1
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Cugudda A, La Manna S, Marasco D. Are peptidomimetics the compounds of choice for developing new modulators of the JAK-STAT pathway? Front Immunol 2024; 15:1406886. [PMID: 38983855 PMCID: PMC11232365 DOI: 10.3389/fimmu.2024.1406886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
Protein-protein interactions (PPIs) play critical roles in a wide range of biological processes including the dysregulation of cellular pathways leading to the loss of cell function, which in turn leads to diseases. The dysfunction of several signaling pathways is linked to the insurgence of pathological processes such as inflammation, cancer development and neurodegeneration. Thus, there is an urgent need for novel chemical modulators of dysregulated PPIs to drive progress in targeted therapies. Several PPIs have been targeted by bioactive compounds, and, often, to properly cover interacting protein regions and improve the biological activities of modulators, a particular focus concerns the employment of macrocycles as proteomimetics. Indeed, for their physicochemical properties, they occupy an intermediate space between small organic molecules and macromolecular proteins and are prominent in the drug discovery process. Peptide macrocycles can modulate fundamental biological mechanisms and here we will focus on peptidomimetics active on the Janus kinase/signal transducers and activators of transcription (JAK-STAT) pathways.
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Affiliation(s)
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
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2
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Lin Y, Horne WS. Backbone Modification in a Protein Hydrophobic Core. Chemistry 2024:e202401890. [PMID: 38753977 DOI: 10.1002/chem.202401890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 05/16/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Targeted protein backbone modification can recreate tertiary structures reminiscent of folds found in nature on artificial scaffolds with improved biostability. Incorporation of altered monomers in such entities is typically limited to sites distant from the hydrophobic core to avoid potential disruptions to folding. This is limiting, as it is advantageous in some applications to incorporate artificial connectivity at buried sites. Here, we report an examination of protein backbone modification targeted specifically to hydrophobic core positions and its impacts on tertiary folded structure and fold stability. Different artificial monomer types are placed at core, core-flanking, or solvent-exposed positions in a compact three-helix protein. Effects on structure and folding energetics are assessed by NMR spectroscopy and biophysical methods. Results show that artificial residues can be well accommodated in the hydrophobic core of a defined tertiary fold, with effects on stability only modestly larger than identical changes at solvent-exposed sites. Collectively, these results provide new insights into folding behavior of protein-like artificial chains as well as strategies for the design of such molecules.
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Affiliation(s)
- Yuhan Lin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
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3
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Angera IJ, Wright MM, Del Valle JR. Beyond N-Alkylation: Synthesis, Structure, and Function of N-Amino Peptides. Acc Chem Res 2024; 57:1287-1297. [PMID: 38626119 DOI: 10.1021/acs.accounts.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The growing list of physiologically important protein-protein interactions (PPIs) has amplified the need for compounds to target topologically complex biomolecular surfaces. In contrast to small molecules, peptide and protein mimics can exhibit three-dimensional shape complementarity across a large area and thus have the potential to significantly expand the "druggable" proteome. Strategies to stabilize canonical protein secondary structures without sacrificing side-chain content are particularly useful in the design of peptide-based chemical probes and therapeutics.Substitution of the backbone amide in peptides represents a subtle chemical modification with profound effects on conformation and stability. Studies focused on N-alkylation have already led to broad-ranging applications in peptidomimetic design. Inspired by nonribosomal peptide natural products harboring amide N-oxidations, we envisioned that main-chain hydrazide and hydroxamate bonds would impose distinct conformational preferences and offer unique opportunities for backbone diversification. This Account describes our exploration of peptide N-amination as a strategy for stabilizing canonical protein folds and for the structure-based design of soluble amyloid mimics.We developed a general synthetic protocol to access N-amino peptides (NAPs) on solid support. In an effort to stabilize β-strand conformation, we designed stitched peptidomimetics featuring covalent tethering of the backbone N-amino substituent to the preceding residue side chain. Using a combination of NMR, X-ray crystallography, and molecular dynamics simulations, we discovered that backbone N-amination alone could significantly stabilize β-hairpin conformation in multiple models of folding. Our studies revealed that the amide NH2 substituent in NAPs participates in cooperative noncovalent interactions that promote β-sheet secondary structure. In contrast to Cα-substituted α-hydrazino acids, we found that N-aminoglycine and its N'-alkylated derivatives instead stabilize polyproline II (PPII) conformation. The reactivity of hydrazides also allows for late-stage peptide macrocyclization, affording novel covalent surrogates of side-chain-backbone H-bonds.The pronounced β-sheet propensity of Cα-substituted α-hydrazino acids prompted us to target amyloidogenic proteins using NAP-based β-strand mimics. Backbone N-amination was found to render aggregation-prone lead sequences soluble and resistant to proteolysis. Inhibitors of Aβ and tau identified through N-amino scanning blocked protein aggregation and the formation of mature fibrils in vitro. We further identified NAP-based single-strand and cross-β tau mimics capable of inhibiting the prion-like cellular seeding activity of recombinant and patient-derived tau fibrils.Our studies establish backbone N-amination as a valuable addition to the peptido- and proteomimetic tool kit. α-Hydrazino acids show particular promise as minimalist β-strand mimics that retain side-chain information. Late-stage derivatization of hydrazides also provides facile entry into libraries of backbone-edited peptides. We anticipate that NAPs will thus find applications in the development of optimally constrained folds and modulators of PPIs.
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Affiliation(s)
- Isaac J Angera
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Durukan C, Arbore F, Klintrot R, Bigiotti C, Ilie IM, Vreede J, Grossmann TN, Hennig S. Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y. Chembiochem 2024; 25:e202400020. [PMID: 38470946 DOI: 10.1002/cbic.202400020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Transcription factors (TFs) play a central role in gene regulation, and their malfunction can result in a plethora of severe diseases. TFs are therefore interesting therapeutic targets, but their involvement in protein-protein interaction networks and the frequent lack of well-defined binding pockets render them challenging targets for classical small molecules. As an alternative, peptide-based scaffolds have proven useful, in particular with an α-helical active conformation. Peptide-based strategies often require extensive structural optimization efforts, which could benefit from a more detailed understanding of the dynamics in inhibitor/protein interactions. In this study, we investigate how truncated stapled α-helical peptides interact with the transcription factor Nuclear Factor-Y (NF-Y). We identified a 13-mer minimal binding core region, for which two crystal structures with an altered C-terminal peptide conformation when bound to NF-Y were obtained. Subsequent molecular dynamics simulations confirmed that the C-terminal part of the stapled peptide is indeed relatively flexible while still showing defined interactions with NF-Y. Our findings highlight the importance of flexibility in the bound state of peptides, which can contribute to overall binding affinity.
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Affiliation(s)
- Canan Durukan
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Federica Arbore
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Rasmus Klintrot
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Carlo Bigiotti
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Ioana M Ilie
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Jocelyne Vreede
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
- Amsterdam Center for Multiscale Modeling (ACMM), University of Amsterdam, P.O. Box, 94157, 1090 GD, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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5
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Yoo SH, Buratto J, Roy A, Pasco M, Pulka-Ziach K, Collie GW, Guichard G. Oligourea helix bundle binds detergents with diverse polar head groups. Org Biomol Chem 2024; 22:731-734. [PMID: 38169016 DOI: 10.1039/d3ob01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Here we report a series of crystal structures (and accompanying biophysical data) of an array of diverse detergent guests bound to an oligourea foldamer helix bundle. These results significantly increase our structural and chemical understanding of aqueous guest recognition by oligourea foldamers and will aid the design of further functionalised oligourea-based self-assemblies.
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Affiliation(s)
- Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jérémie Buratto
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Arup Roy
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Morgane Pasco
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | | | - Gavin W Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK.
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
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6
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Santhouse JR, Leung JMG, Chong LT, Horne WS. Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein. Chem Sci 2024; 15:675-682. [PMID: 38179541 PMCID: PMC10763558 DOI: 10.1039/d3sc03976e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024] Open
Abstract
Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding. In contrast, little is known about how protein mimetic entities transition between an unfolded and folded state. Here, we report effects of altered backbone connectivity on the folding kinetics and mechanism of the B domain of Staphylococcal protein A (BdpA), an ultrafast-folding sequence. A combination of experimental biophysical analysis and atomistic molecular dynamics simulations performed on the prototype protein and several heterogeneous-backbone variants reveal the interplay among backbone flexibility, folding rates, and structural details of the transition state ensemble. Collectively, these findings suggest a significant degree of plasticity in the mechanisms that can give rise to ultrafast folding in the BdpA sequence and provide atomic level insights into how protein mimetic chains adopt an ordered folded state.
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Affiliation(s)
| | - Jeremy M G Leung
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA
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7
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Sobinoff AP, Di Maro S, Low RRJ, Benedetti R, Tomassi S, D'Aniello A, Russo R, Baglivo I, Chianese U, Pedone PV, Chambery A, Cesare AJ, Altucci L, Pickett HA, Cosconati S. Irreversible inhibition of TRF2 TRFH recruiting functions by a covalent cyclic peptide induces telomeric replication stress in cancer cells. Cell Chem Biol 2023; 30:1652-1665.e6. [PMID: 38065101 DOI: 10.1016/j.chembiol.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
The TRF2 shelterin component is an essential regulator of telomere homeostasis and genomic stability. Mutations in the TRF2TRFH domain physically impair t-loop formation and prevent the recruitment of several factors that promote efficient telomere replication, causing telomeric DNA damage. Here, we design, synthesize, and biologically test covalent cyclic peptides that irreversibly target the TRF2TRFH domain. We identify APOD53 as our most promising compound, as it consistently induces a telomeric DNA damage response in cancer cell lines. APOD53 forms a covalent adduct with a reactive cysteine residue present in the TRF2TRFH domain and induces phenotypes consistent with TRF2TRFH domain mutants. These include induction of a telomeric DNA damage response, increased telomeric replication stress, and impaired recruitment of RTEL1 and SLX4 to telomeres. We demonstrate that APOD53 impairs cancer cell growth and find that co-treatment with APOD53 can exacerbate telomere replication stress caused by the G4 stabilizer RHPS4 and low dose aphidicolin (APH).
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Affiliation(s)
- Alexander P Sobinoff
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Salvatore Di Maro
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ronnie R J Low
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Rosaria Benedetti
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy; Azienda Ospedaliera Universitaria "Luigi Vanvitelli", Medical Epigenetics Program
| | - Stefano Tomassi
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy
| | - Antonia D'Aniello
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Rosita Russo
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ilaria Baglivo
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Ugo Chianese
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Paolo V Pedone
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Angela Chambery
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138 Naples, Italy; BIOGEM, 83031 Ariano Irpino, Italy; Azienda Ospedaliera Universitaria "Luigi Vanvitelli", Medical Epigenetics Program; IEOS CNR, Napoli, Italy
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia.
| | - Sandro Cosconati
- DiSTABiF, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy.
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8
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Ferková S, Froehlich U, Nepveu-Traversy MÉ, Murza A, Azad T, Grandbois M, Sarret P, Lavigne P, Boudreault PL. Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System. Int J Mol Sci 2023; 25:166. [PMID: 38203338 PMCID: PMC10778704 DOI: 10.3390/ijms25010166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Medicinal chemistry is constantly searching for new approaches to develop more effective and targeted therapeutic molecules. The design of peptidomimetics is a promising emerging strategy that is aimed at developing peptides that mimic or modulate the biological activity of proteins. Among these, stapled peptides stand out for their unique ability to stabilize highly frequent helical motifs, but they have failed to be systematically reported. Here, we exploit chemically diverse helix-inducing i, i + 4 constraints-lactam, hydrocarbon, triazole, double triazole and thioether-on two distinct short sequences derived from the N-terminal peptidase domain of hACE2 upon structural characterization and in silico alanine scan. Our overall objective was to provide a sequence-independent comparison of α-helix-inducing staples using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. We identified a 9-mer lactam stapled peptide derived from the hACE2 sequence (His34-Gln42) capable of reaching its maximal helicity of 55% with antiviral activity in bioreporter- and pseudovirus-based inhibition assays. To the best of our knowledge, this study is the first comprehensive investigation comparing several cyclization methods with the goal of generating stapled peptides and correlating their secondary structures with PPI inhibitions using a highly topical model system (i.e., the interaction of SARS-CoV-2 Spike RBD with hACE2).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pierre-Luc Boudreault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada; (S.F.); (M.-É.N.-T.); (A.M.); (T.A.)
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9
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Ito T, Yokoo H, Kato T, Doi M, Demizu Y. Sculpting Secondary Structure of a Cyclic Peptide: Conformational Analysis of a Cyclic Hexapeptide Containing a Combination of l-Leu, d-Leu, and Aib Residues. ACS OMEGA 2023; 8:44106-44111. [PMID: 38027316 PMCID: PMC10666233 DOI: 10.1021/acsomega.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
We have previously reported that cyclo(l-Leu-d-Leu-Aib-l-Leu-d-Leu-Aib) (2), a cyclic hexapeptide consisting of heterochiral l-Leu and d-Leu (l-Leu-d-Leu) residues with achiral 2-aminoisobutyric acid (Aib) residues, forms a figure-8 conformation. In this study, we newly designed cyclo(l-Leu-d-Leu-Aib-d-Leu-l-Leu-Aib)+ (4), an epimer of 2, and examined the conformational differences between 2 and 4 by X-ray crystallographic analysis. Peptide 4 formed a planar cyclic conformation with an antiparallel β-sheet hydrogen-bonding pattern. This investigation demonstrates the potential to manipulate the molecular conformation of cyclic peptides by simply arranging the l- and d-amino acids and emphasizes that diverse conformations can be obtained by using cyclic peptides. Harnessing cyclic peptides as platforms for distinct molecular structures is a promising approach to expanding the chemical space for various applications.
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Affiliation(s)
- Takahito Ito
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Yokohama, Kanagawa 236-0027, Japan
| | - Hidetomo Yokoo
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
| | - Takuma Kato
- Faculty
of Pharmacy, Osaka Medical and Pharmaceutical
University, Takatsuki, Osaka 569-8686, Japan
| | - Mitsunobu Doi
- Faculty
of Pharmacy, Osaka Medical and Pharmaceutical
University, Takatsuki, Osaka 569-8686, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Yokohama, Kanagawa 236-0027, Japan
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10
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Nazzaro A, Lu B, Sawyer N, Watkins AM, Arora PS. Macrocyclic β-Sheets Stabilized by Hydrogen Bond Surrogates. Angew Chem Int Ed Engl 2023; 62:e202303943. [PMID: 37170337 PMCID: PMC10592574 DOI: 10.1002/anie.202303943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/13/2023]
Abstract
Mimics of protein secondary and tertiary structure offer rationally-designed inhibitors of biomolecular interactions. β-Sheet mimics have a storied history in bioorganic chemistry and are typically designed with synthetic or natural turn segments. We hypothesized that replacement of terminal inter-β-strand hydrogen bonds with hydrogen bond surrogates (HBS) may lead to conformationally-defined macrocyclic β-sheets without the requirement for natural or synthetic β-turns, thereby providing a minimal mimic of a protein β-sheet. To access turn-less antiparallel β-sheet mimics, we developed a facile solid phase synthesis protocol. We surveyed a dataset of protein β-sheets for naturally observed interstrand side chain interactions. This bioinformatics survey highlighted an over-abundance of aromatic-aromatic, cation-π and ionic interactions in β-sheets. In correspondence with natural β-sheets, we find that minimal HBS mimics show robust β-sheet formation when specific amino acid residue pairings are incorporated. In isolated β-sheets, aromatic interactions endow superior conformational stability over ionic or cation-π interactions. Circular dichroism and NMR spectroscopies, along with high-resolution X-ray crystallography, support our design principles.
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Affiliation(s)
- Alex Nazzaro
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Brandon Lu
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
| | | | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, NY 10013, New York, USA
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11
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Yu Z, Kreitler DF, Chiu YTT, Xu R, Bruchs AT, Bingman CA, Gellman SH. Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Angew Chem Int Ed Engl 2023; 62:e202308100. [PMID: 37587780 PMCID: PMC10668598 DOI: 10.1002/anie.202308100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Yin Ting T Chiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ruiwen Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Austin T Bruchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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12
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Lim D, Lee W, Hong J, Gong J, Choi J, Kim J, Lim S, Yoo SH, Lee Y, Lee HS. Versatile Post-synthetic Modifications of Helical β-Peptide Foldamers Derived from a Thioether-Containing Cyclic β-Amino Acid. Angew Chem Int Ed Engl 2023; 62:e202305196. [PMID: 37309575 DOI: 10.1002/anie.202305196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
We introduce a novel cyclic β-amino acid, trans-(3S,4R)-4-aminotetrahydrothiophene-3-carboxylic acid (ATTC), as a versatile building block for designing peptide foldamers with controlled secondary structures. We synthesized and characterized a series of β-peptide hexamers containing ATTC using various techniques, including X-ray crystallography, circular dichroism, and NMR spectroscopy. Our findings reveal that ATTC-containing foldamers can adopt 12-helical conformations similar to their isosteres and offer the possibility of fine-tuning their properties via post-synthetic modifications. In particular, chemoselective conjugation strategies demonstrate that ATTC provides unique post-synthetic modification opportunities, which expand their potential applications across diverse research areas. Collectively, our study highlights the versatility and utility of ATTC as an alternative to previously reported cyclic β-amino acid building blocks in both structural and functional aspects, paving the way for future research in the realm of peptide foldamers and beyond.
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Affiliation(s)
- Danim Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Wonchul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Current address: Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Jungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jintaek Gong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Current address: Department of Chemistry Education, Sunchon National University, 255 Jungang-ro, Suncheon-si, Jeollanam-do, 57922, Republic of Korea
| | - Jonghoon Choi
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Current address: Department of Chemistry Education, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Jaewook Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seolhee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sung Hyun Yoo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yunho Lee
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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13
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Gibadullin R, Kim TW, Tran LML, Gellman SH. Hormone Analogues with Unique Signaling Profiles from Replacement of α-Residue Triads with β/γ Diads. J Am Chem Soc 2023; 145:20539-20550. [PMID: 37697685 PMCID: PMC10588032 DOI: 10.1021/jacs.3c06703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
We have applied an underexplored backbone modification strategy to generate new analogues of peptides that activate two clinically important class B1 G protein-coupled receptors (GPCRs). Most peptide modification strategies involve changing side chains or, less commonly, changing the configuration at side chain-bearing carbons (i.e., l residues replaced by d residues). In contrast, backbone modifications alter the number of backbone atoms and the identities of backbone atoms relative to a poly-α-amino acid backbone. Starting from the peptide agonists PTH(1-34) (the first 34 residues of the parathyroid hormone, used clinically as the drug teriparatide) and glucagon-like peptide-1 (7-36) (GLP-1(7-36)), we replaced native α-residue triads with a diad composed of a β-amino acid residue and a γ-amino acid residue. The β/γ diad retains the number of backbone atoms in the ααα triad. Because the β and γ residue each bear a single side chain, we implemented ααα→βγ replacements at sites that contained a Gly residue (i.e., at α-residue triads that presented only two side chains). All seven of the α/β/γ-peptides derived from PTH(1-34) or GLP-1(7-36) bind to the cognate receptor (the PTHR1 or the GLP-1R), but they vary considerably in their activity profiles. Outcomes include functional mimicry of the all-α agonist, receptor-selective agonist activity, biased agonism, or strong binding with weak activation, which could lead to antagonist development. Collectively, these findings demonstrate that ααα→βγ replacements, which are easily implemented via solid-phase synthesis, can generate peptide hormone analogues that display unique and potentially useful signaling behavior.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Tae Wook Kim
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lauren My-Linh Tran
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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14
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Shah SKH, Modi U, Patel K, James A, N S, De S, Vasita R, Prabhakaran P. Site-selective post-modification of short α/γ hybrid foldamers: a powerful approach for molecular diversification towards biomedical applications. Biomater Sci 2023; 11:6210-6222. [PMID: 37526301 DOI: 10.1039/d3bm00766a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification approach is successful in peptides, proteins, and polymers to modulate their functions. To the best of our knowledge, site-selective post-modification of a foldamer affording molecules with different pendant functional groups within a molecular scaffold has not yet been reported. We demonstrate for the first time that late-stage site-selective functionalization of short hybrid oligomers is an efficient approach to afford molecules with diverse functional groups. In this article, we report the design and synthesis of hybrid peptides with repeating units of leucine (Leu) and 5-amino salicylic acid (ASA), regioselective post-modification, conformational analyses (based on solution-state NMR, circular dichroism and computational studies) and morphological studies of the peptide nanostructures. As a proof-of-concept, we demonstrate the applications of differently modified peptides as drug delivery agents, imaging probes, and anticancer agents. The novel feature of the work is that the difference in reactivity of two phenolic OH groups in short biomimetic peptides was utilized to achieve site-selective post-modification. It is challenging to apply the same approach to short α-peptides having a poor folding tendency, and their post-functionalization may considerably affect their conformation.
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Affiliation(s)
| | - Unnati Modi
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Anjima James
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi 682022, India
| | - Sreerag N
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut 673635, India
| | - Rajesh Vasita
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
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15
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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16
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Harmon TW, Horne WS. Protein Backbone Alteration in Non-Hairpin β-Turns: Impacts on Tertiary Folded Structure and Folded Stability. Chembiochem 2023; 24:e202300113. [PMID: 36920327 PMCID: PMC10239330 DOI: 10.1002/cbic.202300113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/16/2023]
Abstract
The importance of β-turns to protein folding has motivated extensive efforts to stabilize the motif with non-canonical backbone connectivity. Prior work has focused almost exclusively on turns between strands in a β-sheet (i. e., hairpins). Turns in other structural contexts are also common in nature and have distinct conformational preferences; however, design principles for their mimicry remain poorly understood. Here, we report strategies that stabilize non-hairpin β-turns through systematic evaluation of the impacts of backbone alteration on the high-resolution folded structure and folded stability of a helix-loop-helix prototype protein. Several well-established hairpin turn mimetics are shown detrimental to folded stability and/or hydrophobic core packing, while less-explored modification schemes that reinforce alternate turn types lead to improved stability and more faithful structural mimicry. Collectively, these results have implications in control over protein folding through chemical modification as well as the design of protein mimetics.
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Affiliation(s)
- Thomas W Harmon
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260, USA
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17
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Wang C, Deng R, Weck M. Orthogonal Supramolecular Assemblies Using Side-Chain Functionalized Helical Poly(isocyanide)s. Macromolecules 2023; 56:3507-3516. [PMID: 37251603 PMCID: PMC10210603 DOI: 10.1021/acs.macromol.2c02224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/20/2023] [Indexed: 05/31/2023]
Abstract
Mimicking the structure of proteins using synthetic polymers requires building blocks with structural similarity and the use of various noncovalent and dynamic covalent interactions. We report the synthesis of helical poly(isocyanide)s bearing diaminopyridine and pyridine side-chains and the multistep functionalization of the polymers' side-chains using hydrogen bonding and metal coordination. The orthogonality of the hydrogen bonding and metal coordination was proved by varying the sequence of the multistep assembly. The two side-chain functionalizations are reversible through the use of competitive solvents and/or competing ligands. Throughout the assembly and disassembly, the helical conformation of the polymer backbone is sustained as proved by circular dichroism spectroscopy. These results open the possibility to incorporate helical domains into complex polymer architectures and create a helical scaffold for smart materials.
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18
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Díaz-Perlas C, Oller-Salvia B. Chemically Enhanced Peptide and Protein Therapeutics. Pharmaceutics 2023; 15:pharmaceutics15030827. [PMID: 36986688 PMCID: PMC10053323 DOI: 10.3390/pharmaceutics15030827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Proteins and peptides are on the rise as therapeutic agents and represent a higher percentage of approved drugs each year: 24% in 2021 vs [...]
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19
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Rao SR, Harmon TW, Heath SL, Wolfe JA, Santhouse JR, O'Brien GL, Distefano AN, Reinert ZE, Horne WS. Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States. Pept Sci (Hoboken) 2023; 115:e24297. [PMID: 37397503 PMCID: PMC10312354 DOI: 10.1002/pep2.24297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 03/03/2024]
Abstract
The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.
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Affiliation(s)
- Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Thomas W Harmon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Shelby L Heath
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jacob A Wolfe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Gregory L O'Brien
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexis N Distefano
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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20
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Menke FS, Mazzier D, Wicher B, Allmendinger L, Kauffmann B, Maurizot V, Huc I. Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds. Org Biomol Chem 2023; 21:1275-1283. [PMID: 36645374 DOI: 10.1039/d2ob02109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.
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Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Daniela Mazzier
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Lars Allmendinger
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (UMS3011/US001), CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
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21
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Zhang Y, Guo J, Cheng J, Zhang Z, Kang F, Wu X, Chu Q. High-Throughput Screening of Stapled Helical Peptides in Drug Discovery. J Med Chem 2023; 66:95-106. [PMID: 36580278 DOI: 10.1021/acs.jmedchem.2c01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
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Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
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22
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Imiołek M, Winssinger N. Two-Helix Supramolecular Proteomimetic Binders Assembled via PNA-Assisted Disulfide Crosslinking. Chembiochem 2023; 24:e202200561. [PMID: 36349499 DOI: 10.1002/cbic.202200561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Peptidic motifs folded in a defined conformation are able to inhibit protein-protein interactions (PPIs) covering large interfaces and as such they are biomedical molecules of interest. Mimicry of such natural structures with synthetically tractable constructs often requires complex scaffolding and extensive optimization to preserve the fidelity of binding to the target. Here, we present a novel proteomimetic strategy based on a 2-helix binding motif that is brought together by hybridization of peptide nucleic acids (PNA) and stabilized by a rationally positioned intermolecular disulfide crosslink. Using a solid phase synthesis approach (SPPS), the building blocks are easily accessible and such supramolecular peptide-PNA helical hybrids could be further coiled using precise templated chemistry. The elaboration of the structural design afforded high affinity SARS CoV-2 RBD (receptor binding domain) binders without interference with the underlying peptide sequence, creating a basis for a new architecture of supramolecular proteomimetics.
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Affiliation(s)
- Mateusz Imiołek
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
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23
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Ożga K, Berlicki Ł. Miniprotein-Based Artificial Retroaldolase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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24
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Richaud AD, Zaghouani M, Zhao G, Wangpaichitr M, Savaraj N, Roche SP. Exploiting the Innate Plasticity of the Programmed Cell Death-1 (PD1) Receptor to Design Pembrolizumab H3 Loop Mimics. Chembiochem 2022; 23:e202200449. [PMID: 36082509 PMCID: PMC10029098 DOI: 10.1002/cbic.202200449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/07/2022] [Indexed: 11/08/2022]
Abstract
Checkpoint blockade of the immunoreceptor programmed cell death-1 (PD1) with its ligand-1 (PDL1) by monoclonal antibodies such as pembrolizumab provided compelling clinical results in various cancer types, yet the molecular mechanism by which this drug blocks the PD1/PDL1 interface remains unclear. To address this question, we examined the conformational motion of PD1 associated with the binding of pembrolizumab. Our results revealed that the innate plasticity of both C'D and FG loops is crucial to form a deep binding groove (371 Å3 ) across several distant epitopes of PD1. This analysis ultimately provided a rational-design to create pembrolizumab H3 loop mimics [RDYRFDMGFD] into β-hairpin scaffolds. As a result, a 20-residue long β-hairpin peptide 1 e was identified as a first-in-class potent PD1-inhibitor (EC50 of 0.29 μM; Ki of 41 nM).
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mehdi Zaghouani
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
| | | | - Niramol Savaraj
- Miller School of Medicine, University of Miami, Miami, FL 33458, USA
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, FL 33431, USA
- Center for Molecular Biology and Biotechnology, Florida Atlantic University, Jupiter, FL 33458, USA
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25
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Khatri B, Pramanick I, Malladi SK, Rajmani RS, Kumar S, Ghosh P, Sengupta N, Rahisuddin R, Kumar N, Kumaran S, Ringe RP, Varadarajan R, Dutta S, Chatterjee J. A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein. Nat Chem Biol 2022; 18:1046-1055. [PMID: 35654847 PMCID: PMC9512702 DOI: 10.1038/s41589-022-01060-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022]
Abstract
Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Ishika Pramanick
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Raju S Rajmani
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Sahil Kumar
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Pritha Ghosh
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - Nayanika Sengupta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | - R Rahisuddin
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Narender Kumar
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - S Kumaran
- Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh P Ringe
- Virology Unit, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Somnath Dutta
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India.
| | - Jayanta Chatterjee
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India.
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26
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Shokrani H, Shokrani A, Sajadi SM, Khodadadi Yazdi M, Seidi F, Jouyandeh M, Zarrintaj P, Kar S, Kim SJ, Kuang T, Rabiee N, Hejna A, Saeb MR, Ramakrishna S. Polysaccharide-based nanocomposites for biomedical applications: a critical review. NANOSCALE HORIZONS 2022; 7:1136-1160. [PMID: 35881463 DOI: 10.1039/d2nh00214k] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polysaccharides (PSA) have taken specific position among biomaterials for advanced applications in medicine. Nevertheless, poor mechanical properties are known as the main drawback of PSA, which highlights the need for PSA modification. Nanocomposites PSA (NPSA) are a class of biomaterials widely used as biomedical platforms, but despite their importance and worldwide use, they have not been reviewed. Herein, we critically reviewed the application of NPSA by categorizing them into generic and advanced application realms. First, the application of NPSA as drug and gene delivery systems, along with their role in the field as an antibacterial platform and hemostasis agent is discussed. Then, applications of NPSA for skin, bone, nerve, and cartilage tissue engineering are highlighted, followed by cell encapsulation and more critically cancer diagnosis and treatment potentials. In particular, three features of investigations are devoted to cancer therapy, i.e., radiotherapy, immunotherapy, and photothermal therapy, are comprehensively reviewed and discussed. Since this field is at an early stage of maturity, some other aspects such as bioimaging and biosensing are reviewed in order to give an idea of potential applications of NPSA for future developments, providing support for clinical applications. It is well-documented that using nanoparticles/nanomaterials above a critical concentration brings about concerns of toxicity; thus, their effect on cellular interactions would become critical. We compared nanoparticles used in the fabrication of NPSA in terms of toxicity mechanism to shed more light on future challenging aspects of NPSA development. Indeed, the neutralization mechanisms underlying the cytotoxicity of nanomaterials, which are expected to be induced by PSA introduction, should be taken into account for future investigations.
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Affiliation(s)
- Hanieh Shokrani
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, 210037 Nanjing, China.
- Department of Chemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Amirhossein Shokrani
- Department of Mechanical Engineering, Sharif University of Technology, Azadi Ave., Tehran, Iran
| | - S Mohammad Sajadi
- Department of Nutrition, Cihan University-Erbil, Kurdistan Region, 625, Erbil, Iraq
| | - Mohsen Khodadadi Yazdi
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Farzad Seidi
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, 210037 Nanjing, China.
| | - Maryam Jouyandeh
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078, USA
| | - Saptarshi Kar
- College of Engineering and Technology, American University of the Middle East, Kuwait
| | - Seok-Jhin Kim
- School of Chemical Engineering, Oklahoma State University, Stillwater, OK, USA
| | - Tairong Kuang
- College of Material Science and Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, New South Wales, 2109, Australia
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Alexander Hejna
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Mohammad Reza Saeb
- Department of Polymer Technology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
| | - Seeram Ramakrishna
- Department of Mechanical Engineering, National University Singapore, 10 Kent Ridge, Crescent 119260, Singapore.
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27
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Yoo SH, Buratto J, Roy A, Morvan E, Pasco M, Pulka-Ziach K, Lombardo CM, Rosu F, Gabelica V, Mackereth CD, Collie GW, Guichard G. Adaptive Binding of Alkyl Glycosides by Nonpeptidic Helix Bundles in Water: Toward Artificial Glycolipid Binding Proteins. J Am Chem Soc 2022; 144:15988-15998. [PMID: 35998571 DOI: 10.1021/jacs.2c05234] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphipathic water-soluble helices formed from synthetic peptides or foldamers are promising building blocks for the creation of self-assembled architectures with non-natural shapes and functions. While rationally designed artificial quaternary structures such as helix bundles have been shown to contain preformed cavities suitable for guest binding, there are no examples of adaptive binding of guest molecules by such assemblies in aqueous conditions. We have previously reported a foldamer 6-helix bundle that contains an internal nonpolar cavity able to bind primary alcohols as guest molecules. Here, we show that this 6-helix bundle can also interact with larger, more complex guests such as n-alkyl glycosides. X-ray diffraction analysis of co-crystals using a diverse set of guests together with solution and gas-phase studies reveals an adaptive binding mode whereby the apo form of the 6-helix bundle undergoes substantial conformational change to accommodate the hydrocarbon chain in a manner reminiscent of glycolipid transfer proteins in which the cavity forms upon lipid uptake. The dynamic nature of the self-assembling and molecular recognition processes reported here marks a step forward in the design of functional proteomimetic molecular assemblies.
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Affiliation(s)
- Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Jérémie Buratto
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Arup Roy
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Estelle Morvan
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France
| | - Morgane Pasco
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | | | - Caterina M Lombardo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France.,Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Bordeaux, France
| | - Gavin W Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
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28
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Paulussen FM, Schouten GK, Moertl C, Verheul J, Hoekstra I, Koningstein GM, Hutchins GH, Alkir A, Luirink RA, Geerke DP, van Ulsen P, den Blaauwen T, Luirink J, Grossmann TN. Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex. J Am Chem Soc 2022; 144:15303-15313. [PMID: 35945166 PMCID: PMC9413201 DOI: 10.1021/jacs.2c06304] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The use of antibiotics is threatened by the emergence
and spread
of multidrug-resistant strains of bacteria. Thus, there is a need
to develop antibiotics that address new targets. In this respect,
the bacterial divisome, a multi-protein complex central to cell division,
represents a potentially attractive target. Of particular interest
is the FtsQB subcomplex that plays a decisive role in divisome assembly
and peptidoglycan biogenesis in E. coli. Here, we report the structure-based design of
a macrocyclic covalent inhibitor derived from a periplasmic region
of FtsB that mediates its binding to FtsQ. The bioactive conformation
of this motif was stabilized by a customized cross-link resulting
in a tertiary structure mimetic with increased affinity for FtsQ.
To increase activity, a covalent handle was incorporated, providing
an inhibitor that impedes the interaction between FtsQ and FtsB irreversibly. The covalent inhibitor reduced the growth of an outer
membrane-permeable E. coli strain,
concurrent with the expected loss of FtsB localization, and also affected
the infection of zebrafish larvae by a clinical E.
coli strain. This first-in-class inhibitor of a divisome
protein–protein interaction highlights the potential of proteomimetic
molecules as inhibitors of challenging targets. In particular, the
covalent mode-of-action can serve as an inspiration for future antibiotics
that target protein–protein interactions.
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Affiliation(s)
- Felix M Paulussen
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Gina K Schouten
- Medical Microbiology and Infection Control (MMI), Amsterdam UMC Location VUmc, De Boelelaan 1108, Amsterdam 1081 HZ, Netherlands
| | - Carolin Moertl
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Jolanda Verheul
- Department of Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, Netherlands
| | - Irma Hoekstra
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Gregory M Koningstein
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - George H Hutchins
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Aslihan Alkir
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Rosa A Luirink
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Peter van Ulsen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Tanneke den Blaauwen
- Department of Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, Amsterdam 1098 XH, Netherlands
| | - Joen Luirink
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands.,Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, Netherlands
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29
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Yoshida S, Uehara S, Kondo N, Takahashi Y, Yamamoto S, Kameda A, Kawagoe S, Inoue N, Yamada M, Yoshimura N, Tachibana Y. Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J Med Chem 2022; 65:10655-10673. [PMID: 35904556 DOI: 10.1021/acs.jmedchem.2c00919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, ″Peptide-to-Small Molecule″, which is a combination of rapid identification of high-affinity macrocyclic peptides via peptide display screening followed by pharmacophore-guided de novo design of small molecules, and demonstrate the applicability using nicotinamide N-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide 1 that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided de novo design and further structure-based optimization resulted in highly potent and cell-active small molecule 14 (cell-free IC50 = 0.0011 μM, cell-based IC50 = 0.40 μM), indicating that this strategy could be a new option for drug discovery.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shota Uehara
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Noriyasu Kondo
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yu Takahashi
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shiho Yamamoto
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsushi Kameda
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Soichiro Kawagoe
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Naoko Inoue
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Masami Yamada
- PeptiDream Inc. 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Norito Yoshimura
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yuki Tachibana
- Pharmaceutical Research Division, Shionogi Pharmaceutical Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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30
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Koelman EMR, Yeste-Vázquez A, Grossmann TN. Targeting the interaction of β-catenin and TCF/LEF transcription factors to inhibit oncogenic Wnt signaling. Bioorg Med Chem 2022; 70:116920. [PMID: 35841828 DOI: 10.1016/j.bmc.2022.116920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
The Wnt/β-catenin signaling pathway is crucially involved in embryonic development, stem cell maintenance and tissue renewal. Hyperactivation of this pathway is associated with the development and progression of various types of cancers. The transcriptional coactivator β-catenin represents a pivotal component of the pathway and its interaction with transcription factors of the TCF/LEF family is central to pathway activation. Inhibition of this crucial protein-protein interaction via direct targeting of β-catenin is considered a promising strategy for the inactivation of oncogenic Wnt signaling. This review summarizes advances in the development of Wnt antagonists that have been shown to directly bind β-catenin.
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Affiliation(s)
- Emma M R Koelman
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands.
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31
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Learte-Aymamí S, Martin-Malpartida P, Roldán-Martín L, Sciortino G, Couceiro JR, Maréchal JD, Macias MJ, Mascareñas JL, Vázquez ME. Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide. Commun Chem 2022; 5:75. [PMID: 36697641 PMCID: PMC9814687 DOI: 10.1038/s42004-022-00691-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/10/2022] [Indexed: 01/28/2023] Open
Abstract
RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascade.
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Affiliation(s)
- Soraya Learte-Aymamí
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Pau Martin-Malpartida
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain
| | - Lorena Roldán-Martín
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Giuseppe Sciortino
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain ,grid.473715.30000 0004 6475 7299Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007 Spain
| | - José R. Couceiro
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - Jean-Didier Maréchal
- grid.7080.f0000 0001 2296 0625Insilichem, Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, 08193 Spain
| | - Maria J. Macias
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, 08028 Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010 Spain
| | - José L. Mascareñas
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
| | - M. Eugenio Vázquez
- grid.11794.3a0000000109410645Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, 15705 Spain
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32
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Li B, Wan Z, Zheng H, Cai S, Tian HW, Tang H, Chu X, He G, Guo DS, Xue XS, Chen G. Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine. J Am Chem Soc 2022; 144:10080-10090. [PMID: 35639413 DOI: 10.1021/jacs.2c04620] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.
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Affiliation(s)
- Bo Li
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhao Wan
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanliang Zheng
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Shaokun Cai
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Han-Wen Tian
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hong Tang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Chu
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Gang He
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Dong-Sheng Guo
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Gong Chen
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.,Frontiers Science Center for New Organic Matter, Nankai University, Tianjin 300071, China
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33
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Niu J, Cederstrand AJ, Eddinger GA, Yin B, Checco JW, Bingman CA, Outlaw VK, Gellman SH. Trimer-to-Monomer Disruption Mechanism for a Potent, Protease-Resistant Antagonist of Tumor Necrosis Factor-α Signaling. J Am Chem Soc 2022; 144:9610-9617. [PMID: 35613436 PMCID: PMC9749406 DOI: 10.1021/jacs.1c13717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aberrant tumor necrosis factor-α (TNFα) signaling is associated with many inflammatory diseases. The homotrimeric quaternary structure of TNFα is essential for receptor recognition and signal transduction. Previously, we described an engineered α/β-peptide inhibitor that potently suppresses TNFα activity and resists proteolysis. Here, we present structural evidence that both the α/β-peptide inhibitor and an all-α analogue bind to a monomeric form of TNFα. Calorimetry data support a 1:1 inhibitor/TNFα stoichiometry in solution. In contrast, previous cocrystal structures involving peptide or small-molecule inhibitors have shown the antagonists engaging a TNFα dimer. The structural data reveal why our inhibitors favor monomeric TNFα. Previous efforts to block TNFα-induced cell death with peptide inhibitors revealed that surfactant additives to the assay conditions cause a more rapid manifestation of inhibitory activity than is observed in the absence of additives. We attributed this effect to a loose surfactant TNFα association that lowers the barrier to trimer dissociation. Here, we used the new structural data to design peptide inhibitors bearing a surfactant-inspired appendage intended to facilitate TNFα trimer dissociation. The appendage modified the time course of protection from cell death.
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Affiliation(s)
- Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Annika J. Cederstrand
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Geoffrey A. Eddinger
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Boyu Yin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - James W. Checco
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Victor K. Outlaw
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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34
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Nelson B, Hong SH, Lupoli TJ. Protein Cofactor Mimics Disrupt Essential Chaperone Function in Stressed Mycobacteria. ACS Infect Dis 2022; 8:901-910. [PMID: 35412813 DOI: 10.1021/acsinfecdis.1c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial DnaK is an ATP-dependent molecular chaperone important for maintaining cellular proteostasis in concert with cofactor proteins. The cofactor DnaJ delivers non-native client proteins to DnaK and activates its ATPase activity, which is required for protein folding. In the bacterial pathogen Mycobacterium tuberculosis, DnaK is assisted by two DnaJs, DnaJ1 and DnaJ2. Functional protein-protein interactions (PPIs) between DnaK and at least one DnaJ are essential for survival of mycobacteria; hence, these PPIs represent untapped antibacterial targets. Here, we synthesize peptide-based mimetics of DnaJ1 and DnaJ2 N-terminal domains as rational inhibitors of DnaK-cofactor interactions. We find that covalently stabilized DnaJ mimetics are capable of disrupting DnaK-cofactor activity in vitro and prevent mycobacterial recovery from proteotoxic stress in vivo, leading to cell death. Since chaperones and cofactors are highly conserved, we anticipate these results will inform the design of other mimetics to modulate chaperone function across cell types.
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Affiliation(s)
- Brock Nelson
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, New York 10003, United States
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35
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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36
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Cabalteja CC, Lin Q, Harmon TW, Rao SR, Di YP, Horne WS. Heterogeneous-Backbone Proteomimetic Analogues of Lasiocepsin, a Disulfide-Rich Antimicrobial Peptide with a Compact Tertiary Fold. ACS Chem Biol 2022; 17:987-997. [PMID: 35290019 PMCID: PMC9039985 DOI: 10.1021/acschembio.2c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emergence of resistance to clinically used antibiotics by bacteria presents a significant problem in public health. Natural antimicrobial peptides (AMPs) are a valuable source of antibiotics that act by a mechanism less prone to the evolutionary development of resistance. In an effort to realize the promise of AMPs while overcoming limitations such as poor biostability, researchers have sought sequence-defined oligomers with artificial amide-based backbones that show membrane-disrupting functions similar to natural agents. Most of this precedent has focused on short peptidomimetic analogues of unstructured chains or secondary folds; however, the natural antimicrobial arsenal includes a number of small- and medium-sized proteins that act via an ordered tertiary structure. Generating proteomimetic analogues of these scaffolds poses a challenge due to the increased complexity of the target for mimicry. Here, we report the development of heterogeneous-backbone variants of lasiocepsin, a 27-residue disulfide-rich AMP found in bee venom that adopts a compact tertiary fold. Iterative cycles of design, synthesis, and biological evaluation yielded analogues of the natural domain with ∼30 to 40% artificial backbone content, comparable antibacterial activity, reduced host cell toxicity, and improved stability to proteolytic degradation. High-resolution structures determined for several variants by NMR provide insights into the interplay among backbone composition, tertiary fold, and biological properties. Collectively, the results reported here broaden the scope of protein functional mimicry by artificial backbone analogues of tertiary folding patterns and suggest protein backbone engineering as a means to tune protein function by exerting site-specific control over protein folded structure.
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Affiliation(s)
- Chino C. Cabalteja
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Qiao Lin
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Thomas W. Harmon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Shilpa R. Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Y. Peter Di
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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37
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Heinz-Kunert SL, Pandya A, Dang VT, Tran PN, Ghosh S, McElheny D, Santarsiero BD, Ren Z, Nguyen AI. Assembly of π-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework. J Am Chem Soc 2022; 144:7001-7009. [PMID: 35390261 DOI: 10.1021/jacs.2c02146] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The evolution of proteins from simpler, self-assembled peptides provides a powerful blueprint for the design of complex synthetic materials. Previously, peptide-metal frameworks using short sequences (≤3 residues) have shown great promise as proteomimetic materials that exhibit sophisticated capabilities. However, their development has been hindered due to few variable residues and restricted choice of side-chains that are compatible with metal ions. Herein, we developed a noncovalent strategy featuring π-stacking bipyridyl residues to assemble much longer peptides into crystalline frameworks that tolerate even previously incompatible acidic and basic functionalities and allow an unprecedented level of pore variations. Single-crystal X-ray structures are provided for all variants to guide and validate rational design. These materials exhibit hallmark proteomimetic behaviors such as guest-selective induced fit and assembly of multimetallic units. Significantly, we demonstrate facile optimization of the framework design to substantially increase affinity toward a complex organic molecule.
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Affiliation(s)
- Sherrie L Heinz-Kunert
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Ashma Pandya
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Sabari Ghosh
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Bernard D Santarsiero
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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38
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Santhouse JR, Leung JMG, Chong LT, Horne WS. Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics. Chem Sci 2022; 13:11798-11806. [PMID: 36320921 PMCID: PMC9580521 DOI: 10.1039/d2sc04427g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 12/28/2022] Open
Abstract
Sequence-encoded folding is the foundation of protein structure and is also possible in synthetic chains of artificial chemical composition. In natural proteins, the characteristics of the unfolded state are as important as those of the folded state in determining folding energetics. While much is known about folded structures adopted by artificial protein-like chains, corresponding information about the unfolded states of these molecules is lacking. Here, we report the consequences of altered backbone composition on the structure, stability, and dynamics of the folded and unfolded states of a compact helix-rich protein. Characterization through a combination of biophysical experiments and atomistic simulation reveals effects of backbone modification that depend on both the type of artificial monomers employed and where they are applied in sequence. In general, introducing artificial connectivity in a way that reinforces characteristics of the unfolded state ensemble of the prototype natural protein minimizes the impact of chemical changes on folded stability. These findings have implications in the design of protein mimetics and provide an atomically detailed picture of the unfolded state of a natural protein and artificial analogues under non-denaturing conditions. Biophysical experiments and atomistic simulation reveal impacts of protein backbone alteration on the ensemble that defines the unfolded state. These effects have implications on folded stability of protein mimetics.![]()
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Affiliation(s)
| | - Jeremy M. G. Leung
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15211, USA
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39
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Suwal S, Rahman M, O’Brien G, Karambizi VG, Wrotny M, Scott Goodman M. Chemo-selective syntheses of N-t-boc-protected amino ester analogs through Buchwald–Hartwig amination. NEW J CHEM 2022. [DOI: 10.1039/d1nj05596h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We showcased a library of amino ester molecules created through the BHA reaction. The product formation is more facile in the esters where nitrogen is present ortho to the halo substituent in the heteroaromatic ring.
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Affiliation(s)
- Sujit Suwal
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
| | - Mahmuda Rahman
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
| | - Gregory O’Brien
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
| | - Victoire G. Karambizi
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
| | - Matthew Wrotny
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
| | - M. Scott Goodman
- Department of Chemistry, SUNY-Buffalo State College, 1300 Elmwood Avenue, Buffalo, NY 14222, USA
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40
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Sun H, Qiao B, Choi W, Hampu N, McCallum NC, Thompson MP, Oktawiec J, Weigand S, Ebrahim OM, de la Cruz MO, Gianneschi NC. Origin of Proteolytic Stability of Peptide-Brush Polymers as Globular Proteomimetics. ACS CENTRAL SCIENCE 2021; 7:2063-2072. [PMID: 34963898 PMCID: PMC8704038 DOI: 10.1021/acscentsci.1c01149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Indexed: 05/03/2023]
Abstract
Peptide-brush polymers (PBPs), wherein every side-chain of the polymers is peptidic, represent a new class of proteomimetic with unusually high proteolytic resistance while maintaining bioactivity. Here, we sought to determine the origin of this behavior and to assess its generality via a combined theory and experimental approach. A series of PBPs with various polymer backbone structures were prepared and examined for their proteolytic stability and bioactivity. We discovered that an increase in the hydrophobicity of the polymer backbones is predictive of an elevation in proteolytic stability of the side-chain peptides. Computer simulations, together with small-angle X-ray scattering (SAXS) analysis, revealed globular morphologies for these polymers, in which pendant peptides condense around hydrophobic synthetic polymer backbones driven by the hydrophobic effect. As the hydrophobicity of the polymer backbones increases, the extent of solvent exposure of peptide cleavage sites decreases, reducing their accessibility to proteolytic enzymes. This study provides insight into the important factors driving PBP aqueous-phase structures to behave as globular, synthetic polymer-based proteomimetics.
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Affiliation(s)
- Hao Sun
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Chemistry and Chemical & Biomedical Engineering, University of New Haven, West Haven, Connecticut 06516, United States
| | - Baofu Qiao
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Wonmin Choi
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Nicholas Hampu
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Naneki C. McCallum
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew P. Thompson
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julia Oktawiec
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Steven Weigand
- Dupont-Northwestern-Dow
Collaborative Access Team (DND-CAT) Synchrotron Research Center, Northwestern University, Argonne, Illinois 60208, United States
| | - Omar M. Ebrahim
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Chemical & Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry, International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Materials Science & Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Biomedical Engineering, Department of Pharmacology, Chemistry of
Life Processes Institute, Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
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41
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Kuepper A, McLoughlin NM, Neubacher S, Yeste-Vázquez A, Collado Camps E, Nithin C, Mukherjee S, Bethge L, Bujnicki JM, Brock R, Heinrichs S, Grossmann TN. Constrained peptides mimic a viral suppressor of RNA silencing. Nucleic Acids Res 2021; 49:12622-12633. [PMID: 34871435 PMCID: PMC8682738 DOI: 10.1093/nar/gkab1149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 10/01/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.
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Affiliation(s)
- Arne Kuepper
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
| | - Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
| | - Estel Collado Camps
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Lucas Bethge
- Silence Therapeutics GmbH, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen Medical Center, Nijmegen 6525 GA, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 293, Bahrain
| | - Stefan Heinrichs
- University Hospital Essen, Institute for Transfusion Medicine, Essen 45147, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund 44227, Germany
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Dortmund 44227, Germany
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, The Netherlands
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42
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Singh H, Chenna A, Gangwar U, Borah J, Goel G, Haridas V. Bispidine as a β-strand nucleator: from a β-arch to self-assembled cages and vesicles. Chem Sci 2021; 12:15757-15764. [PMID: 35003608 PMCID: PMC8654037 DOI: 10.1039/d1sc04860k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic scaffolds that nucleate well-folded secondary structures is highly challenging. Herein, we designed and synthesized a series of core-modified peptides (F1, F2, F3, and F4) that fold into β-strand structures. These bispidine-scaffolded peptides were studied by CD, IR, NMR, single crystal XRD, and Molecular Dynamics (MD) simulations to investigate their conformational preferences. Solid-state and solution studies revealed that bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating the β-strand structure. Scaffolds that nucleate an isolated β-strand conformation are rare. Bispidine placed at the C-terminus of the peptide chain could nucleate a β-strand conformation, while bispidine placed at the middle resulted in a β-arch conformation. This nucleation activity stems from the ability to restrict the psi torsion angle (ψ) through intramolecular C5 hydrogen bonding between the equatorial hydrogen(s) of bispidine and the carbonyl oxygen(s) of the amino acid close to the scaffold. Furthermore, the bispidine peptidomimetic with a super secondary structure, namely β-arch, assembled into single-hole submicron cages and spherical vesicles as evident from microscopic studies. The design logic defined here will be a significant strategy for the development of β-strand mimetics and super secondary structures.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Julie Borah
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
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43
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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021; 60:24870-24874. [PMID: 34519402 DOI: 10.1002/anie.202110978] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Indexed: 12/31/2022]
Abstract
Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.,Present Address: École Centrale School of Engineering, Mahindra University, Hyderabad, 500043, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - R Rahisuddin
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | - S Kumaran
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | | | | | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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44
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Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
- Present Address: École Centrale School of Engineering Mahindra University Hyderabad 500043 India
| | - Sohini Chakraborti
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - R. Rahisuddin
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | - S. Kumaran
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | | | | | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
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45
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Yin H, Zhou X, Huang YH, King GJ, Collins BM, Gao Y, Craik DJ, Wang CK. Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy. J Am Chem Soc 2021; 143:18536-18547. [PMID: 34661406 DOI: 10.1021/jacs.1c08132] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Peptides have potential to be developed into immune checkpoint inhibitors, but the target interfaces are difficult to inhibit. Here, we explored an approach to mimic the binding surface of PD-1 to design inhibitors. Mimicking native PD-1 resulted in a mimetic with no activity. However, mimicking an affinity-optimized PD-1 resulted in the peptide mimetic MOPD-1 that displayed nanomolar affinity to PD-L1 and could inhibit PD-1:PD-L1 interactions in both protein- and cell-based assays. Mutagenesis and structural characterization using NMR spectroscopy and X-ray crystallography revealed that binding residues from the high affinity PD-1 are crucial for the bioactivity of MOPD-1. Furthermore, MOPD-1 was extremely stable in human serum and inhibited tumor growth in vivo, suggesting it has potential for use in cancer immunotherapy. The successful design of an inhibitor of PD-1:PD-L1 using the mimicry approach described herein illustrates the value of placing greater emphasis on optimizing the target interface before inhibitor design and is an approach that could have broader utility for the design of peptide inhibitors for other complex protein-protein interactions.
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Affiliation(s)
- Huawu Yin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland 4072, Australia
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46
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DeStefano A, Segalman RA, Davidson EC. Where Biology and Traditional Polymers Meet: The Potential of Associating Sequence-Defined Polymers for Materials Science. JACS AU 2021; 1:1556-1571. [PMID: 34723259 PMCID: PMC8549048 DOI: 10.1021/jacsau.1c00297] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/08/2023]
Abstract
Polymers with precisely defined monomeric sequences present an exquisite tool for controlling material properties by harnessing both the robustness of synthetic polymers and the ability to tailor the inter- and intramolecular interactions so crucial to many biological materials. While polymer scientists traditionally synthesized and studied the physics of long molecules best described by their statistical nature, many biological polymers derive their highly tailored functions from precisely controlled sequences. Therefore, significant effort has been applied toward developing new methods of synthesizing, characterizing, and understanding the physics of non-natural sequence-defined polymers. This perspective considers the synergistic advantages that can be achieved via tailoring both precise sequence control and attributes of traditional polymers in a single system. Here, we focus on the potential of sequence-defined polymers in highly associating systems, with a focus on the unique properties, such as enhanced proton conductivity, that can be attained by incorporating sequence. In particular, we examine these materials as key model systems for studying previously unresolvable questions in polymer physics including the role of chain shape near interfaces and how to tailor compatibilization between dissimilar polymer blocks. Finally, we discuss the critical challenges-in particular, truly scalable synthetic approaches, characterization and modeling tools, and robust control and understanding of assembly pathways-that must be overcome for sequence-defined polymers to attain their potential and achieve ubiquity.
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Affiliation(s)
- Audra
J. DeStefano
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
| | - Emily C. Davidson
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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47
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Li X, Sabol AL, Wierzbicki M, Salveson PJ, Nowick JS. An Improved Turn Structure for Inducing β‐Hairpin Formation in Peptides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xingyue Li
- Department of Chemistry University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
| | - Andrew L. Sabol
- Department of Chemistry University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
| | - Michał Wierzbicki
- Department of Chemistry University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
| | - Patrick J. Salveson
- Department of Chemistry University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
| | - James S. Nowick
- Department of Chemistry University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
- Department of Pharmaceutical Sciences University of California Irvine 4126 Natural Sciences I Irvine CA 92697-2025 USA
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48
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Li X, Sabol AL, Wierzbicki M, Salveson PJ, Nowick JS. An Improved Turn Structure for Inducing β-Hairpin Formation in Peptides. Angew Chem Int Ed Engl 2021; 60:22776-22782. [PMID: 34258835 DOI: 10.1002/anie.202105559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/14/2021] [Indexed: 11/05/2022]
Abstract
Although β-hairpins are widespread in proteins, there is no tool to coax any small peptide to adopt a β-hairpin conformation, regardless of sequence. Here, we report that δ-linked γ(R)-methyl-ornithine (δ MeOrn) provides an improved β-turn template for inducing a β-hairpin conformation in peptides. We developed a synthesis of protected δ MeOrn as a building block suitable for use in Fmoc-based solid-phase peptide synthesis. The synthesis begins with l-leucine and affords gram quantities of the Nα -Boc-Nδ -Fmoc-γ(R)-methyl-ornithine building block. X-ray crystallography confirms that the δ MeOrn turn unit adopts a folded structure in a macrocyclic β-hairpin peptide. CD and NMR spectroscopy allow comparison of the δ MeOrn turn template to the δ-linked ornithine (δ Orn) turn template that we previously introduced and to the popular d-Pro-Gly turn template. These studies show that the folding of the δ MeOrn turn template is substantially better than that of δ Orn and is comparable to d-Pro-Gly.
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Affiliation(s)
- Xingyue Li
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA
| | - Andrew L Sabol
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA
| | - Michał Wierzbicki
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA
| | - Patrick J Salveson
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA
| | - James S Nowick
- Department of Chemistry, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA.,Department of Pharmaceutical Sciences, University of California Irvine, 4126 Natural Sciences I, Irvine, CA, 92697-2025, USA
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49
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Collie GW, Lombardo CM, Yoo SH, Pułka-Ziach K, Gabelica V, Mackereth CD, Rosu F, Guichard G. Crystal structures capture multiple stoichiometric states of an aqueous self-assembling oligourea foldamer. Chem Commun (Camb) 2021; 57:9514-9517. [PMID: 34546254 DOI: 10.1039/d1cc03604a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here an oligourea foldamer able to self-assemble in aqueous conditions into helix bundles of multiple stoichiometries. Importantly, we report crystal structures of several of these stoichiometries, providing a series of high-resolution snap-shots of the structural polymorphism of this foldamer and uncovering a novel self-assembly.
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Affiliation(s)
| | - Caterina M Lombardo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
| | | | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
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50
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Haim A, Neubacher S, Grossmann TN. Protein Macrocyclization for Tertiary Structure Stabilization. Chembiochem 2021; 22:2672-2679. [PMID: 34060202 PMCID: PMC8453710 DOI: 10.1002/cbic.202100111] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Proteins possess unique molecular recognition capabilities and enzymatic activities, features that are usually tied to a particular tertiary structure. To make use of proteins for biotechnological and biomedical purposes, it is often required to enforce their tertiary structure in order to ensure sufficient stability under the conditions inherent to the application of interest. The introduction of intramolecular crosslinks has proven efficient in stabilizing native protein folds. Herein, we give an overview of methods that allow the macrocyclization of expressed proteins, discussing involved reaction mechanisms and structural implications.
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Affiliation(s)
- Anissa Haim
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Incircular B.V.De Boelelaan 11081081 HZAmsterdamThe Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical SciencesVU University AmsterdamAmsterdamThe Netherlands
- Amsterdam Institute of Molecular and Life SciencesVU University AmsterdamAmsterdamThe Netherlands
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