de Vega MJ, García-Aranda MI, González-Muñiz R. A role for ring-closing metathesis in medicinal chemistry: Mimicking secondary architectures in bioactive peptides. Med Res Rev 2010; 31:677-715. [DOI: 10.1002/med.20199] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
92
|
Liu F, Stephen AG, Waheed AA, Freed EO, Fisher RJ, Burke TR. Application of ring-closing metathesis macrocyclization to the development of Tsg101-binding antagonists. Bioorg Med Chem Lett 2010; 20:318-21. [PMID: 19914066 PMCID: PMC2818493 DOI: 10.1016/j.bmcl.2009.10.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/23/2009] [Accepted: 10/26/2009] [Indexed: 11/18/2022]
Abstract
HIV-1 viral budding involves binding of the viral Gag(p6) protein to the ubiquitin E2 variant domain of the human tumor susceptibility gene 101 protein (Tsg101). Recognition of p6 by Tsg101 is mediated in part by a proline-rich motif that contains the sequence 'Pro-Thr-Ala-Pro' ('PTAP'). Using the p6-derived 9-mer sequence 'PEPTAPPEE', we had previously improved peptide binding affinity by employing N-alkylglycine ('peptoid') residues. The current study applies ring-closing metathesis macrocyclization strategies to Tsg101-binding peptide-peptoid hybrids as an approach to stabilize binding conformations and to observe the effects of such macrocyclization on Tsg101-binding affinity and bioavailability.
Collapse
Affiliation(s)
- Fa Liu
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Andrew G. Stephen
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc. NCI-Frederick, Frederick, MD 21702
| | - Abdul A. Waheed
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Eric O. Freed
- HIV Drug Resistance Program, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| | - Robert J. Fisher
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc. NCI-Frederick, Frederick, MD 21702
| | - Terrence R. Burke
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute-Frederick, National Institutes of Health Frederick, MD 21702
| |
Collapse
|