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Miao Q, Dekkers R, Gupta KBSS, Overhand M, Dasgupta R, Ubbink M. Rigidified and Hydrophilic DOTA-like Lanthanoid Ligands: Design, Synthesis, and Dynamic Properties. Inorg Chem 2023; 62:3776-3787. [PMID: 36802549 PMCID: PMC9996828 DOI: 10.1021/acs.inorgchem.2c03768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Limiting the dynamics of paramagnetic tags is crucial for the accuracy of the structural information derived from paramagnetic nuclear magnetic resonance (NMR) experiments. A hydrophilic rigid 2,2',2″,2‴-(1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrayl)tetraacetic acid (DOTA)-like lanthanoid complex was designed and synthesized following a strategy that allows the incorporation of two sets of two adjacent substituents. This resulted in a C2 symmetric hydrophilic and rigid macrocyclic ring, featuring four chiral hydroxyl-methylene substituents. NMR spectroscopy was used to investigate the conformational dynamics of the novel macrocycle upon complexation with europium and compared to DOTA and its derivatives. The twisted square antiprismatic and square antiprismatic conformers coexist, but the former is favored, which is different from DOTA. Two-dimensional 1H exchange spectroscopy shows that ring flipping of the cyclen-ring is suppressed due to the presence of the four chiral equatorial hydroxyl-methylene substituents at proximate positions. The reorientation of the pendant arms causes conformational exchange between two conformers. The reorientation of the coordination arms is slower when the ring flipping is suppressed. This indicates that these complexes are suitable scaffolds to develop rigid probes for paramagnetic NMR of proteins. Due to their hydrophilic nature, it is anticipated that they are less likely to cause protein precipitation than their more hydrophobic counterparts.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands.,College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - René Dekkers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Karthick Babu Sai Sankar Gupta
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Rubin Dasgupta
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, Stockholm 17177, Sweden
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Skinner SP, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. Corrigendum: A Two-Armed Probe for In-Cell DEER Measurements on Proteins. Chemistry 2021; 27:6994. [PMID: 33887092 DOI: 10.1002/chem.202100954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Miao Q, Zurlo E, de Bruin D, Wondergem JAJ, Timmer M, Blok A, Heinrich D, Overhand M, Huber M, Ubbink M. A Two-Armed Probe for In-Cell DEER Measurements on Proteins*. Chemistry 2020; 26:17128-17133. [PMID: 33200852 PMCID: PMC7839491 DOI: 10.1002/chem.202002743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022]
Abstract
The application of double electron‐electron resonance (DEER) with site‐directed spin labeling (SDSL) to measure distances in proteins and protein complexes in living cells puts rigorous restraints on the spin‐label. The linkage and paramagnetic centers need to resist the reducing conditions of the cell. Rigid attachment of the probe to the protein improves precision of the measured distances. Here, three two‐armed GdIII complexes, GdIII‐CLaNP13a/b/c were synthesized. Rather than the disulfide linkage of most other CLaNP molecules, a thioether linkage was used to avoid reductive dissociation of the linker. The doubly GdIII labeled N55C/V57C/K147C/T151C variants of T4Lysozyme were measured by 95 GHz DEER. The constructs were measured in vitro, in cell lysate and in Dictyostelium discoideum cells. Measured distances were 4.5 nm, consistent with results from paramagnetic NMR. A narrow distance distribution and typical modulation depth, also in cell, indicate complete and durable labeling and probe rigidity due to the dual attachment sites.
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Affiliation(s)
- Qing Miao
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Enrico Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Donny de Bruin
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Joeri A J Wondergem
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Doris Heinrich
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands.,Fraunhofer Institute for Silicate Research ISC, 97082, Würzburg, Germany
| | - Mark Overhand
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO box 9504, 2300, RA, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333, CC, Leiden, The Netherlands
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Miao Q, Liu WM, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019; 58:13093-13100. [PMID: 31314159 PMCID: PMC6771572 DOI: 10.1002/anie.201906049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/15/2019] [Indexed: 01/20/2023]
Abstract
Synthetic metal complexes can be used as paramagnetic probes for the study of proteins and protein complexes. Herein, two transition metal NMR probes (TraNPs) are reported. TraNPs are attached through two arms to a protein to generate a pseudocontact shift (PCS) using cobalt(II), or paramagnetic relaxation enhancement (PRE) with manganese(II). The PCS analysis of TraNPs attached to three different proteins shows that the size of the anisotropic component of the magnetic susceptibility depends on the probe surroundings at the surface of the protein, contrary to what is observed for lanthanoid‐based probes. The observed PCS are relatively small, making cobalt‐based probes suitable for localized studies, such as of an active site. The obtained PREs are stronger than those obtained with nitroxide spin labels and the possibility to generate both PCS and PRE offers advantages. The properties of TraNPs in comparison with other cobalt‐based probes are discussed.
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Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Wei-Min Liu
- Department of Chemistry, Fu Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New, Taipei City, 24205, Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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6
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Miao Q, Liu W, Kock T, Blok A, Timmer M, Overhand M, Ubbink M. A Double‐Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Qing Miao
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Wei‐Min Liu
- Department of Chemistry Fu Jen Catholic University No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City 24205 Taiwan
| | - Thomas Kock
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anneloes Blok
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Monika Timmer
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mark Overhand
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Marcellus Ubbink
- Gorlaeus Laboratories Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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Nabuurs RJ, Kapoerchan VV, Metaxas A, Hafith S, de Backer M, Welling MM, Jiskoot W, van den Nieuwendijk AM, Windhorst AD, Overkleeft HS, van Buchem MA, Overhand M, van der Weerd L. Bis-pyridylethenyl benzene as novel backbone for amyloid-β binding compounds. Bioorg Med Chem 2016; 24:6139-6148. [DOI: 10.1016/j.bmc.2016.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 04/28/2016] [Accepted: 05/14/2016] [Indexed: 11/16/2022]
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8
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Schilder J, Liu WM, Kumar P, Overhand M, Huber M, Ubbink M. Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement. Phys Chem Chem Phys 2016; 18:5729-42. [DOI: 10.1039/c5cp03781f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The effect of spin label mobility on the accuracy of protein–protein docking calculations was investigated using inter- and intra-molecular PRE data.
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Affiliation(s)
- Jesika Schilder
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Wei-Min Liu
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Pravin Kumar
- Department of Physics
- Huygens-Kamerlingh Onnes Laboratory
- Leiden University
- 2333 CA Leiden
- The Netherlands
| | - Mark Overhand
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
| | - Martina Huber
- Department of Physics
- Huygens-Kamerlingh Onnes Laboratory
- Leiden University
- 2333 CA Leiden
- The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry
- Leiden University
- Gorlaeus Laboratories
- 2333 CC Leiden
- The Netherlands
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Liu W, Skinner SP, Timmer M, Blok A, Hass MAS, Filippov DV, Overhand M, Ubbink M. A Two‐Armed Lanthanoid‐Chelating Paramagnetic NMR Probe Linked to Proteins via Thioether Linkages. Chemistry 2014; 20:6256-8. [DOI: 10.1002/chem.201400257] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Wei‐Min Liu
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Simon P. Skinner
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Anneloes Blok
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Mathias A. S. Hass
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Mark Overhand
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden (The Netherlands)
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Nabuurs RJA, Kapoerchan VV, Metaxas A, de Jongh S, de Backer M, Welling MM, Jiskoot W, Windhorst AD, Overkleeft HS, van Buchem MA, Overhand M, van der Weerd L. Polyfluorinated bis-styrylbenzenes as amyloid-β plaque binding ligands. Bioorg Med Chem 2014; 22:2469-81. [PMID: 24657049 DOI: 10.1016/j.bmc.2014.02.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 02/25/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
Detection of cerebral β-amyloid (Aβ) by targeted contrast agents remains of great interest to aid the in vivo diagnosis of Alzheimer's disease (AD). Bis-styrylbenzenes have been previously reported as potential Aβ imaging agents. To further explore their potency as (19)F MRI contrast agents we synthetized several novel fluorinated bis-styrylbenzenes and studied their fluorescent properties and amyloid-β binding characteristics. The compounds showed a high affinity for Aβ plaques on murine and human brain sections. Interestingly, competitive binding experiments demonstrated that they bound to a different binding site than chrysamine G. Despite their high logP values, many bis-styrylbenzenes were able to enter the brain and label murine amyloid in vivo. Unfortunately initial post-mortem (19)F NMR studies showed that these compounds as yet do not warrant further MRI studies due to the reduction of the (19)F signal in the environment of the brain.
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Affiliation(s)
- Rob J A Nabuurs
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands.
| | - Varsha V Kapoerchan
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | | | - Sanne de Jongh
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Maaike de Backer
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Mick M Welling
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Wim Jiskoot
- Division of Drug Delivery Technology, Leiden Academic Center for Drug Research, Leiden University, Netherlands
| | | | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Mark A van Buchem
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands
| | - Mark Overhand
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Louise van der Weerd
- Department of Radiology CS2, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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Cavalli S, Overhand M, Kros A. Assembly into β-Sheet Structures upon Peptide-Liposome Conjugation through Copper(I)-Catalyzed [3+2] Azide-Alkyne Cycloaddition. Chempluschem 2014; 79:564-568. [DOI: 10.1002/cplu.201300354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 01/03/2014] [Indexed: 11/12/2022]
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Luo J, Otero JM, Yu C, Wärmländer SKTS, Gräslund A, Overhand M, Abrahams JP. Inhibiting and Reversing Amyloid‐β Peptide (1–40) Fibril Formation with Gramicidin S and Engineered Analogues. Chemistry 2013; 19:17338-48. [DOI: 10.1002/chem.201301535] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 09/12/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Jinghui Luo
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The Netherlands)
| | - José M. Otero
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The Netherlands)
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia y Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Campus Vida, Universidad de Santiago de Compostela, 15782 Santiago de Compostela (Spain)
| | - Chien‐Hung Yu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The Netherlands)
| | - Sebastian K. T. S. Wärmländer
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm (Sweden)
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, 10691 Stockholm (Sweden)
| | - Mark Overhand
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The Netherlands)
| | - Jan Pieter Abrahams
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden (The Netherlands)
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Guisado-Barrios G, Muñoz BK, Kamer PCJ, Lastdrager B, van der Marel G, Overhand M, Vega-Vázquez M, Martin-Pastor M. Cyclic decapeptide gramicidin S derivatives containing phosphines: novel ligands for asymmetric catalysis. Dalton Trans 2013; 42:1973-8. [DOI: 10.1039/c2dt31782f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Knijnenburg AD, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, Grotenbreg GM, van der Marel GA, Overkleeft HS, Overhand M. Ring-Extended Gramicidin S Analogs Containingcis δ-Sugar Amino Acid Turn Mimetics with Varying Ring Size. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200497] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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van der Knaap M, Basalan F, van de Mei HC, Busscher HJ, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and Biological Evaluation of Gramicidin S-Inspired Cyclic Mixedα/β-Peptides. Chem Biodivers 2012; 9:2494-506. [DOI: 10.1002/cbdv.201200277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Indexed: 11/06/2022]
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Liu WM, Keizers PHJ, Hass MAS, Blok A, Timmer M, Sarris AJC, Overhand M, Ubbink M. A pH-sensitive, colorful, lanthanide-chelating paramagnetic NMR probe. J Am Chem Soc 2012; 134:17306-13. [PMID: 22994925 DOI: 10.1021/ja307824e] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Paramagnetic lanthanides ions are broadly used in NMR spectroscopy. The effects of unpaired electrons on NMR spectral parameters provide a powerful tool for the characterization of macromolecular structures and dynamics. Here, a new lanthanide-chelating NMR probe, Caged Lanthanide NMR Probe-7 (CLaNP-7), is presented. It can be attached to protein surfaces via two disulfide bridges, yielding a probe that is rigid relative to the protein backbone. CLaNP-7 extends the application range of available probes. It has a yellow color, which is helpful for sample preparation. Its effects are comparable to those of CLaNP-5, but its charge is two units lower (+1) than that of CLaNP-5 (+3), reducing the change in surface potential after probe attachment. It also has a different magnetic susceptibility tensor, so by using both tags, two sets of structural restraints can be obtained per engineered cysteine pair. Moreover, it was found that the orientation of the magnetic susceptibility tensor is pH dependent (pK(a) ≈ 7) when a histidine residue is located in the neighborhood of the probe attachment site. The results show that the His imidazole group interacts with the CLaNP-7 tag. It is proposed that the histidine residue forms a hydrogen bond to a water/hydroxyl molecule that occupies the ninth coordination position on the lanthanide, thus breaking the two-fold symmetry of the CLaNP tag in a pH-dependent way.
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Affiliation(s)
- Wei-Min Liu
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
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Kapoerchan VV, Knijnenburg AD, Keizer P, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, van der Marel GA, Overkleeft HS, Overhand M. ‘Inverted’ analogs of the antibiotic gramicidin S with an improved biological profile. Bioorg Med Chem 2012; 20:6059-62. [DOI: 10.1016/j.bmc.2012.08.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 08/21/2012] [Accepted: 08/21/2012] [Indexed: 10/28/2022]
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van der Knaap M, Otero JM, Llamas-Saiz A, van Raaij MJ, Lageveen LI, Busscher HJ, Grotenbreg GM, van der Marel GA, Overkleeft HS, Overhand M. Design, synthesis and structural analysis of mixed α/β-peptides that adopt stable cyclic hairpin-like conformations. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Li J, Girard G, Florea BI, Geurink PP, Li N, van der Marel GA, Overhand M, Overkleeft HS, van Wezel GP. Identification and isolation of lantibiotics from culture: a bioorthogonal chemistry approach. Org Biomol Chem 2012; 10:8677-83. [DOI: 10.1039/c2ob26050f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dasgupta S, Hu X, Keizers PHJ, Liu WM, Luchinat C, Nagulapalli M, Overhand M, Parigi G, Sgheri L, Ubbink M. Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains. J Biomol NMR 2011; 51:253-263. [PMID: 21826520 DOI: 10.1007/s10858-011-9532-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained by substitution of three paramagnetic lanthanide ions to the calcium ion in the second calcium binding loop of the N-terminal domain. The analysis shows that the availability of paramagnetic restraints arising from metal ions placed on both domains, reduces the MO of the conformations to different extents, thereby helping to identify those conformations that can be mostly sampled by the protein.
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Affiliation(s)
- Soumyasri Dasgupta
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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21
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Carstensen EV, Duynstee HI, van der Marel GA, van Boom JH, Nielsen J, Overkleeft HS, Overhand M. Synthesis of Highly Functionalized Piperidines via a Tandem Retro‐Michael‐[2 + 3]‐Cycloaddition. J Carbohydr Chem 2011. [DOI: 10.1081/car-120021703] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | - Howard I. Duynstee
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Gijs A. van der Marel
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Jacques H. van Boom
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - John Nielsen
- b The Royal Veterinary and Agricultural University , Thorvald Sense, VEJ‐40, DK‐1871 , Frederiksberg C , Denmark
| | - Herman S. Overkleeft
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
| | - Mark Overhand
- a Leiden Institute of Chemistry , P. O. Box 9502, 2300 RA , Leiden , The Netherlands
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Knijnenburg AD, Kapoerchan VV, Grotenbreg GM, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, Ravensbergen B, Nibbering PH, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and evaluation of strand and turn modified ring-extended gramicidin S derivatives. Bioorg Med Chem 2011; 19:3402-9. [PMID: 21561781 DOI: 10.1016/j.bmc.2011.04.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/05/2011] [Accepted: 04/13/2011] [Indexed: 11/16/2022]
Abstract
In this paper, we describe the crystal structure of previously reported ring-extended gramicidin S (GS) derivative 2 (GS14K4), containing a d-amino acid residue in one of the β-strand regions. This structure is in agreement with a previously reported modeling study of the same molecule. The polar side chain of the additional d-amino acid residue is positioned at the same face of the molecule as the hydrophobic side chains, and we believe that because of this compound 2 is considerably less hydrophobic than extended GS derivatives in which the strand regions are exclusively composed of l-amino acids. Using this backbone structure as our benchmark we prepared a small series of ring-extended GS analogues featuring sugar amino acid dipeptide isosteres of varied hydrophobicity at the turn region. We show that via this approach hydrophobicity of extended GS analogues can be tuned without affecting the secondary structure (as observed from NMR and CD spectra). Biological evaluation reveals that hydrophobicity correlates to cell toxicity, but still bacteriolysis is induced with GS analogues that are too hydrophilic to efficiently lyse human red blood cells.
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van der Knaap M, Lageveen LT, Busscher HJ, Mars-Groenendijk R, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, van der Marel GA, Overkleeft HS, Overhand M. Evaluation of Readily Accessible Azoles as Mimics of the Aromatic Ring of D-Phenylalanine in the Turn Region of Gramicidin S. ChemMedChem 2011; 6:840-7. [DOI: 10.1002/cmdc.201000539] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 01/26/2011] [Indexed: 11/06/2022]
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24
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Knijnenburg AD, Tuin AW, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, van der Marel GA, Overkleeft HS, Overhand M. Exploring the Conformational and Biological Versatility of β-Turn-Modified Gramicidin S by Using Sugar Amino Acid Homologues that Vary in Ring Size. Chemistry 2011; 17:3995-4004. [DOI: 10.1002/chem.201002895] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Indexed: 11/11/2022]
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25
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Knijnenburg AD, Kapoerchan VV, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, van der Marel GA, Overkleeft HS, Overhand M. Tuning hydrophobicity of highly cationic tetradecameric Gramicidin S analogues using adamantane amino acids. Bioorg Med Chem 2010; 18:8403-9. [DOI: 10.1016/j.bmc.2010.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 11/25/2022]
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26
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Canalle LA, van der Knaap M, Overhand M, van Hest JCM. A comparison of triazole-forming bioconjugation techniques for constructing comb-shaped peptide-polymer bioconjugates. Macromol Rapid Commun 2010; 32:203-8. [PMID: 21433141 DOI: 10.1002/marc.201000507] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 09/06/2010] [Indexed: 12/18/2022]
Abstract
The grafting-to of a peptide to a side chain functional polymer was investigated using "click" chemistry. Two click reactions were compared: the copper-free strain-promoted azide-alkyne 1,3-cycloaddition (SPAAC) and the traditional copper-catalyzed azide-alkyne 1,3-cycloaddition (CuAAC). For the resulting comb-shaped products, it was found that the steric bulk of the conjugation moiety used in SPAAC limits the degree of grafting for these highly dense systems, whereas CuAAC gives (near) quantitative functionalization.
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Affiliation(s)
- Luiz A Canalle
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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27
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Risseeuw MD, Florea BI, van der Marel GA, Overkleeft HS, Overhand M. Sugar amino acid based peptide epoxyketones as potential proteasome inhibitors. Bioorg Chem 2010; 38:202-9. [DOI: 10.1016/j.bioorg.2010.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 04/20/2010] [Accepted: 04/22/2010] [Indexed: 01/30/2023]
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Kapoerchan VV, Knijnenburg AD, Niamat M, Spalburg E, de Neeling AJ, Nibbering PH, Mars-Groenendijk RH, Noort D, Otero JM, Llamas-Saiz AL, van Raaij MJ, van der Marel GA, Overkleeft HS, Overhand M. An Adamantyl Amino Acid Containing Gramicidin S Analogue with Broad Spectrum Antibacterial Activity and Reduced Hemolytic Activity. Chemistry 2010; 16:12174-81. [DOI: 10.1002/chem.201001686] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Linders J, Kokje J, Overhand M, Lie T, Maat L. Diels-Alder reaction of 6-demethoxy-β-dihydrothebaine with methyl vinyl ketone using microwave heating; preparation and pharmacology of 3-hydroxy-α,α, 17-trimethyl-6β,14β-ethenomorphinan-7β-methanol, a novel deoxygenated diprenorphine analogue (chemistry. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881070610] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Boons GJPH, Overhand M, van der Marel GA, van Boom JH. Synthesis of two branched heptopyranoside- (L,D-Hepp)-containing trisaccharides of the inner-core region of Citrobacter PCM 1487. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19921110306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Keizers PHJ, Mersinli B, Reinle W, Donauer J, Hiruma Y, Hannemann F, Overhand M, Bernhardt R, Ubbink M. A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy. Biochemistry 2010; 49:6846-55. [PMID: 20695524 DOI: 10.1021/bi100598f] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lanthanide tags offer the opportunity to retrieve long-range distance information from NMR experiments that can be used to guide protein docking. To determine whether sufficient restraints can be retrieved for proteins with low solubility and availability, Ln tags were applied in the study of the 65 kDa membrane-associated protein complex formed by the electron carrier adrenodoxin and its electron donor, adrenodoxin reductase. The reductase is only monomeric at low concentration, and the paramagnetic iron-sulfur cluster of adrenodoxin broadens many of the resonances of nuclei in the interface. Guided by the paramagnetic restraints obtained using two Ln-tag attachment sites, protein docking yields a cluster of solutions with an rmsd of 3.2 A. The mean structure is close to the crystal structure of the cross-linked complex, with an rmsd of 4.0 A. It is concluded that with the application of Ln tags paramagnetic NMR restraints for structure determination can be retrieved even for difficult, low-concentration protein complexes.
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Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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32
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Kapoerchan V, Spalburg E, de Neeling A, Mars-Groenendijk R, Noort D, Otero J, Ferraces-Casais P, Llamas-Saiz A, van Raaij M, van Doorn J, van der Marel G, Overkleeft H, Overhand M. Gramicidin S Derivatives Containingcis- andtrans-Morpholine Amino Acids (MAAs) as Turn Mimetics. Chemistry 2010; 16:4259-65. [DOI: 10.1002/chem.200902984] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Kapoerchan VV, Wiesner M, Hillaert U, Drijfhout JW, Overhand M, Alard P, van der Marel GA, Overkleeft HS, Koning F. Design, synthesis and evaluation of high-affinity binders for the celiac disease associated HLA-DQ2 molecule. Mol Immunol 2009; 47:1091-7. [PMID: 19962195 DOI: 10.1016/j.molimm.2009.10.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 10/29/2009] [Indexed: 11/26/2022]
Abstract
Celiac disease is caused by uncontrolled CD4 T-cell responses directed to wheat-derived gluten peptides bound to the disease predisposing HLA-DQ molecules. The only available treatment is a life-long gluten-free diet which is complicated by the widespread use of wheat-derived gluten in the food industry. As the binding of gluten-derived peptides is a prerequisite for the induction of the inflammatory T-cell response, blockers that would prevent gluten peptide binding to the HLA-DQ molecules might be used as an alternative to the gluten-free diet. In the present study we have analyzed the binding properties of a set of previously identified natural ligands for HLA-DQ2, the primary disease predisposing allele. An in silico method, Epibase, ranked these peptides and the top one, a peptide with a nine amino acid core FVAEYEPVL, was measured among these peptides as the peptide with the highest binding affinity for HLA-DQ2. In a stepwise approach we subsequently tested the impact of N-terminal extensions and systematic single amino acid substitutions within the core of this peptide which revealed that an N-terminal extension with the tripeptide sequence ADA increased binding affinity 5- to 6-fold. In addition the substitution analysis indicated which amino acids were most preferred at anchor residues in the lead peptide, generally leading to an increase of binding affinity with a factor of 2. Next we tested which combinations of such preferred amino acids yielded the best results. The combined results indicate that a peptide with sequence ADAYDYESEELFAA (core in bold) had superior binding properties. This peptide was chosen as a lead peptide for further optimization with non-natural amino acids at the p1 position, since molecular modeling indicated that none of the natural amino acids is able to optimally occupy the p1 pocket. A set of 8 non-proteinogenic amino acids was designed, synthesized and incorporated in the lead peptide (and in two control peptides) and tested for binding to HLA-DQ2. The results indicate that the effect of the incorporation of these non-proteinogenic amino acids depended on the peptide in which they were incorporated and that the maximum increase in binding affinity obtained was approximately 2-fold. Altogether lead sequences were obtained that have a binding affinity for HLA-DQ2 that is 100- to 200-fold higher compared to that of the gluten-derived peptide that has the highest affinity for HLA-DQ2. Such peptides are candidate lead peptides for further optimization. Our results, however, also indicate that in order to obtain further significant increases in binding affinity alternative approaches will have to be explored.
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Affiliation(s)
- Varsha V Kapoerchan
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden, The Netherlands
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34
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Knijnenburg A, Spalburg E, de Neeling A, Mars-Groenendijk R, Noort D, Grotenbreg G, van der Marel G, Overkleeft H, Overhand M. Ring-Extended Derivatives of Gramicidin S with Furanoid Sugar Amino Acids in the Turn Region Have Enhanced Antimicrobial Activity. ChemMedChem 2009; 4:1976-9. [DOI: 10.1002/cmdc.200900379] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Risseeuw MDP, van den Berg RJBHN, Donker-Koopman WE, van der Marel GA, Aerts JMFG, Overhand M, Overkleeft HS. Synthesis and evaluation of D-gluco-pyranocyclopropyl amines as potential glucosidase inhibitors. Bioorg Med Chem Lett 2009; 19:6600-3. [PMID: 19853441 DOI: 10.1016/j.bmcl.2009.10.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 10/05/2009] [Accepted: 10/06/2009] [Indexed: 10/20/2022]
Abstract
In the recent past sugar-derived cyclopropylamines were proposed as structurally new glycosidase inhibitors. In this Letter we report our efforts in the synthesis of a set of alpha-glucose configured oxabicyclo[4.1.0] heptanes, based on this hypothesis, bearing an amine substituent on the propyl ring and reveal that their inhibitory potential towards a range of mammalian glucosidases is modest.
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Affiliation(s)
- Martijn D P Risseeuw
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands
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36
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Tuin AW, Palachanis DK, Buizert A, Grotenbreg GM, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and Biological Evaluation of Novel Gramicidin S Analogues (Eur. J. Org. Chem. 25/2009). European J Org Chem 2009. [DOI: 10.1002/ejoc.200990069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Tuin AW, Palachanis DK, Buizert A, Grotenbreg GM, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, Noort D, van der Marel GA, Overkleeft HS, Overhand M. Synthesis and Biological Evaluation of Novel Gramicidin S Analogues. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900460] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Burck S, van Assema SG, Lastdrager B, Slootweg JC, Ehlers A, Otero J, Dacunha-Marinho B, Llamas-Saiz A, Overhand M, van Raaij M, Lammertsma K. Bisphosphine-Functionalized Cyclic Decapeptides Based on the Natural Product Gramicidin S: A Potential Scaffold for Transition-Metal Coordination. Chemistry 2009; 15:8134-45. [DOI: 10.1002/chem.200901127] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Tuin AW, Grotenbreg GM, Spalburg E, de Neeling AJ, Mars-Groenendijk RH, van der Marel GA, Noort D, Overkleeft HS, Overhand M. Structural and biological evaluation of some loloatin C analogues. Bioorg Med Chem 2009; 17:6233-40. [PMID: 19679485 DOI: 10.1016/j.bmc.2009.07.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/22/2009] [Indexed: 11/18/2022]
Abstract
Loloatin C is a cyclic cationic antimicrobial peptide which is active against gram positive as well as certain gram negative bacteria. Unfortunately, it is equally potent against human erythrocytes. To probe the structure-activity relationship of this promising antibiotic peptide, amino acid substitution and/or incorporation of a constraint sugar amino acid dipeptide isoster has been applied. Six new derivatives have been synthesized using SPPS and their solution structure investigated using NMR studies. Finally, the antimicrobial and the hemolytic activities have been determined.
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Affiliation(s)
- Adriaan W Tuin
- Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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40
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Risseeuw MD, van der Marel GA, Overkleeft HS, Overhand M. Pyranocyclopropanyl sugar amino acids, a new class of constrained (di)peptide isosteres. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.tetasy.2009.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Keizers PHJ, Saragliadis A, Hiruma Y, Overhand M, Ubbink M. Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment. J Am Chem Soc 2008; 130:14802-12. [PMID: 18826316 DOI: 10.1021/ja8054832] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Immobilized lanthanide ions offer the opportunity to refine structures of proteins and the complexes they form by using restraints obtained from paramagnetic NMR experiments. We report the design, synthesis, and spectroscopic evaluation of the lanthanide chelator, Caged Lanthanide NMR Probe 5 (CLaNP-5) readily attachable to a protein surface via two cysteine residues. The probe causes tunable pseudocontact shifts, alignment, paramagnetic relaxation enhancement, and luminescence, by chelating it to the appropriate lanthanide ion. The observation of single shifts and the finding that the magnetic susceptibility tensors obtained from shifts and alignment analyses are highly similar strongly indicate that the probe is rigid with respect to the protein backbone. By placing the probe at various positions on a model protein it is demonstrated that the size and orientation of the magnetic susceptibility tensor of the probe are independent of the local protein environment. Consequently, the effects of the probe are readily predictable using a protein structure only. These findings designate CLaNP-5 as a protein probe to deliver unambiguous high quality structural restraints in studies on protein-protein and protein-ligand interactions.
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Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands
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42
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43
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Röhrig CH, Loch C, Guan JY, Siegal G, Overhand M. Fragment-Based Synthesis and SAR of Modified FKBP Ligands: Influence of Different Linking on Binding Affinity. ChemMedChem 2007; 2:1054-70. [PMID: 17541991 DOI: 10.1002/cmdc.200600296] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The viability of the fragment-based approach for lead discovery depends on reliable fragment-screening methods combined with straightforward fragment-linking- or fragment-growing-chemistry. In the present study we sought a flexible synthetic approach that would allow efficient synthesis of a variety of linkers that can subsequently be tested for biological activity. We applied this approach to fragments known to bind to FKBP12 (FK506 binding protein), a peptidyl-prolyl isomerase involved in immunosuppression and neural functioning. In our set of linked FKBP ligands, ester and thioester linkages resulted in high-affinity ligands, whereas an amide linkage decreased affinity remarkably; oxime and triazole linkages were not tolerated by the target protein's binding pocket, rendering these ligands ineffective. By investigating corresponding derivatized non-linked fragments and docking studies of linked fragments, we were able to evaluate the effect of the linker region on ligand binding affinity.
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Affiliation(s)
- Christoph H Röhrig
- Leiden Institute of Chemistry, Gorlaeus Laboratories, University of Leiden, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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44
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Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Leiden, The Netherlands
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45
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Lastdrager B, Timmer MSM, van der Marel GA, Overkleeft HS, Overhand M. Transformation of Glucose into a Novel Carbasugar Amino Acid Dipeptide Isostere. J Carbohydr Chem 2007. [DOI: 10.1080/07328300701252623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Bas Lastdrager
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
| | - Mattie S. M. Timmer
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
| | | | | | - Mark Overhand
- a Leiden Institute of Chemistry, Leiden University , Leiden, The Netherlands
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46
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Llamas-Saiz AL, Grotenbreg GM, Overhand M, van Raaij MJ. Double-stranded helical twisted beta-sheet channels in crystals of gramicidin S grown in the presence of trifluoroacetic and hydrochloric acids. Acta Crystallogr D Biol Crystallogr 2007; 63:401-7. [PMID: 17327677 DOI: 10.1107/s0907444906056435] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Accepted: 12/28/2006] [Indexed: 11/10/2022]
Abstract
Gramicidin S is a nonribosomally synthesized cyclic decapeptide antibiotic with twofold symmetry (Val-Orn-Leu-D-Phe-Pro)(2); a natural source is Bacillus brevis. Gramicidin S is active against Gram-positive and some Gram-negative bacteria. However, its haemolytic toxicity in humans limits its use as an antibiotic to certain topical applications. Synthetically obtained gramicidin S was crystallized from a solution containing water, methanol, trifluoroacetic acid and hydrochloric acid. The structure was solved and refined at 0.95 A resolution. The asymmetric unit contains 1.5 molecules of gramicidin S, two trifluoroacetic acid molecules and ten water molecules located and refined in 14 positions. One gramicidin S molecule has an exact twofold-symmetrical conformation; the other deviates from the molecular twofold symmetry. The cyclic peptide adopts an antiparallel beta-sheet secondary structure with two type II' beta-turns. These turns have the residues D-Phe and Pro at positions i + 1 and i + 2, respectively. In the crystals, the gramicidin S molecules line up into double-stranded helical channels that differ from those observed previously. The implications of the supramolecular structure for several models of gramicidin S conformation and assembly in the membrane are discussed.
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Affiliation(s)
- Antonio L Llamas-Saiz
- Unidad de Difracción de Rayos X (RIAIDT), Laboratorio Integral de Dinámica y Estructura de Biomoléculas José R. Carracido, Edificio CACTUS, Campus Sur, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain.
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Vlasie MD, Comuzzi C, van den Nieuwendijk AMCH, Prudêncio M, Overhand M, Ubbink M. Long-Range-Distance NMR Effects in a Protein Labeled with a Lanthanide–DOTA Chelate. Chemistry 2007; 13:1715-23. [PMID: 17115462 DOI: 10.1002/chem.200600916] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.
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Affiliation(s)
- Monica D Vlasie
- Leiden Institute of Chemistry, Gorlaeus Laboratories Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Risseeuw MDP, Mazurek J, van Langenvelde A, van der Marel GA, Overkleeft HS, Overhand M. Synthesis of alkylated sugar amino acids: conformationally restricted l-Xaa-l-Ser/Thr mimics. Org Biomol Chem 2007; 5:2311-4. [PMID: 17609763 DOI: 10.1039/b705750d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two synthetic strategies for the generation of delta-substituted pyranoid sugar amino acids (SAAs) are evaluated. The first employs chiral nonracemic tert-butane sulfinamides as key reagents. Regardless of the stereochemistry of the applied sulfinamide, the product formed has a stereochemistry resembling that of a d amino acid at C7. Direct Grignard reaction on formyl-tetra-O-benzyl-beta-D-C-glucopyranoside in the second strategy and subsequent Mitsunobu inversion, yields the l,l-dipeptide isosters.
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Affiliation(s)
- Martijn D P Risseeuw
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis, PO box 9502, 2300 RA, Leiden, The Netherlands
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Cavalli S, Handgraaf JW, Tellers EE, Popescu DC, Overhand M, Kjaer K, Vaiser V, Sommerdijk NAJM, Rapaport H, Kros A. Two-Dimensional Ordered β-Sheet Lipopeptide Monolayers. J Am Chem Soc 2006; 128:13959-66. [PMID: 17044724 DOI: 10.1021/ja065479v] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of amphiphilic lipopeptides, ALPs, consisting of an alternating hydrophilic and hydrophobic amino acid residue sequence coupled to a phospholipid tail, was designed to form supramolecular assemblies composed of beta-sheet monolayers decorated by lipid tails at the air-water interface. A straightforward synthetic approach based on solid-phase synthesis, followed by an efficient purification protocol was used to prepare the lipid-peptide conjugates. Structural insight into the organization of monolayers was provided by surface pressure versus area isotherms, circular dichroism, Fourier transform infrared spectroscopy, and Brewster angle microscopy. In situ grazing-incidence X-ray diffraction (GIXD) revealed that lipopeptides six to eight amino acids in length form a new type of 2D self-organized monolayers that exhibit beta-sheet ribbons segregated by lipid tails. The conclusions drawn from the experimental findings were supported by a representative model based on molecular dynamics simulations of amphiphilic lipopeptides at the vacuum-water interface.
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Affiliation(s)
- Silvia Cavalli
- Contribution from the Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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Risseeuw MDP, Grotenbreg GM, Witte MD, Tuin AW, Leeuwenburgh MA, Van der Marel GA, Overkleeft HS, Overhand M. The Synthesis ofcis- andtrans-Fused Bicyclic Sugar Amino Acids. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600228] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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