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Wall BJ, Sharma KK, O’Brien EA, Donovan A, VanVeller B. General Installation of (4 H)-Imidazolone cis-Amide Bioisosteres Along the Peptide Backbone. J Am Chem Soc 2024; 146:11648-11656. [PMID: 38629317 PMCID: PMC11062833 DOI: 10.1021/jacs.3c13825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Imidazolones represent an important class of heterocycles present in a wide range of pharmaceuticals, metabolites, and bioactive natural products and serve as the active chromophore in green fluorescent protein. Recently, imidazolones have received attention for their ability to act as a nonaromatic amide bond bioisotere which improves pharmacological properties. Herein, we present a tandem amidine installation and cyclization with an adjacent ester to yield (4H)-imidazolone products. Using amino acid building blocks, we can access the first examples of α-chiral imidazolones that have been previously inaccessible. Additionally, our method is amenable to on-resin installation which can be seamlessly integrated into existing solid-phase peptide synthesis protocols. Finally, we show that peptide imidazolones are potent cis-amide bond surrogates that preorganize linear peptides for head-to-tail macrocyclization. This work represents the first general approach to the backbone and side-chain insertion of imidazolone bioisosteres at various positions in linear and cyclic peptides.
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Affiliation(s)
- Brendan J. Wall
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | | | - Aaron Donovan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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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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Contreras-Montoya R, Smith JP, Boothroyd SC, Aguilar JA, Mirzamani M, Screen MA, Yufit DS, Robertson M, He L, Qian S, Kumari H, Steed JW. Pathway complexity in fibre assembly: from liquid crystals to hyper-helical gelmorphs. Chem Sci 2023; 14:11389-11401. [PMID: 37886106 PMCID: PMC10599479 DOI: 10.1039/d3sc03841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Pathway complexity results in unique materials from the same components according to the assembly conditions. Here a chiral acyl-semicarbazide gelator forms three different gels of contrasting fibre morphology (termed 'gelmorphs') as well as lyotropic liquid crystalline droplets depending on the assembly pathway. The gels have morphologies that are either hyperhelical (HH-Gel), tape-fibre (TF-Gel) or thin fibril derived from the liquid crystalline phase (LC-Gels) and exhibit very different rheological properties. The gelator exists as three slowly interconverting conformers in solution. All three gels are comprised of an unsymmetrical, intramolecular hydrogen bonded conformer. The kinetics show that formation of the remarkable HH-Gel is cooperative and is postulated to involve association of the growing fibril with a non-gelling conformer. This single molecule dynamic conformational library shows how very different materials with different morphology and hence very contrasting materials properties can arise from pathway complexity as a result of emergent interactions during the assembly process.
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Affiliation(s)
| | - James P Smith
- Department of Chemistry, Durham University Durham DH1 3LE UK
| | | | - Juan A Aguilar
- Department of Chemistry, Durham University Durham DH1 3LE UK
| | - Marzieh Mirzamani
- James L. Winkle College of Pharmacy, University of Cincinnati 231 Albert Sabin Way, Medical Science Building 3109C Cincinnati OH 45267-0514 USA
| | - Martin A Screen
- Department of Chemistry, Durham University Durham DH1 3LE UK
| | - Dmitry S Yufit
- Department of Chemistry, Durham University Durham DH1 3LE UK
| | - Mark Robertson
- School of Polymer Science and Engineering, University of Southern Mississippi 118 College Dr. Hattiesburg MS 39406 USA
| | - Lilin He
- Neutron Scattering Division, Oak Ridge National Laboratory 1 Bethel Valley Rd. Oak Ridge TN 37831 USA
| | - Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory 1 Bethel Valley Rd. Oak Ridge TN 37831 USA
| | - Harshita Kumari
- James L. Winkle College of Pharmacy, University of Cincinnati 231 Albert Sabin Way, Medical Science Building 3109C Cincinnati OH 45267-0514 USA
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrierte Helizität: Zusammenführung divergierender Enden einer stabilen aromatischen Amid‐Helix zu einem fluxionalen Makrocyclus. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Yann Ferrand
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 München Deutschland
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrated Helicity: Joining the Diverging Ends of a Stable Aromatic Amide Helix to Form a Fluxional Macrocycle. Angew Chem Int Ed Engl 2018; 57:7888-7892. [DOI: 10.1002/anie.201802159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Yann Ferrand
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1–33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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8
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Loeffler JR, Ehmki ESR, Fuchs JE, Liedl KR. Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design. J Comput Aided Mol Des 2016; 30:391-400. [PMID: 27272323 PMCID: PMC4912590 DOI: 10.1007/s10822-016-9913-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 05/02/2016] [Indexed: 11/25/2022]
Abstract
Urea derivatives are ubiquitously found in many chemical disciplines. N,N'-substituted ureas may show different conformational preferences depending on their substitution pattern. The high energetic barrier for isomerization of the cis and trans state poses additional challenges on computational simulation techniques aiming at a reproduction of the biological properties of urea derivatives. Herein, we investigate energetics of urea conformations and their interconversion using a broad spectrum of methodologies ranging from data mining, via quantum chemistry to molecular dynamics simulation and free energy calculations. We find that the inversion of urea conformations is inherently slow and beyond the time scale of typical simulation protocols. Therefore, extra care needs to be taken by computational chemists to work with appropriate model systems. We find that both knowledge-driven approaches as well as physics-based methods may guide molecular modelers towards accurate starting structures for expensive calculations to ensure that conformations of urea derivatives are modeled as adequately as possible.
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Affiliation(s)
- Johannes R Loeffler
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Emanuel S R Ehmki
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Julian E Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria.
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
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Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [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: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
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Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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