1
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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Byerly-Duke J, O'Brien EA, Wall BJ, VanVeller B. Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres. Methods Enzymol 2024; 698:27-55. [PMID: 38886036 DOI: 10.1016/bs.mie.2024.04.012] [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] [Indexed: 06/20/2024]
Abstract
Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brendan J Wall
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA, United States.
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3
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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4
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Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [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: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
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Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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5
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Gibadullin R, Morris RK, Niu J, Sidney J, Sette A, Gellman SH. Thioamide Analogues of MHC I Antigen Peptides. J Am Chem Soc 2023; 145:25559-25569. [PMID: 37968794 PMCID: PMC10782604 DOI: 10.1021/jacs.3c05300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.
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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
| | - Rylie K. Morris
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
- Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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6
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Fiore KE, Patist MJ, Giannakoulias S, Huang CH, Verma H, Khatri B, Cheng RP, Chatterjee J, Petersson EJ. Structural impact of thioamide incorporation into a β-hairpin. RSC Chem Biol 2022; 3:582-591. [PMID: 35656485 PMCID: PMC9092430 DOI: 10.1039/d1cb00229e] [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: 11/29/2021] [Accepted: 03/24/2022] [Indexed: 11/21/2022] Open
Abstract
The thioamide is a naturally-occurring single atom substitution of the canonical amide bond. The exchange of oxygen to sulfur alters the amide's physical and chemical characteristics, thereby expanding its functionality. Incorporation of thioamides in prevalent secondary structures has demonstrated that they can either have stabilizing, destabilizing, or neutral effects. We performed a systematic investigation of the structural impact of thioamide incorporation in a β-hairpin scaffold with nuclear magnetic resonance (NMR). Thioamides as hydrogen bond donors did not increase the foldedness of the more stable "YKL" variant of this scaffold. In the less stable "HPT" variant of the scaffold, the thioamide could be stabilizing as a hydrogen bond donor and destabilizing as a hydrogen bond acceptor, but the extent of the perturbation depended upon the position of incorporation. To better understand these effects we performed structural modelling of the macrocyclic folded HPT variants. Finally, we compare the thioamide effects that we observe to previous studies of both side-chain and backbone perturbations to this β-hairpin scaffold to provide context for our observations.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Martijn J Patist
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
| | - Cheng-Hsin Huang
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Richard P Cheng
- Department of Chemistry, National Taiwan University No. 1, Sec. 4, Roosevelt Road Taipei 10617 Taiwan
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia 19104 USA
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7
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Cong Y, Zhai Y, Yang J, Grofe A, Gao J, Li H. Quantum vibration perturbation approach with polyatomic probe in simulating infrared spectra. Phys Chem Chem Phys 2021; 24:1174-1182. [PMID: 34932049 DOI: 10.1039/d1cp04490g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The quantitative prediction of vibrational spectra of chromophore molecules in solution is challenging and numerous methods have been developed. In this work, we present a quantum vibration perturbation (QVP) approach, which is a procedure that combines molecular quantum vibration and molecular dynamics with perturbation theory. In this framework, an initial Newtonian molecular dynamics simulation is performed, followed by a substitution process to embed molecular quantum vibrational wave functions into the trajectory. The instantaneous vibrational frequency shift at each time step is calculated using the Rayleigh-Schrödinger perturbation theory, where the perturbation operator is the difference in the vibrational potential between the reference chromophore and the perturbed chromophore in the environment. Semi-classical statistical mechanics is employed to obtain the spectral lineshape function. We validated our method using HCOOH·nH2O (n = 1-2) clusters and HCOOH aqueous solution as examples. The QVP method can be employed for rapid prediction of the vibrational spectrum of a specific mode in solution.
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Affiliation(s)
- Yang Cong
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People's Republic of China.
| | - Yu Zhai
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People's Republic of China.
| | - Jitai Yang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People's Republic of China.
| | - Adam Grofe
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People's Republic of China.
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, MN 55455, USA. .,Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Hui Li
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2519 Jiefang Road, Changchun 130023, People's Republic of China.
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8
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Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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9
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Li C, Hilgeroth P, Hasan N, Ströhl D, Kressler J, Binder WH. Comparing C2=O and C2=S Barbiturates: Different Hydrogen-Bonding Patterns of Thiobarbiturates in Solution and the Solid State. Int J Mol Sci 2021; 22:12679. [PMID: 34884482 PMCID: PMC8657569 DOI: 10.3390/ijms222312679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 12/17/2022] Open
Abstract
Carbonyl-centered hydrogen bonds with various strength and geometries are often exploited in materials to embed dynamic and adaptive properties, with the use of thiocarbonyl groups as hydrogen-bonding acceptors remaining only scarcely investigated. We herein report a comparative study of C2=O and C2=S barbiturates in view of their differing hydrogen bonds, using the 5,5-disubstituted barbiturate B and the thiobarbiturate TB as model compounds. Owing to the different hydrogen-bonding strength and geometries of C2=O vs. C2=S, we postulate the formation of different hydrogen-bonding patterns in C2=S in comparison to the C2=O in conventional barbiturates. To study differences in their association in solution, we conducted concentration- and temperature-dependent NMR experiments to compare their association constants, Gibbs free energy of association ∆Gassn., and the coalescence behavior of the N-H‧‧‧S=C bonded assemblies. In Langmuir films, the introduction of C2=S suppressed 2D crystallization when comparing B and TB using Brewster angle microscopy, also revealing a significant deviation in morphology. When embedded into a hydrophobic polymer such as polyisobutylene, a largely different rheological behavior was observed for the barbiturate-bearing PB compared to the thiobarbiturate-bearing PTB polymers, indicative of a stronger hydrogen bonding in the thioanalogue PTB. We therefore prove that H-bonds, when affixed to a polymer, here the thiobarbiturate moieties in PTB, can reinforce the nonpolar PIB matrix even better, thus indicating the formation of stronger H-bonds among the thiobarbiturates in polymers in contrast to the effects observed in solution.
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Affiliation(s)
- Chenming Li
- Macromolecular Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany; (C.L.); (P.H.)
| | - Philipp Hilgeroth
- Macromolecular Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany; (C.L.); (P.H.)
| | - Nazmul Hasan
- Physical Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany; (N.H.); (J.K.)
| | - Dieter Ströhl
- Organic Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120 Halle (Saale), Germany;
| | - Jörg Kressler
- Physical Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany; (N.H.); (J.K.)
| | - Wolfgang H. Binder
- Macromolecular Chemistry, Institute of Chemistry, Martin-Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, D-06120 Halle (Saale), Germany; (C.L.); (P.H.)
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10
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Spekowius J, Pfister R, Helbing J. Folding and Unfolding of the Tryptophan Zipper in the Presence of Two Thioamide Substitutions. J Phys Chem B 2021; 125:7662-7670. [PMID: 34232040 DOI: 10.1021/acs.jpcb.1c03327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.
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Affiliation(s)
- Jasmin Spekowius
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Rolf Pfister
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jan Helbing
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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11
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Khatri B, Raj N, Chatterjee J. Opportunities and challenges in the synthesis of thioamidated peptides. Methods Enzymol 2021; 656:27-57. [PMID: 34325789 DOI: 10.1016/bs.mie.2021.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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12
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Ronchi E, Paradine SM, Jacobsen EN. Enantioselective, Catalytic Multicomponent Synthesis of Homoallylic Amines Enabled by Hydrogen-Bonding and Dispersive Interactions. J Am Chem Soc 2021; 143:7272-7278. [PMID: 33949857 PMCID: PMC8547772 DOI: 10.1021/jacs.1c03024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a one-step catalytic, enantioselective method for the preparation of homoallylic N-Boc amines directly from acetals. Reactive iminium ion intermediates are generated in situ through the combination of an acetal, a chiral thiourea catalyst, trialkylsilyl triflate, and N-Boc carbamate and are subsequently trapped by a variety of allylsilane nucleophiles. No homoallylic ether byproducts are detected, consistent with allylation of the iminium intermediate being highly favored over allylation of the intermediate oxocarbenium ion. Acetals derived from aromatic aldehydes possessing a variety of functional groups and substitution patterns yield homoallylic amines with excellent levels of enantiomeric enrichment. Experimental and computational data are consistent with an anchoring hydrogen-bond interaction between the protioiminium ion and the amide of the catalyst in the enantiodetermining transition state, and with stereodifferentiation achieved through specific noncovalent interactions (NCIs) with the catalyst pyrenyl moiety. Evidence is provided that the key NCI in the major pathway is a π-stacking interaction, contrasting with the cation-π interactions invoked in previously studied reactions promoted by the same family of aryl-pyrrolidino-H-bond-donor catalysts.
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Affiliation(s)
| | | | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
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13
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Yang P, Wang X, Ma Y, Sun Y, Zhang L, Yue J, Fu K, Zhou JS, Tang B. Nickel-catalyzed C-alkylation of thioamide, amides and esters by primary alcohols through a hydrogen autotransfer strategy. Chem Commun (Camb) 2020; 56:14083-14086. [PMID: 33107876 DOI: 10.1039/d0cc06468h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A simple catalyst of Ni(OAc)2 and P(t-Bu)3 enables selective C-alkylation of thioacetamides and primary acetamides with alcohols for the first time. Monoalkylation of thioamides, amides and t-butyl esters occurs in excellent yields (>95%). Mechanistic studies reveal that the reaction proceeds via a hydrogen autotransfer pathway.
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Affiliation(s)
- Peng Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Xiuhua Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Yu Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Yaxin Sun
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Li Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Jieyu Yue
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Kaiyue Fu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
| | - Jianrong Steve Zhou
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Room F312, 2199 Lishui Road, Nanshan District, Shenzhen 518055, China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, P. R. China.
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14
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Khatri B, Majumder P, Nagesh J, Penmatsa A, Chatterjee J. Increasing protein stability by engineering the n → π* interaction at the β-turn. Chem Sci 2020; 11:9480-9487. [PMID: 34094214 PMCID: PMC8161691 DOI: 10.1039/d0sc03060k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abundant n → π* interactions between adjacent backbone carbonyl groups, identified by statistical analysis of protein structures, are predicted to play an important role in dictating the structure of proteins. However, experimentally testing the prediction in proteins has been challenging due to the weak nature of this interaction. By amplifying the strength of the n → π* interaction via amino acid substitution and thioamide incorporation at a solvent exposed β-turn within the GB1 proteins and Pin 1 WW domain, we demonstrate that an n → π* interaction increases the structural stability of proteins by restricting the ϕ torsion angle. Our results also suggest that amino acid side-chain identity and its rotameric conformation play an important and decisive role in dictating the strength of an n → π* interaction. Amino acid residues adopt a right-handed α-helical conformation with increasing strength of the n → π* interaction. We also demonstrate a direct consequence of n → π* interactions on enhancing the structural stability of proteins.![]()
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science Bangalore 560012 India
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15
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Khatri B, Bhat P, Chatterjee J. Convenient synthesis of thioamidated peptides and proteins. J Pept Sci 2020; 26:e3248. [PMID: 32202029 DOI: 10.1002/psc.3248] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 12/13/2022]
Abstract
The unique physicochemical properties of a thioamide bond, which is an ideal isostere of an amide bond, have not been fully exploited because of the tedious synthesis of thionated amino acid building blocks. Here, we report a purification-free and highly efficient synthesis of thiobenzotriazolides of Fmoc-protected and orthogonally protected 20 naturally occurring amino acids including asparagine, glutamine, and histidine. The near-quantitative conversion to the respective thioamidated peptides on solid support demonstrates the robustness of the synthetic route. Furthermore, the unaltered incorporation efficiency of thiobenzotriazolides from their stock solution till 48 h suggests their compatibility toward automated peptide synthesis. Finally, utilizing an optimized cocktail of 2% DBU + 5% piperazine for fast Fmoc-deprotection, we report the synthesis of a thioamidated Pin1 WW domain and thioamidated GB1 directly on solid support.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Prabhat Bhat
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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16
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Yang J, Wang C, Yao C, Chen C, Hu Y, He G, Zhao J. Site-Specific Incorporation of Multiple Thioamide Substitutions into a Peptide Backbone via Solid Phase Peptide Synthesis. J Org Chem 2019; 85:1484-1494. [DOI: 10.1021/acs.joc.9b02486] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jinhua Yang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Changliu Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Chaochao Yao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Chunqiu Chen
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Yafang Hu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Guifeng He
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
| | - Junfeng Zhao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, P. R. China
- Key Laboratory of Chemical Biology of Jiangxi Province, Nanchang 330022, Jiangxi, P. R. China
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17
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18
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Acharyya A, DiGiuseppi D, Stinger BL, Schweitzer-Stenner R, Vaden TD. Structural Destabilization of Azurin by Imidazolium Chloride Ionic Liquids in Aqueous Solution. J Phys Chem B 2019; 123:6933-6945. [DOI: 10.1021/acs.jpcb.9b04113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, Pennsylvania 19104, United States
| | - David DiGiuseppi
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Brittany L. Stinger
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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19
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Saito M, Kobayashi Y, Takemoto Y. Divergent and Chemoselective Transformations of Thioamides with Designed Carbene Equivalents. Chemistry 2019; 25:10314-10318. [DOI: 10.1002/chem.201902699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Masato Saito
- Graduate School of Pharmaceutical SciencesKyoto University 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku Kyoto 606-8501 Japan
| | - Yusuke Kobayashi
- Graduate School of Pharmaceutical SciencesKyoto University 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku Kyoto 606-8501 Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical SciencesKyoto University 46-29 Shimoadachi-cho, Yoshida, Sakyo-ku Kyoto 606-8501 Japan
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20
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Oppermann M, Spekowius J, Bauer B, Pfister R, Chergui M, Helbing J. Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics. J Phys Chem Lett 2019; 10:2700-2705. [PMID: 31059267 DOI: 10.1021/acs.jpclett.9b01253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combining transient CD spectroscopy in the deep-UV with thioamide substitution, we demonstrate a method to overcome this difficulty. We investigated a dipeptide whose two carbonyl oxygen atoms were replaced by sulfur, red-shifting the strong lowest-lying ππ* transitions into the more accessible 250-370 nm spectral window. Coupling of the two thioamide units cannot be resolved by achiral 2D-UV spectroscopy, but it gives rise to a pronounced bisignate CD spectrum. The transient CD spectra reveal weakening of this coupling in the electronically excited state, where conformational constraints are released. Our results show that direct local probing of fast backbone conformational change via CD spectroscopy is possible in combination with site-selective thio substitution in peptides and proteins.
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Affiliation(s)
- Malte Oppermann
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Jasmin Spekowius
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Benjamin Bauer
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Rolf Pfister
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Majed Chergui
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Jan Helbing
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
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21
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Mahanta N, Szantai-Kis DM, Petersson EJ, Mitchell DA. Biosynthesis and Chemical Applications of Thioamides. ACS Chem Biol 2019; 14:142-163. [PMID: 30698414 PMCID: PMC6404778 DOI: 10.1021/acschembio.8b01022] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Thioamidation as a posttranslational modification is exceptionally rare, with only a few reported natural products and exactly one known protein example (methyl-coenzyme M reductase from methane-metabolizing archaea). Recently, there has been significant progress in elucidating the biosynthesis and function of several thioamide-containing natural compounds. Separate developments in the chemical installation of thioamides into peptides and proteins have enabled cell biology and biophysical studies to advance the current understanding of natural thioamides. This review highlights the various strategies used by Nature to install thioamides in peptidic scaffolds and the potential functions of this rare but important modification. We also discuss synthetic methods used for the site-selective incorporation of thioamides into polypeptides with a brief discussion of the physicochemical implications. This account will serve as a foundation for the further study of thioamides in natural products and their various applications.
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Affiliation(s)
| | - D Miklos Szantai-Kis
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
| | - E James Petersson
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , Pennsylvania 19104 , United States
- Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104 , United States
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22
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Lahiri P, Verma H, Ravikumar A, Chatterjee J. Protein stabilization by tuning the steric restraint at the reverse turn. Chem Sci 2018; 9:4600-4609. [PMID: 29899953 PMCID: PMC5969505 DOI: 10.1039/c7sc05163h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
The incorporation of pseudoallylic strain by N-methylation at the solvent exposed loop in proteins leads to a stark increase in their thermodynamic stability that can be tuned by altering the amino acid composition.
Reverse turns are solvent-exposed motifs in proteins that are crucial in nucleating β-sheets and drive the protein folding. The solvent-exposed nature makes reverse turns more amenable to chemical modifications than α-helices or β-sheets towards modulating the stability of re-engineered proteins. Here, we utilize van der Waals repulsive forces in tuning the steric restraint at the reverse turn. The steric restraint induced upon N-methylation of the i+1–i+2 amide bond at the reverse turn results in well-folded and stable β-sheets in aqueous solution at room temperature. The developed superactive turn inducing motif is tolerant to a wide variety of functional groups present on coded amino acids making the designed turn fully compatible with bioactive loops in proteins. We demonstrate that the steric restraint and the functional groups at the reverse turn act in synergy to modulate the folding of re-engineered β-sheets. Introduction of the turn motifs onto a three-stranded β-sheet protein, Pin 1 WW domain, resulted in various analogs showing a cooperative two-state transition with thermal stability (TM) ranging from 62 °C to 82 °C. Despite modulating the stability of Pin 1 variants by ∼2.8 kcal mol–1 (ΔΔGf), the native fold in all the protein variants was found to be unperturbed. This structural stability is brought about by conformational preorganization at the engineered reverse turn that results in strong intramolecular hydrogen bonds along the three dimensional structure of the protein. Thus, this simple loop engineering strategy via two amino acid substitution provides us a “toolkit” to modulate the stability of β-sheet containing peptides and proteins in aqueous solution that will greatly expand the scope of de novo protein and foldamer design.
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Affiliation(s)
- Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Ashraya Ravikumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
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23
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Soares P, Lucas X, Ciulli A. Thioamide substitution to probe the hydroxyproline recognition of VHL ligands. Bioorg Med Chem 2018; 26:2992-2995. [PMID: 29650462 PMCID: PMC6008493 DOI: 10.1016/j.bmc.2018.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 11/28/2022]
Abstract
Thioamide substitution influences hydrogen bond and n → π∗ interactions involved in the conformational stability of protein secondary structures and oligopeptides. Hydroxyproline is the key recognition element of small molecules targeting the von Hippel-Lindau (VHL) E3 ligase, which are of interest as probes of hypoxia signaling and ligands for PROTAC conjugation. We hypothesized that VHL ligands could be a privileged model system to evaluate the contribution of these interactions to protein:ligand complex formation. Herein we report the synthesis of VHL ligands bearing thioamide substitutions at the central hydroxyproline moiety, and characterize their binding by fluorescence polarization, isothermal titration calorimetry, X-ray crystallography and molecular modeling. In spite of a conserved binding mode, the substitution pattern had a pronounced impact on the ligand affinities. Together the results underscore the role of hydrogen bond and n → π∗ interactions in fine tuning hydroxyproline recognition by VHL.
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Affiliation(s)
- Pedro Soares
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Xavier Lucas
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
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24
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Walters CR, Ferrie JJ, Petersson EJ. Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin. Chem Commun (Camb) 2018; 54:1766-1769. [PMID: 29383362 PMCID: PMC5845795 DOI: 10.1039/c8cc00104a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Thioamide substitutions in the backbones of proteins can modulate their structure and thermostability, or serve as spectroscopic probes in fluorescence quenching experiments. Using native chemical ligation, we have produced the first examples of a protein (calmodulin) containing two thioamides. Dithioamide variants were made to explore the effects of combining stabilizing, neutral, and destabilizing single thioamide substitutions. One of the dithioamide calmodulin variants exhibited stabilization greater than any monothioamide variant, although the effect could not easily be anticipated from the results of single substitutions. Each of the calmodulin variants retained the ability to bind a target peptide, and the dithioamide proteins exhibited an increase in fluorescence quenching of tryptophan relative to their single thioamide counterparts. These results show that multiply thioamidated proteins can be synthesized, and that properly placed thioamides can be used to increase protein thermostability or enhance fluorecsence quenching in peptide binding experiments.
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Affiliation(s)
- Christopher R Walters
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
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25
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Huang Y, Ferrie JJ, Chen X, Zhang Y, Szantai-Kis DM, Chenoweth DM, Petersson EJ. Electronic interactions of i, i + 1 dithioamides: increased fluorescence quenching and evidence for n-to-π* interactions. Chem Commun (Camb) 2018; 52:7798-801. [PMID: 27229876 DOI: 10.1039/c6cc00105j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Thioamide residues can be effective, minimally-perturbing fluorescence quenching probes for studying protein folding and proteolysis. In order to increase the level of quenching, we have here explored the use of adjacent dithioamides. We have found that they are more effective fluorescence quenchers, as expected, but we have also observed unexpected changes in the thioamide absorption spectra that may arise from n-to-π* interactions of the thiocarbonyls. We have made use of the increased quenching to improve the fluorescence turn-on of thioamide protease sensors.
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Affiliation(s)
- Yun Huang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - Xing Chen
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - Yitao Zhang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - D Miklos Szantai-Kis
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA. and Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Perelman School of Medicine, 3700 Hamilton Walk, Philadelphia, PA 19104, USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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26
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Verma H, Khatri B, Chakraborti S, Chatterjee J. Increasing the bioactive space of peptide macrocycles by thioamide substitution. Chem Sci 2018; 9:2443-2451. [PMID: 29732120 PMCID: PMC5909342 DOI: 10.1039/c7sc04671e] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
We show that substituting a single atom, O to S (amide to thioamide), in a peptide bond results in global restriction of the conformational flexibility in peptide macrocycles with minimal perturbation of the parent conformation. The van der Waals interactions between the C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 S group and the surrounding atoms are the major driving force in inducing the conformational restriction, resulting in well-defined structures of these cyclic peptides with static 3-D presentation of the pharmacophores. Utilizing this property of thioamides, we report the development of a superactive antagonist of pro-angiogenic αvβ3, αvβ5 and α5β1 integrins, which are responsible for cancer cell proliferation and survival. Using simple thio-scanning and spatial screening of a non-efficacious and conformationally flexible cyclic peptide, we could achieve a more than 105 fold enhancement in its efficacy in cellulo via a single O to S substitution. The developed peptide shows better efficacy in inhibiting the pro-angiogenic integrins than the drug candidate cilengitide, with a significantly enhanced serum half-life of 36 h compared to that of cilengitide (12 h). The long shelf-life, absence of non-specific toxicity and resistance to degradation of the thioamidated macrocyclic peptides in human serum suggest the promise of thioamides in markedly improving the affinity, efficacy and pharmacology of peptide macrocycles.
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Affiliation(s)
- Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Bhavesh Khatri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Sohini Chakraborti
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India . .,NMR Research Centre , Indian Institute of Science , Bangalore 560012 , India
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27
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Chen X, Mietlicki-Baase EG, Barrett TM, McGrath LE, Koch-Laskowski K, Ferrie JJ, Hayes MR, Petersson EJ. Thioamide Substitution Selectively Modulates Proteolysis and Receptor Activity of Therapeutic Peptide Hormones. J Am Chem Soc 2017; 139:16688-16695. [PMID: 29130686 PMCID: PMC7744120 DOI: 10.1021/jacs.7b08417] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peptide hormones are attractive as injectable therapeutics and imaging agents, but they often require extensive modification by mutagenesis and/or chemical synthesis to prevent rapid in vivo degradation. Alternatively, the single-atom, O-to-S modification of peptide backbone thioamidation has the potential to selectively perturb interactions with proteases while preserving interactions with other proteins, such as target receptors. Here, we use the validated diabetes therapeutic, glucagon-like peptide-1 (GLP-1), and the target of clinical investigation, gastric inhibitory polypeptide (GIP), as proof-of-principle peptides to demonstrate the value of thioamide substitution. In GLP-1 and GIP, a single thioamide near the scissile bond renders these peptides up to 750-fold more stable than the corresponding oxopeptides toward cleavage by dipeptidyl peptidase 4, the principal regulator of their in vivo stability. These stabilized analogues are nearly equipotent with their parent peptide in cyclic AMP activation assays, but the GLP-1 thiopeptides have much lower β-arrestin potency, making them novel agonists with altered signaling bias. Initial tests show that a thioamide GLP-1 analogue is biologically active in rats, with an in vivo potency for glycemic control surpassing that of native GLP-1. Taken together, these experiments demonstrate the potential for thioamides to modulate specific protein interactions to increase proteolytic stability or tune activation of different signaling pathways.
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Affiliation(s)
- Xing Chen
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Elizabeth G. Mietlicki-Baase
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Philadelphia, PA 19104
- Current Address: Department of Exercise and Nutrition Sciences, State University of New York at Buffalo, Buffalo, G10G Farber Hall, NY 14214
| | - Taylor M. Barrett
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Lauren E. McGrath
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Philadelphia, PA 19104
| | - Kieran Koch-Laskowski
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Philadelphia, PA 19104
| | - John J. Ferrie
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
| | - Matthew R. Hayes
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, 125 South 31st Street, Philadelphia, PA 19104
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104
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28
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Mundlapati VR, Gautam S, Sahoo DK, Ghosh A, Biswal HS. Thioamide, a Hydrogen Bond Acceptor in Proteins and Nucleic Acids. J Phys Chem Lett 2017; 8:4573-4579. [PMID: 28876948 DOI: 10.1021/acs.jpclett.7b01810] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···S═C H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···S═C H-bond is ∼-30 kJ/mol, which suggests that the amide-N-H···S═C H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···S═C H-bonds in nucleobase pairing and protein folding.
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Affiliation(s)
- V Rao Mundlapati
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanjeev Gautam
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arindam Ghosh
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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29
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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30
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Walters CR, Szantai-Kis DM, Zhang Y, Reinert ZE, Horne WS, Chenoweth DM, Petersson EJ. The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts. Chem Sci 2017; 8:2868-2877. [PMID: 28553525 PMCID: PMC5428018 DOI: 10.1039/c6sc05580j] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/24/2017] [Indexed: 12/17/2022] Open
Abstract
Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.
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Affiliation(s)
- Christopher R Walters
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - D Miklos Szantai-Kis
- Biochemistry and Molecular Biophysics Graduate Group , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , PA 19104 , USA
| | - Yitao Zhang
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - Zachary E Reinert
- 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
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - E James Petersson
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
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31
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Xue RJ, Grofe A, Yin H, Qu Z, Gao J, Li H. Perturbation Approach for Computing Infrared Spectra of the Local Mode of Probe Molecules. J Chem Theory Comput 2017; 13:191-201. [PMID: 28068771 DOI: 10.1021/acs.jctc.6b00733] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Linear and two-dimensional infrared (IR) spectroscopy of site-specific probe molecules provides an opportunity to gain a molecular-level understanding of the local hydrogen-bonding network, conformational dynamics, and long-range electrostatic interactions in condensed-phase and biological systems. A challenge in computation is to determine the time-dependent vibrational frequencies that incorporate explicitly both nuclear quantum effects of vibrational motions and an electronic structural representation of the potential energy surface. In this paper, a nuclear quantum vibrational perturbation (QVP) method is described for efficiently determining the instantaneous vibrational frequency of a chromophore in molecular dynamics simulations. Computational efficiency is achieved through the use of (a) discrete variable representation of the vibrational wave functions, (b) a perturbation theory to evaluate the vibrational energy shifts due to solvent dynamic fluctuations, and (c) a combined QM/MM potential for the systems. It was found that first-order perturbation is sufficiently accurate, enabling time-dependent vibrational frequencies to be obtained on the fly in molecular dynamics. The QVP method is illustrated in the mode-specific linear and 2D-IR spectra of the H-Cl stretching frequency in the HCl-water clusters and the carbonyl stretching vibration of acetone in aqueous solution. To further reduce computational cost, a hybrid strategy was proposed, and it was found that the computed vibrational spectral peak position and line shape are in agreement with experimental results. In addition, it was found that anharmonicity is significant in the H-Cl stretching mode, and hydrogen-bonding interactions further enhance anharmonic effects. The present QVP method complements other computational approaches, including path integral-based molecular dynamics, and represents a major improvement over the electrostatics-based spectroscopic mapping procedures.
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Affiliation(s)
- Rui-Jie Xue
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Adam Grofe
- Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - He Yin
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Zexing Qu
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
| | - Jiali Gao
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China.,Department of Chemistry and Supercomputing Institute, University of Minnesota , 207 Pleasant Street, SE, Minneapolis, Minnesota 55455, United States
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University , 2519 Jiefang Road, Changchun 130023, People's Republic of China
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32
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Park HS, Kang YK. Effects of isosteric substitutions on the conformational preference and cis–trans isomerization of proline-containing peptides. NEW J CHEM 2017. [DOI: 10.1039/c7nj01403a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Isosteric substitutions of the peptide CO group by CS and CSe groups increased thetranspopulation and rotational barrier to the prolylcis–transisomerization of proline-containing peptides.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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33
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Liu W, Huang B, Kuang Y, Liu G. Molecular dynamics simulations elucidate conformational selection and induced fit mechanisms in the binding of PD-1 and PD-L1. MOLECULAR BIOSYSTEMS 2017; 13:892-900. [DOI: 10.1039/c7mb00036g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PD-L1 binds PD-1 through a complex mechanism including both the conformational selection and induced fit pathways.
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Affiliation(s)
- Wenping Liu
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
- Division of Birth Cohort Study
| | - Bing Huang
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006
- China
| | - Yashu Kuang
- Division of Birth Cohort Study
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou 510623
- China
| | - Guangjian Liu
- Division of Birth Cohort Study
- Guangzhou Women and Children's Medical Center
- Guangzhou Medical University
- Guangzhou 510623
- China
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34
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Mukherjee S, Chatterjee J. Suppressing the epimerization of endothioamide peptides during Fmoc/t-Bu-based solid phase peptide synthesis. J Pept Sci 2016; 22:664-672. [DOI: 10.1002/psc.2929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Somnath Mukherjee
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
- NMR Research Centre; Indian Institute of Science; Bangalore 560012 India
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35
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Lin W, Erdmann F, Quintero A, Fischer G, Zhang Y. Thioxylated cyclosporin A for studying protein-drug interactions. Bioorg Med Chem Lett 2016; 26:5754-5756. [PMID: 27815116 DOI: 10.1016/j.bmcl.2016.10.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 12/20/2022]
Abstract
Single atom substitution of cyclosporin A (CsA) through thioxylation has been used to study the structure-activity relationship of the immunosuppressive complex, involving the CsA receptor protein cyclophilin 18 (Cyp18) and the immunological target protein phosphatase calcineurin (CaN), illustrating the contributions of peptide backbone in protein-drug interaction. Moreover, the subtle difference between thioxylation positions in CsA has led to a remarkable change in the quenching effect on Cyp18 intrinsic fluorescence. Using the thioxylated compound Cs7 as an isosteric derivative of CsA in competition assay, the experiment has led to the determination of koff value in solution. Whereas the conformational heterogeneity of CsA has been found to be associated with its two-phase binding kinetics to Cyp18, the dissociation rate of CsA from complex is independent from the initial ligand structure.
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Affiliation(s)
- Weilin Lin
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Frank Erdmann
- Institute for Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Andres Quintero
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany
| | - Gunter Fischer
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, BO Halle (Saale) Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Yixin Zhang
- B CUBE Center for Molecular Bioengineering, Technical University Dresden, Arnoldstr. 18, 01307 Dresden, Germany.
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36
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A prevalent intraresidue hydrogen bond stabilizes proteins. Nat Chem Biol 2016; 12:1084-1088. [PMID: 27748749 PMCID: PMC5110370 DOI: 10.1038/nchembio.2206] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/10/2016] [Indexed: 11/08/2022]
Abstract
Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds. Biophysical analyses demonstrate that selective attenuation or enhancement of these C5 hydrogen bonds affects the stability of synthetic β-sheets. These interactions are common, affecting approximately 5% of all residues and 94% of proteins, and their cumulative impact provides several kcal/mol of conformational stability to a typical protein. C5 hydrogen bonds stabilize, especially, the flat β-sheets of the amyloid state, which is linked with Alzheimer’s disease and other neurodegenerative disorders. Inclusion of these interactions in computational force fields would improve models of protein folding, function, and dysfunction.
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37
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De Zotti M, Peggion C, Biondi B, Crisma M, Formaggio F, Toniolo C. Endothioxopeptides: A conformational overview. Biopolymers 2016; 106:697-713. [DOI: 10.1002/bip.22899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/08/2016] [Accepted: 06/25/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Marta De Zotti
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Cristina Peggion
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
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38
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Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
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39
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Ghosh D, Lahiri P, Verma H, Mukherjee S, Chatterjee J. Engineering β-sheets employing N-methylated heterochiral amino acids. Chem Sci 2016; 7:5212-5218. [PMID: 29449932 PMCID: PMC5784515 DOI: 10.1039/c6sc00518g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/19/2016] [Indexed: 01/01/2023] Open
Abstract
There is a lack of functional group diversity in the reverse turn motifs nucleating a β-sheet conformation in designed peptides, proteins and foldamers. The majority of these sequences consist of d-Pro-l-Pro, d-Pro-Gly or Asn-Gly as the turn inducing motif restricting their biological application and physicochemical modulation. In this report, for the first time we elucidate that N-methylation of heterochiral amino acids in linear peptides nucleates β-sheet conformation without the necessity of having a ring or covalent constraint at the reverse turn. Our results show that d-Pro can be conveniently substituted by any other N-methylated d-amino acid followed by an N-methylated l-amino acid or sarcosine to adopt a βII' turn inducing the β-sheet folding. Furthermore, we reveal that a single amino acid either at the i + 1 or i + 2 site of the reverse turn can modulate the right-handed twist, which eventually dictates the extent of the foldedness of the β-hairpin.
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Affiliation(s)
- Dipan Ghosh
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Somnath Mukherjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
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40
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Wang YJ, Szantai-Kis DM, Petersson EJ. Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins. Org Biomol Chem 2016; 14:6262-9. [PMID: 27264841 DOI: 10.1039/c6ob01020b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Thioamides are single-atom substitutions of canonical amide bonds, and have been proven to be versatile and minimally perturbing probes in protein folding studies. Previously, our group showed that thioamides can be incorporated into proteins by native chemical ligation (NCL) with Cys as a ligation handle. In this study, we report the expansion of this strategy into non-Cys ligation sites, utilizing radical initiated desulfurization to "erase" the side chain thiol after ligation. The reaction exhibited high chemoselectivity against thioamides, which can be further enhanced with thioacetamide as a sacrificial scavenger. As a proof-of-concept example, we demonstrated the incorporation of a thioamide probe into a 56 amino acid protein, the B1 domain of Protein G (GB1). Finally, we showed that the method can be extended to β-thiol amino acid analogs and selenocysteine.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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41
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Ding B, Hilaire MR, Gai F. Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function. J Phys Chem B 2016; 120:5103-13. [PMID: 27183318 DOI: 10.1021/acs.jpcb.6b03199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While folding or performing functions, a protein can sample a rich set of conformational space. However, experimentally capturing all of the important motions with sufficient detail to allow a mechanistic description of their dynamics is nontrivial since such conformational events often occur over a wide range of time and length scales. Therefore, many methods have been employed to assess protein conformational dynamics, and depending on the nature of the conformational transition in question, some may be more advantageous than others. Herein, we describe our recent efforts, and also those of others, wherever appropriate, to use infrared- and fluorescence-based techniques to interrogate protein folding and functional dynamics. Specifically, we focus on discussing how to use extrinsic spectroscopic probes to enhance the structural resolution of these techniques and how to exploit various cross-linking strategies to acquire dynamic and mechanistic information that was previously difficult to attain.
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Affiliation(s)
- Bei Ding
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Mary Rose Hilaire
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry and ‡The Ultrafast Optical Processes Laboratory, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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42
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Wang YJ, Szantai-Kis DM, Petersson EJ. Semi-synthesis of thioamide containing proteins. Org Biomol Chem 2016; 13:5074-81. [PMID: 25811732 DOI: 10.1039/c5ob00224a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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43
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Milen M, Slégel P, Keglevich P, Keglevich G, Simig G, Volk B. Efficient synthesis of N b -thioacyltryptamine derivatives by a three-component Willgerodt–Kindler reaction, and their transformation to 1-substituted-3,4-dihydro-β-carbolines. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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44
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Fang B, Wang T, Chen X, Jin T, Zhang R, Zhuang W. Modeling Vibrational Spectra of Ester Carbonyl Stretch in Water and DMSO Based on Molecular Dynamics Simulation. J Phys Chem B 2015; 119:12390-6. [PMID: 26335032 DOI: 10.1021/acs.jpcb.5b06541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
On the basis of molecular dynamics simulation, we model the ester carbonyl stretch FTIR signals of methyl acetate in D2O and DMSO. An ab initio map is constructed at the B3LYP/6-311++G** level to relate the carbonyl stretch frequency to the external electric field. Using this map, fluctuating Hamiltonian of the carbonyl stretch is constructed from the MD simulation trajectory. The IR spectra calculated based on this Hamiltonian are found to be in good agreement with the experiment. For methyl acetate in D2O, hydrogen bonding on alkoxy oxygen causes a blue shift of frequency, while that on carbonyl oxygen causes a red shift. Two peaks observed in FTIR signals originate from the balance of these two effects. Furthermore, in both D2O and DMSO solutions, correlations are found between the instantaneous electric field on C═O and the frequencies. Broader line width of the signal in D2O suggests a more inhomogeneous electric field distribution due to the complicated hydrogen-bonding environment.
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Affiliation(s)
- Bin Fang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Tianjun Wang
- Department of Chemistry, ShanghaiTech University , 19 Yueyang Road, Shanghai 200031, China
| | - Xian Chen
- Key Laboratory of Physics and Technology for Advanced Batteries (Ministry of Education), Department of Physics, Jilin University , 2699 Qianjin Street, ChangChun 130012, China
| | - Tan Jin
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road, Dalian 116023, Liaoning, China
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45
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Sequence, structure, and cooperativity in folding of elementary protein structural motifs. Proc Natl Acad Sci U S A 2015. [PMID: 26216963 DOI: 10.1073/pnas.1506309112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Residue-level unfolding of two helix-turn-helix proteins--one naturally occurring and one de novo designed--is reconstructed from multiple sets of site-specific (13)C isotopically edited infrared (IR) and circular dichroism (CD) data using Ising-like statistical-mechanical models. Several model variants are parameterized to test the importance of sequence-specific interactions (approximated by Miyazawa-Jernigan statistical potentials), local structural flexibility (derived from the ensemble of NMR structures), interhelical hydrogen bonds, and native contacts separated by intervening disordered regions (through the Wako-Saitô-Muñoz-Eaton scheme, which disallows such configurations). The models are optimized by directly simulating experimental observables: CD ellipticity at 222 nm for model proteins and their fragments and (13)C-amide I' bands for multiple isotopologues of each protein. We find that data can be quantitatively reproduced by the model that allows two interacting segments flanking a disordered loop (double sequence approximation) and incorporates flexibility in the native contact maps, but neither sequence-specific interactions nor hydrogen bonds are required. The near-identical free energy profiles as a function of the global order parameter are consistent with expected similar folding kinetics for nearly identical structures. However, the predicted folding mechanism for the two motifs is different, reflecting the order of local stability. We introduce free energy profiles for "experimental" reaction coordinates--namely, the degree of local folding as sensed by site-specific (13)C-edited IR, which highlight folding heterogeneity and contrast its overall, average description with the detailed, local picture.
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46
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Mukherjee S, Verma H, Chatterjee J. Efficient Site-Specific Incorporation of Thioamides into Peptides on a Solid Support. Org Lett 2015; 17:3150-3. [DOI: 10.1021/acs.orglett.5b01484] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Somnath Mukherjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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47
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Nelli YR, Antunes S, Salaün A, Thinon E, Massip S, Kauffmann B, Douat C, Guichard G. Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site-Specific Perturbation of the Helix Geometry. Chemistry 2014; 21:2870-80. [DOI: 10.1002/chem.201405792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 01/05/2023]
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48
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Yu Z, Selvam S, Mao H. Intermediates Stabilized by Tryptophan Pairs Exist in Trpzip Beta-Hairpins. Biochemistry 2014; 53:5978-86. [DOI: 10.1021/bi500194g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zhongbo Yu
- Department
of Chemistry and
Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Sangeetha Selvam
- Department
of Chemistry and
Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department
of Chemistry and
Biochemistry, Kent State University, Kent, Ohio 44242, United States
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49
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Mout R, Tonga GY, Ray M, Moyano DF, Xing Y, Rotello VM. Environmentally responsive histidine-carboxylate zipper formation between proteins and nanoparticles. NANOSCALE 2014; 6:8873-7. [PMID: 24960536 PMCID: PMC4113908 DOI: 10.1039/c4nr02097a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interfacing synthetic materials with biomacromolecules provides new systems for biological applications. We report the creation of a reversible multivalent supramolecular "zipper" recognition motif between gold nanoparticles and proteins. In this assembly, carboxylate-functionalized nanoparticles interact strongly with oligohistidine tags. This interaction can be tuned through His-tag length, and offers unique binding profiles based on the pH and electrolyte concentration of the medium.
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Affiliation(s)
- Rubul Mout
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, Massachusetts 01003, USA.
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50
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Petersson EJ, Goldberg JM, Wissner RF. On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability. Phys Chem Chem Phys 2014; 16:6827-37. [PMID: 24598971 DOI: 10.1039/c3cp55525a] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our laboratory has developed thioamide analogs of the natural amino acids as minimally-perturbing fluorescence quenching probes that can be placed at many locations in a protein sequence. We have shown that the mechanism of quenching can be either Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), depending on the identity of the donor fluorophore. Furthermore, we have shown that one can use a combination of semi-synthetic methods to label full-sized proteins with fluorophore-thioamide pairs. These probes can be used to study protein-protein interactions, protein folding or misfolding, and proteolysis.
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Affiliation(s)
- E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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