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Bryant SJ, Garvey CJ, Darwish TA, Georgii R, Bryant G. Molecular interactions with bilayer membrane stacks using neutron and X-ray diffraction. Adv Colloid Interface Sci 2024; 326:103134. [PMID: 38518550 DOI: 10.1016/j.cis.2024.103134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/24/2024]
Abstract
Lamellar unit cell reconstruction from neutron and X-ray diffraction data provides information about the disposition and position of molecules and molecular segments with respect to the bilayer. When supplemented with the judicious use of molecular deuteration, the technique probes the molecular interactions and conformations within the bilayer membrane and the water layer which constitute the crystallographic unit cell. The perspective is model independent, and potentially, with a higher degree of resolution than is available with other techniques. In the case of neutron diffraction the measurement consists of carefully normalised diffracted intensity under conditions of contrast variation of the water layer. The subsequent Fourier reconstruction of the unit cell is made using the phase information from variation of peak intensities with contrast. Although the phase problem is not as easily solved for the corresponding X-ray measurements, an intuitive approach can often suffice. Here we discuss the two complimentary techniques as probes of scattering length density profiles of a bilayer, and how such a perspective provides information about the location and orientation of molecules within or between lipid bilayers. Within the basic paradigm of lamellar phases this method has provided, for example, detailed insights into the location and interaction of cryoprotectants and stress proteins, of the mechanisms of actions of viral proteins, antimicrobial compounds and drugs, and the underlying structure of the stratum corneum. In this paper we review these techniques and provide examples of the systems that have been examined. We finish with a future outlook on the use of these techniques to improve our understanding of the interactions of membranes with biomolecules.
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Affiliation(s)
- Saffron J Bryant
- School of Science, College of STEM, RMIT University, Melbourne, Australia
| | - Christopher J Garvey
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Tamim A Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organization, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia; Faculty of Science and Technology, University of Canberra, ACT 2617, Australia
| | - Robert Georgii
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Gary Bryant
- School of Science, College of STEM, RMIT University, Melbourne, Australia.
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2
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Katsyuba SA, Burganov TI. Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine. Spectrochim Acta A Mol Biomol Spectrosc 2024; 309:123832. [PMID: 38190776 DOI: 10.1016/j.saa.2023.123832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/26/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121-24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [J. Phys. Chem. B, 2020, 124, 6664-6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute-solvent and solvent-solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest.
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Affiliation(s)
- Sergey A Katsyuba
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia.
| | - Timur I Burganov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Centre of RAS, Arbuzov st. 8, 420088 Kazan, Russia
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3
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Zhu Y, He D, Wang C, Han X, Liu Z, Wang K, Zhang J, Shen X, Li J, Lin Y, Wang C, He Y, Zhao F. Suppressing Exciton-Vibration Coupling to Prolong Exciton Lifetime of Nonfullerene Acceptors Enables High-Efficiency Organic Solar Cells. Angew Chem Int Ed Engl 2024; 63:e202316227. [PMID: 38179837 DOI: 10.1002/anie.202316227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
The limited exciton lifetime (τ, generally <1 ns) leads to short exciton diffusion length (LD ) of organic semiconductors, which is the bottleneck issue impeding the further improvement of power conversion efficiencies (PCEs) for organic solar cells (OSCs). However, efficient strategies to prolong intrinsic τ are rare and vague. Herein, we propose a facile method to efficiently reduce vibrational frequency of molecular skeleton and suppress exciton-vibration coupling to decrease non-radiative decay rate and thus prolong τ via deuterating nonfullerene acceptors. The τ remarkably increases from 0.90 ns (non-deuterated L8-BO) to 1.35 ns (deuterated L8-BO-D), which is the record for organic photovoltaic materials. Besides, the inhibited molecular vibration improves molecular planarity of L8-BO-D for enhanced exciton diffusion coefficient. Consequently, the LD increases from 7.9 nm (L8-BO) to 10.7 nm (L8-BO-D). The prolonged LD of L8-BO-D enables PM6 : L8-BO-D-based bulk heterojunction OSCs to acquire higher PCEs of 18.5 % with more efficient exciton dissociation and weaker charge carrier recombination than PM6 : L8-BO-based counterparts. Moreover, benefiting from the prolonged LD , D18/L8-BO-D-based pseudo-planar heterojunction OSCs achieve an impressive PCE of 19.3 %, which is among the highest values. This work provides an efficient strategy to increase the τ and thus LD of organic semiconductors, boosting PCEs of OSCs.
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Affiliation(s)
- Yufan Zhu
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, P. R. China
| | - Dan He
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, P. R. China
| | - Chong Wang
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xiao Han
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Zesheng Liu
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Ke Wang
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, P. R. China
| | - Jianqi Zhang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, P. R. China
| | - Xingxing Shen
- College of Chemical Engineering, Hebei Normal University of Science & Technology, Qinhuangdao, 066004, P. R. China
| | - Jie Li
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yuze Lin
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Chunru Wang
- University of Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Organic Solids and Laboratory of Molecular Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yuehui He
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, P. R. China
| | - Fuwen Zhao
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, 410083, P. R. China
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4
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Taylor T, Gillette W. Production of Isotopically Labeled KRAS4b. Methods Mol Biol 2024; 2797:23-34. [PMID: 38570450 DOI: 10.1007/978-1-0716-3822-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Isotopically labelled proteins are important reagents in structural biology as well as in targeted drug development. The field continues to advance with complex multi-isotope labeling. We have combined our experience in high-level soluble KRAS4b expression with protocols for isotope incorporation, to achieve reliable and efficient approaches for several labeling strategies. Typical experiments achieve nearly 100% 15N incorporation, with yields in the range of 1.3-24.6 mg/L (median = 6.4 mg/L, n = 53). Improvements in the growth parameters in the presence of deuterium reduce the standard time of fermentation from 5 days to 3 days by modifying the medium used during the weaning process. The methods described are compatible with multi-isotope labeling and site-specific labeling.
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Affiliation(s)
- Troy Taylor
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Chen L, Chen Y, Wang B, Yang Z, Cai Z, Wang X, Sun L, Li Z, Wang G. Design, synthesis, and biological evaluation of deuterated indolepropionic acid derivatives as novel long-acting pan PPARα/γ/δ agonists. Bioorg Med Chem 2023; 96:117533. [PMID: 37976807 DOI: 10.1016/j.bmc.2023.117533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/17/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
Metabolic syndrome is a complex disease with diverse symptoms, but current pharmacological interventions have limited efficacy. Indeglitazar, a pan-agonist targeting the three-peroxisome proliferator activated receptors (PPAR), exhibits significant therapeutic effects on both diabetic and fatty liver animal models. However, its short half-life limits the in vivo efficacy, which might be attributed to the β-oxidation of indolepropionic acid at Indeglitazar. To overcome this metabolic instability, two deuterium atoms were introduced to the α-position of indolepropionic acid to block the β-oxidation. In this study, several deuterated derivatives were found to sustain PPARs activity and extend the half-life of liver microsomes. In oral glucose tolerance tests, I-1 exhibited the strongest glucose-lowering effect on ob/ob mice in this series. In db/db mice, I-1 reduced lipid levels, liver steatosis and promoted UCP1 expression in white adipose tissue. Mechanistic studies further revealed that I-1 exerts stronger effects than Indeglitazar on the regulation of genes related to lipid metabolism, mitochondrial function, and oxidative stress. Furthermore, I-1 significantly reduced liver steatosis, hepatocellular ballooning, inflammation, and fibrosis in NASH model induced by HFD + CCl4, and even exerted better therapeutic effect than that of Indeglitazar. With the above attractive efficacy, deuterated derivative I-1 is considered as a promising treatment for metabolic syndrome.
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Affiliation(s)
- Lianru Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Ya Chen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Laboratory of New Drug Discovery and Evaluation of the Guangdong Provincial Education Department, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Bin Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Laboratory of New Drug Discovery and Evaluation of the Guangdong Provincial Education Department, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Zhongcheng Yang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Zongyu Cai
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangzhou Key Laboratory of Construction and Application of New Drug Screening Model Systems, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Xuekun Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, Shandong 252059, PR China
| | - Lidan Sun
- Department of Pharmaceutics, Jiaxing Key Laboratory for Photonanomedicine and Experimental Therapeutics, College of Medicine, Jiaxing University, Jiaxing, Zhejiang, PR China.
| | - Zheng Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Key Laboratory of New Drug Discovery and Evaluation of the Guangdong Provincial Education Department, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangzhou Key Laboratory of Construction and Application of New Drug Screening Model Systems, Guangdong Pharmaceutical University, Guangzhou 510006, PR China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, PR China.
| | - Guangji Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
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6
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Ban K, Imai K, Oyama S, Tokunaga J, Ikeda Y, Uchiyama H, Kadota K, Tozuka Y, Akai S, Sawama Y. Sulfonium Salt Reagents for the Introduction of Deuterated Alkyl Groups in Drug Discovery. Angew Chem Int Ed Engl 2023; 62:e202311058. [PMID: 37726202 DOI: 10.1002/anie.202311058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/21/2023]
Abstract
The pharmacokinetics of pharmaceutical drugs can be improved by replacing C-H bonds with the more stable C-D bonds at the α-position to heteroatoms, which is a typical metabolic site for cytochrome P450 enzymes. However, the application of deuterated synthons is limited. Herein, we established a novel concept for preparing deuterated reagents for the successful synthesis of complex drug skeletons with deuterium atoms at the α-position to heteroatoms. (dn -Alkyl)diphenylsulfonium salts prepared from the corresponding nondeuterated forms using inexpensive and abundant D2 O as the deuterium source with a base, were used as electrophilic alkylating reagents. Additionally, these deuterated sulfonium salts were efficiently transformed into dn -alkyl halides and a dn -alkyl azide as coupling reagents and a dn -alkyl amine as a nucleophile. Furthermore, liver microsomal metabolism studies revealed deuterium kinetic isotope effects (KIE) in 7-(d2 -ethoxy)flavone. The present concept for the synthesis of deuterated reagents and the first demonstration of a KIE in a d2 -ethoxy group will contribute to drug discovery research based on deuterium chemistry.
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Affiliation(s)
- Kazuho Ban
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Keisuke Imai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Shuki Oyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Jin Tokunaga
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yui Ikeda
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Hiromasa Uchiyama
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kazunori Kadota
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yuichi Tozuka
- Department of Formulation Design and Pharmaceutical Technology, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka, 565-0871, Japan
- Deuterium Science Research Unit, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
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7
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Russo C, Leech MC, Walsh JM, Higham JI, Giannessi L, Lambert E, Kiaku C, Poole DL, Mason J, Goodall CAI, Devo P, Giustiniano M, Radi M, Lam K. eHydrogenation: Hydrogen-free Electrochemical Hydrogenation. Angew Chem Int Ed Engl 2023; 62:e202309563. [PMID: 37540528 DOI: 10.1002/anie.202309563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/05/2023]
Abstract
Hydrogenation reactions are staple transformations commonly used across scientific fields to synthesise pharmaceuticals, natural products, and various functional materials. However, the vast majority of these reactions require the use of a toxic and costly catalyst leading to unpractical, hazardous and often functionally limited conditions. Herein, we report a new, general, practical, efficient, mild and high-yielding hydrogen-free electrochemical method for the reduction of alkene, alkyne, nitro and azido groups. Finally, this method has been applied to deuterium labelling.
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Affiliation(s)
- Camilla Russo
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Matthew C Leech
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Jamie M Walsh
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Joe I Higham
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Lisa Giannessi
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
- Department of Food and Drug, University of Parma Parco area delle, Scienze 27°, Parma, Italy
| | - Emmanuelle Lambert
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Cyrille Kiaku
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Darren L Poole
- Discovery High-Throughput Chemistry, Medicinal Chemistry, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Joseph Mason
- Discovery High-Throughput Chemistry, Medicinal Chemistry, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Charles A I Goodall
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Perry Devo
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Mariateresa Giustiniano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Napoli, Italy
| | - Marco Radi
- Department of Food and Drug, University of Parma Parco area delle, Scienze 27°, Parma, Italy
| | - Kevin Lam
- School of Science, Faculty of Engineering and Science, University of Greenwich, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
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8
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Corucci G, Batchu KC, Luchini A, Santamaria A, Frewein MPK, Laux V, Haertlein M, Yamaryo-Botté Y, Botté CY, Sheridan T, Tully M, Maestro A, Martel A, Porcar L, Fragneto G. Developing advanced models of biological membranes with hydrogenous and deuterated natural glycerophospholipid mixtures. J Colloid Interface Sci 2023; 645:870-881. [PMID: 37178564 DOI: 10.1016/j.jcis.2023.04.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/23/2022] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Cellular membranes are complex systems that consist of hundreds of different lipid species. Their investigation often relies on simple bilayer models including few synthetic lipid species. Glycerophospholipids (GPLs) extracted from cells are a valuable resource to produce advanced models of biological membranes. Here, we present the optimisation of a method previously reported by our team for the extraction and purification of various GPL mixtures from Pichia pastoris. The implementation of an additional purification step by High Performance Liquid Chromatography-Evaporative Light Scattering Detector (HPLC-ELSD) enabled for a better separation of the GPL mixtures from the neutral lipid fraction that includes sterols, and also allowed for the GPLs to be purified according to their different polar headgroups. Pure GPL mixtures at significantly high yields were produced through this approach. For this study, we utilised phoshatidylcholine (PC), phosphatidylserine (PS) and phosphatidylglycerol (PG) mixtures. These exhibit a single composition of the polar head, i.e., PC, PS or PG, but contain several molecular species consisting of acyl chains of varying length and unsaturation, which were determined by Gas Chromatography (GC). The lipid mixtures were produced both in their hydrogenous (H) and deuterated (D) versions and were used to form lipid bilayers both on solid substrates and as vesicles in solution. The supported lipid bilayers were characterised by quartz crystal microbalance with dissipation monitoring (QCM-D) and neutron reflectometry (NR), whereas the vesicles by small angle X-ray (SAXS) and neutron scattering (SANS). Our results show that despite differences in the acyl chain composition, the hydrogenous and deuterated extracts produced bilayers with very comparable structures, which makes them valuable to design experiments involving selective deuteration with techniques such as NMR, neutron scattering or infrared spectroscopy.
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Affiliation(s)
- Giacomo Corucci
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France
| | | | - Alessandra Luchini
- European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden; Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andreas Santamaria
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Departamento de Química Física, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Moritz Paul Karl Frewein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, 8010, Austria
| | - Valèrie Laux
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Cyrille Y Botté
- ApicoLipid Team & GEMELI Lipidomics Platform, Institute for Advanced Biosciences, CNRS UMR5309, INSERM (-National Institute for Health and Medical Research) U1209, Université Grenoble Alpes, 38000 Grenoble, France
| | - Thomas Sheridan
- University College Dublin, Belfield, Dublin 4, Dublin, Ireland; AbbVie, Clonshaugh, Dublin 7, Co. Dublin, Ireland
| | - Mark Tully
- European Synchrotron Radiation Facility (ESRF), 71 avenue des Martyrs, CS 40220, 38043, Grenoble, France
| | - Armando Maestro
- Centro de Física de Materiales (CSIC, UPV/EHU) - Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; IKERBASQUE - Basque Foundation for Science, Plaza Euskadi 5, E-48009 Bilbao, Spain
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble, France; École doctorale de Physique, Université Grenoble Alpes, 38400 Saint-Martin-d'Héres, France; European Spallation Source ERIC, P.O. Box 176, SE-221 00 Lund, Sweden.
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9
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Tortajada A, Hevia E. Uncovering the Untapped Potential of the Use of Sodium Amides for Regioselective Arene Functionalisation. Chimia (Aarau) 2023; 77:225-229. [PMID: 38047801 DOI: 10.2533/chimia.2023.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 12/05/2023] Open
Abstract
Alkali-metal amides have become key reagents in synthetic chemistry, with special focus in deprotonation reactions. Despite the higher reactivity found in the heavier sodium and potassium amides, their insolubility and low stability has favoured the use of the more soluble lithium analogues, converting them into the most used non-nucleophilic bases. Studying the coordination effects of Lewis donor molecules such as tridentate amine PMDETA (N,N,N',N'',N''-pentamethyldiethylenetriamine) in combination with the sodium amide NaTMP (TMP = 2,2',6,6'-tetramethylpiperidide), we have been able to unlock the use of these reagents for the functionalisation of arenes, i.e. the deuterium incorporation by hydrogen isotope exchange and the deprotonative borylation of unactivated arenes. These findings show how sodium amides are not just a simple more sustainable replacement of their lithium counterparts, but also that they can display significantly enhanced reactivities allowing for the development of new transformations.
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Affiliation(s)
- Andreu Tortajada
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, CH-3012 Bern.
| | - Eva Hevia
- Departement für Chemie, Biochemie und Pharmazie, Universität Bern, CH-3012 Bern.
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10
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Du HZ, Fan JZ, Wang ZZ, Strotman NA, Yang H, Guan BT. Cesium Amide-Catalyzed Selective Deuteration of Benzylic C-H Bonds with D 2 and Application for Tritiation of Pharmaceuticals. Angew Chem Int Ed Engl 2023; 62:e202214461. [PMID: 36289047 DOI: 10.1002/anie.202214461] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Hydrogen isotope exchange (HIE) represents one of the most attractive labeling methods to synthesize deuterium- and tritium-labeled compounds. Catalytic HIE methods that enable site-selective C-H bond activation and exchange labeling with gaseous isotopes D2 and T2 are of vital importance, in particular for high-specific-activity tritiation of pharmaceuticals. As part of our interest in exploring s-block metals for catalytic transformations, we found CsN(SiMe3 )2 to be an efficient catalyst for selective HIE of benzylic C-H bonds with D2 gas. The reaction proceeds through a kinetic deprotonative equilibrium that establishes an exchange pathway between C-H bonds and D2 gas. By virtue of multiple C-H bonds activation and high activity (isotope enrichment up to 99 %), the simple cesium amide catalyst provided a very powerful and practically convenient labeling protocol for synthesis of highly deuterated compounds and high-specific-activity tritiation of pharmaceuticals.
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Affiliation(s)
- Hui-Zhen Du
- State Key Laboratory and Institute of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, China
| | - Jun-Zhen Fan
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Zhong-Zhen Wang
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Neil A Strotman
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, USA
| | - Haifeng Yang
- Process Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, USA
| | - Bing-Tao Guan
- Department of Chemistry, Fudan University, Shanghai, 200438, China
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11
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Omelchenko AN, Igonina TN, Brusentsev EY, Okotrub KA, Amstislavsky SY, Surovtsev NV. Cryopreservation increases accumulation of exogenous stearic acid in mouse embryos. Cryobiology 2022; 109:44-52. [PMID: 36179820 DOI: 10.1016/j.cryobiol.2022.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/03/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 01/16/2023]
Abstract
Cryopreservation of preimplantation embryos is a widely used technique, but this procedure might impact the subsequent embryo development. The effect of slow freezing and vitrification on the lipid metabolism in preimplantation mammalian embryos is not well studied. In this work, we applied Raman spectroscopy of isotopically labeled molecules to address the effects of cryopreservation on fatty acid accumulation in mouse embryos. Embryos after slow freezing or vitrification were cultured for 20 h in a medium supplemented with bovine serum albumin saturated with deuterated stearic acid (dSA). After this period the concentration of dSA estimated from Raman spectra of frozen-thawed and vitrified-warmed embryos at the morula stage was almost twice higher compared to non-cryopreserved morulas. At the same time, frozen-thawed and vitrified-warmed 4-cell embryos did not demonstrate any difference in the level of stearic acid uptake from non-cryopreserved embryos of the same stage. After an additional 24 h culture, cryopreserved and non-cryopreserved embryos demonstrated similar dSA uptake.
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Affiliation(s)
- A N Omelchenko
- Novosibirsk State University, Novosibirsk, 630090, Russia; Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - T N Igonina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - E Y Brusentsev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - K A Okotrub
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - S Y Amstislavsky
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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12
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Wang XM, Wang J, Fokina V, Patrikeeva S, Rytting E, Ahmed MS, La JH, Nanovskaya T. Effect of deuteration on the single dose pharmacokinetic properties and postoperative analgesic activity of methadone. Drug Metab Pharmacokinet 2022; 47:100477. [PMID: 36368298 PMCID: PMC9886271 DOI: 10.1016/j.dmpk.2022.100477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/01/2023]
Abstract
Although methadone is effective in the management of acute pain, the complexity of its absorption-distribution-metabolism-excretion profile limits its use as an opioid of choice for perioperative analgesia. Because deuteration is known to improve the pharmacokinetic, pharmacodynamic and toxicological properties of some drugs, here we characterized the single dose pharmacokinetic properties and post-operative analgesic efficacy of d9-methadone. The pharmacokinetic profiles of d9-methadone and methadone administered intravenously to CD-1 male mice revealed that deuteration leads to a 5.7- and 4.4-fold increase in the area under the time-concentration curve and maximum concentration in plasma, respectively, as well as reduction in clearance (0.9 ± 0.3 L/h/kg vs 4.7 ± 0.8 L/h/kg). The lower brain-to-plasma ratio of d9-methadone compared to that of methadone (0.35 ± 0.12 vs 2.05 ± 0.62) suggested that deuteration decreases the transfer of the drug across the blood-brain barrier. The estimated LD50 value for a single intravenous dose of d9-methadone was 2.1-fold higher than that for methadone. Moreover, d9-methadone outperformed methadone in the efficacy against postoperative pain by primarily activating peripheral opioid receptors. Collectively, these data suggest that the replacement of three hydrogen atoms in three methyl groups of methadone altered its pharmacokinetic properties, improved safety, and enhanced its analgesic efficacy.
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Affiliation(s)
- Xiao-Ming Wang
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jigong Wang
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Valentina Fokina
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Svetlana Patrikeeva
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Erik Rytting
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Mahmoud S Ahmed
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jun-Ho La
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Tatiana Nanovskaya
- Maternal-Fetal Pharmacology and Bio-Development Laboratories, Department of Obstetrics & Gynecology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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13
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Gabel F. Observing protein degradation in solution by the PAN-20S proteasome complex: Astate-of-the-art example of bio-macromolecular TR-SANS. Methods Enzymol 2023; 678:97-120. [PMID: 36641218 DOI: 10.1016/bs.mie.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the present book chapter we illustrate the state-of-the-art of time-resolved small-angle neutron scattering (TR-SANS) by a concrete example of a dynamic bio-macromolecular system, i.e., regulated protein degradation by the archaeal PAN-20S proteasome complex. We present the specific and unique structural information that can be obtained by this approach, in combination with bio-macromolecular deuteration and online spectrophotometric measurements of a fluorescent substrate (GFP). The complementarity with atomic-resolution structural biology techniques (SAXS, NMR, crystallography and cryo-EM) and with the advent of atomic structure prediction are discussed, as well as the respective limitations and future perspectives.
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14
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Shi Y, Dinh J, Pelletier R, Raccor B, Yusuff N, Morgan AJ, Harbeson S, Uttamsingh V, Totah RA. Selective deuteration of bupropion slows epimerization and reduces metabolism. Bioorg Med Chem Lett 2022; 76:129009. [PMID: 36174836 DOI: 10.1016/j.bmcl.2022.129009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/31/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Strategically replacing hydrogen with deuterium at sites of metabolism in small molecule drugs can significantly alter clearance and potentially enhance clinical safety. Bupropion is an antidepressant and smoking cessation medication with the potential to cause seizures. We hypothesized that incorporating deuterium at specific sites in bupropion may greatly reduce epimerization, potentially slow metabolism, and reduce the formation of toxic metabolites, namely hydroxybupropion which has been associated with bupropion's toxicity. Four deuterated analogues were synthesized incorporating deuterium at sites of metabolism and epimerization with the aim of altering the metabolic profile of bupropion. Spectroscopic binding and metabolism studies with bupropion and R-or S-d4 and R-or S-d10 analogs were performed with recombinant CYP2B6, human liver microsomes, and human hepatocytes. Results demonstrate that deuterated bupropion analogues exhibited 20-25% decrease in racemization and displayed a significant decrease in the formation of CYP2B6-mediated R,R - or S,S-hydroxybupropion with recombinant protein and human liver microsomes. In primary human hepatocytes, metabolism of deuterated analogs to R,R - and S,S-hydroxybupropion and threo- and erythro-hydrobupropion was significantly less than R/S-d0 bupropion. Selective deuterium substitution at metabolic soft spots in bupropion has the potential to provide a drug with a simplified pharmacokinetic profile, reduced toxicity and improved tolerability in patients.
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Affiliation(s)
- Yuanyuan Shi
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA 98195, United States
| | - Jean Dinh
- Certara UK Limited, Simcyp Division, Level 2 Acero, 1 Concourse Way, Sheffield S1 2BJ, United Kingdom
| | - Robert Pelletier
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA 98195, United States
| | - Brianne Raccor
- Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Campbell University, Buies Creek, NC 27506, United States
| | - Naeem Yusuff
- Concert Pharmaceuticals, Inc., 65 Hayden Ave. Suite 3000N, Lexington, MA 02421, United States
| | - Adam J Morgan
- Concert Pharmaceuticals, Inc., 65 Hayden Ave. Suite 3000N, Lexington, MA 02421, United States
| | - Scott Harbeson
- Concert Pharmaceuticals, Inc., 65 Hayden Ave. Suite 3000N, Lexington, MA 02421, United States
| | - Vinita Uttamsingh
- Concert Pharmaceuticals, Inc., 65 Hayden Ave. Suite 3000N, Lexington, MA 02421, United States
| | - Rheem A Totah
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA 98195, United States.
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15
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Sherman MM, Tarantino PM, Morrison DN, Lin CH, Parente RM, Sippy BC. A double-blind, randomized, two-part, two-period crossover study to evaluate the pharmacokinetics of caffeine versus d9-caffeine in healthy subjects. Regul Toxicol Pharmacol 2022; 133:105194. [PMID: 35690181 DOI: 10.1016/j.yrtph.2022.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/02/2021] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022]
Abstract
The deuterium kinetic isotope effect has been used to affect the cytochrome P450 metabolism of the deuterated versions of substances. This study compares the pharmacokinetics of caffeine, a Generally Recognized As Safe food and beverage ingredient, versus d9-caffeine, a potential caffeine alternative, and their respective metabolites at two dose levels in 20 healthy adults. A single dose of 50 mg or 250 mg of caffeine, or a molar-equivalent dose of d9-caffeine, were orally administered in solution with blood samples collected for up to 48 h post-dose. Plasma concentrations of parent and metabolites were analyzed using validated LC-MS/MS methods. Both d9-caffeine and caffeine were rapidly absorbed; however, d9-caffeine exhibited a higher (ca. 29%-43%) Cmax and 4-5-fold higher AUClast than caffeine, and lower Cmax, lower AUClast, and a 5-10-fold reduction in the relative exposure to the active metabolites of caffeine. Results were consistent in normal and rapid metabolizers, and both substances were well tolerated.
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Affiliation(s)
| | | | - Dennis N Morrison
- QPS LLC (Bio-Kinetic Clinical Applications, LLC), Springfield, MO, USA
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16
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Parente RM, Tarantino PM, Sippy BC, Burdock GA. Pharmacokinetic, pharmacological, and genotoxic evaluation of deuterated caffeine. Food Chem Toxicol 2021; 160:112774. [PMID: 34974129 DOI: 10.1016/j.fct.2021.112774] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/24/2021] [Accepted: 12/17/2021] [Indexed: 01/27/2023]
Abstract
Altering caffeine's negative physiological effects and extending its duration of activity is an active area of research; however, deuteration as a means of achieving these goals is unexplored. Deuteration substitutes one or more of the hydrogen atoms of a substance with deuterium, a stable isotope of hydrogen that contains an extra neutron. Deuteration can potentially alter the metabolic profile of a substance, while maintaining its pharmacodynamic properties. d9-Caffeine is a deuterated isotopologue of caffeine with the nine hydrogens contained in the 1, 3, and 7 methyl groups of caffeine substituted with deuterium. d9-Caffeine may prove to be an alternative to caffeine that may be consumed with less frequency, at lower doses, and with less exposure to downstream active metabolites of caffeine. Characterization of d9-caffeine's genotoxic potential, pharmacodynamic, and pharmacokinetic behavior is critical in establishing how it may differ from caffeine. d9-Caffeine was non-genotoxic with and without metabolic activation in both a bacterial reverse mutation assay and a human mammalian cell micronucleus assay at concentrations up to the ICH concentration limits. d9-Caffeine exhibited a prolonged systemic and brain exposure time in rats as compared to caffeine following oral administration. The adenosine receptor antagonist potency of d9-caffeine was similar to caffeine.
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Affiliation(s)
| | - Paul M Tarantino
- Lennham Pharmaceuticals, Inc., 53 Main Street Suite 206 Concord, MA, 01742, USA
| | - Bradford C Sippy
- Lennham Pharmaceuticals, Inc., 53 Main Street Suite 206 Concord, MA, 01742, USA
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17
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Weiss KL, Fan Y, Abraham P, Odom M, Pant S, Zhang Q, O'Neill H. Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation. Methods Enzymol 2021; 659:219-40. [PMID: 34752287 DOI: 10.1016/bs.mie.2021.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D2O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D2O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.
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18
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Schneider F, Stamler D, Bradbury MJ, Loupe PS, Gordon MF, Rabinovich-Guilatt L. The effect of potent CYP2D6 inhibition on the pharmacokinetics and safety of deutetrabenazine in healthy volunteers. Eur J Clin Pharmacol 2021; 78:11-18. [PMID: 34491372 PMCID: PMC8724172 DOI: 10.1007/s00228-021-03202-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/18/2021] [Accepted: 08/12/2021] [Indexed: 11/05/2022]
Abstract
Purpose Deutetrabenazine is a deuterated form of tetrabenazine with a confirmed lower rate of CYP2D6 metabolism of the active metabolites, α- and β-HTBZ. In this study, we assessed the effect of paroxetine, a potent CYP2D6 inhibitor, on the pharmacokinetics and safety of deutetrabenazine and its metabolites. Methods In this open-label sequential drug-drug-interaction study, 24 healthy adults who were CYP2D6 extensive or intermediate metabolizers received a single deutetrabenazine 22.5-mg oral dose on days 1 and 11 and a single paroxetine 20-mg oral daily dose on days 4–12. Pharmacokinetics of deutetrabenazine and its metabolites were assessed on days 1–4 and 11–14. Paroxetine trough concentrations were obtained pre-dose on days 9–13. Safety examinations occurred throughout the study. Results Paroxetine administered under steady-state conditions, increased exposure of the deuterated active metabolites, α-HTBZ (1.2-fold Cmax and 1.8-fold AUC0–∞) and β-HTBZ (2.1-fold Cmax and 5.6-fold AUC0–∞), and correspondingly, 1.6-fold Cmax and threefold AUC0–∞ for total (α + β)-HTBZ. Sixteen subjects reported 45 adverse events and most were mild. Headache was the most common AE reported 8 times by 7 subjects (5 following paroxetine alone; 2 following deutetrabenazine + paroxetine). Conclusions Paroxetine-induced increases in exposure to the active deutetrabenazine metabolites were less than those previously reported for tetrabenazine, a finding expected to reduce the burden of drug interaction. In addition, single doses of 22.5 mg deutetrabenazine, when given alone or in the presence of steady-state paroxetine (20 mg daily), were safe. Supplementary information The online version contains supplementary material available at 10.1007/s00228-021-03202-0.
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Affiliation(s)
- F Schneider
- Teva Pharmaceutical Industries Ltd, Ratiopharm GmbH, Ulm, Germany.
| | - D Stamler
- Formerly of Teva Pharmaceutical Industries Ltd, Currently Alterity Therapeutics Limited, Newark, CA, USA
| | - M J Bradbury
- Formerly of Teva Pharmaceutical Industries Ltd, Currently Alterity Therapeutics Limited, Newark, CA, USA
| | - P S Loupe
- Teva Pharmaceutical Industries Ltd, West Chester, PA, USA
| | - M F Gordon
- Teva Pharmaceutical Industries Ltd, West Chester, PA, USA
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Aggarwal S, Wachenfeldt CV, Fisher SZ, Oksanen E. A protocol for production of perdeuterated OmpF porin for neutron crystallography. Protein Expr Purif 2021; 188:105954. [PMID: 34416360 DOI: 10.1016/j.pep.2021.105954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/26/2021] [Revised: 07/31/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
Hydrogen atoms are at the limit of visibility in X-ray structures even at high resolution. Neutron macromolecular crystallography (NMX) is an unambiguous method to locate hydrogens and study the significance of hydrogen bonding interactions in biological systems. Since NMX requires very large crystals, very few neutron structures of proteins have been determined yet. In addition, the most common hydrogen isotope 1H gives rise to significant background due to its large incoherent scattering cross-section. Therefore, it is advantageous to substitute as many hydrogens as possible with the heavier isotope 2H (deuterium) to reduce the sample volume requirement. While the solvent exchangeable hydrogens can be substituted by dissolving the protein in heavy water, complete deuterium labelling - perdeuteration - requires the protein to be expressed in heavy water with a deuterated carbon source. In this work, we developed an optimized method for large scale production of deuterium-labelled bacterial outer membrane protein F (OmpF) for NMX. OmpF was produced using deuterated media with different carbon sources. Mass spectrometry verified the integrity and level of deuteration of purified OmpF. Perdeuterated OmpF crystals diffracted X-rays to a resolution of 1.9 Å. This work lays the foundation for structural studies of membrane protein by neutron diffraction in future.
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Affiliation(s)
- Swati Aggarwal
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; University Grenoble Alpes, CEA, CNRS, IBS, FR-380 00, Grenoble, France
| | | | - Suzanne Zoë Fisher
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden; Department of Biology, Lund University, Sölvegatan 35, Lund, SE-22 362, Sweden
| | - Esko Oksanen
- European Spallation Source ERIC, Odarslövsvägen 113, SE-225 92, Lund, Sweden.
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20
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Wu Y, Weiss KL, Lieberman RL. Preparation of a Deuterated Membrane Protein for Small-Angle Neutron Scattering. Methods Mol Biol 2021; 2302:219-35. [PMID: 33877630 DOI: 10.1007/978-1-0716-1394-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter outlines a protocol developed to prepare a purified deuterated membrane protein for a small-angle neutron scattering (SANS) experiment. SANS is a noninvasive technique well suited to studying membrane protein solution structures, and deuteration enhances the signal from the protein over the background (Breyton et al., Eur Phys J E Soft Matter 36 (7):71, 2013; Garg et al., Biophys J 101 (2):370-377, 2011). We present our workflow: transformation of our plasmid into E. coli, cell growth and expression of our deuterated protein, membrane isolation, detergent solubilization, protein purification, purity assessment, and final preparation for SANS.
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21
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Akbey Ü. Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H- 13C MAS NMR approach. J Magn Reson 2021; 327:106974. [PMID: 33823335 DOI: 10.1016/j.jmr.2021.106974] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
We describe a 2H based MAS nuclear magnetic resonance (NMR) method to obtain site-specific molecular dynamics of biomolecules. The method utilizes the use of deuterium nucleus as a spin label that is proven to be very useful in dynamics studies of solid biological and functional materials. The aim is to understand overall characteristics of protein backbone and side-chain motions for CD3, CD2 and CD groups, in terms of timescale, type and activation energy of the underlying processes. Variable temperature two-dimensional (2D) 2H-13C correlation MAS NMR spectra were recorded for the uniformly 2H,13C,15N labelled Alanine and microcrystalline SH3 at a broad temperature range, from 320 K down to 100 K. First, the deuterium quadrupolar-coupling constant from specific D-C sites is obtained with the 2D experiment by utilizing carbon chemical shifts. Second, the static quadrupolar patterns are obtained at 100 K. Third, variable temperature approach enabled the observation of quadrupolar pattern over different motional regimes; slow, intermediate and fast. And finally, the apparent activation energies for C-D sites are determined and compared, by evaluating the temperature induced signal intensities. This information led to the determination of the dynamic processes for different D-C sites at a broad range of temperature and motional timescales. This is a first representation of 2D 2H-13C MAS NMR approach applied to fully isotope labelled deuterated protein covering 220 K temperature range.
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Affiliation(s)
- Ümit Akbey
- Weizmann Institute of Science, Department of Chemical and Biological Physics, Perlman Chemical Sciences Building, P.O. Box 26, Rehovot 76100, Israel.
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22
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Li A, Wang X, Li D, Li X, Li R, Yang X, Li X. Deuteration enhances the anti-tumor effects and relative anti-inflammatory effects via affecting proliferation and apoptosis. Heliyon 2021; 7:e06391. [PMID: 33732929 PMCID: PMC7941159 DOI: 10.1016/j.heliyon.2021.e06391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/12/2020] [Revised: 02/10/2021] [Accepted: 02/25/2021] [Indexed: 11/26/2022] Open
Abstract
Apigenin (AP) is a plant flavonoid with potential biomedical applications. To enhance the anti-tumour effect, AP was deuterated via hydrogen–deuterium exchange under hydrothermal conditions. The anti-tumor effects of deuterated AP (D-AP) were then tested on HCT116 cells and on a murine model of turpentine-induced inflammation. Cell cycle progression and cell proliferation were measured by flow cytometry, and in vivo immuno-inflammation was evaluated by quantitating glucose metabolism using 18F-fluorodeoxyglucose positron emission tomography. According to the mass spectral results, the efficiency of AP deuteration was 62.96%. For both the two groups of AP and D-AP at 24 h and 48 h, there were an obvious increase on perception of G2 phage. Apigenin showed the ability of blocking in G2 phage to inhibit cellular proliferation. Additionally, D-AP induced early apoptosis in more cells than did AP (12.1% vs. 10.4%). Moreover, D-AP induced a more severe process of anti-inflammation during the early period, resulting in a more effective anti-inflammatory response. Therefore, given the innate ability of D-AP to block cell proliferation and induce early apoptosis, we conclude that deuteration enhances the systemic anti-cancer effect of this flavonoid.
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Affiliation(s)
- Ao Li
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China.,Southwest University of Science and Technology, Mianyang 621010, China
| | - Xiaojiao Wang
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China
| | - Danni Li
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China
| | - Xiaohong Li
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China
| | - Rou Li
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China
| | - Xuejuan Yang
- Department of Cardiology, Yinchuan Second People's Hospital, Yinchuan 750004, China
| | - Xiao Li
- Department of Nuclear Medicine, Shanghai Changhai Hospital, Shanghai 200433, China
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Kambayashi R, Goto A, Nunoi Y, Hagiwara-Nagasawa M, Izumi-Nakaseko H, Venkatesan G, Takei Y, Matsumoto A, Chan ECY, Sugiyama A. An exploratory analysis of effects of poyendarone, a deuterated analogue of dronedarone, on the canine model of paroxysmal atrial fibrillation. Naunyn Schmiedebergs Arch Pharmacol 2021; 394:1103-1112. [PMID: 33427928 DOI: 10.1007/s00210-020-02047-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/28/2020] [Indexed: 11/26/2022]
Abstract
Poyendarone, a deuterated analogue of dronedarone, is expected to reduce the onset of cardiovascular adverse events of dronedarone, including congestive heart failure and excessive QT-interval prolongation. Since information is still lacking on the anti-atrial fibrillatory property of poyendarone, we assessed it along with effects on the inter-atrial conduction time (IACT) and atrial effective refractory period (AERP) using the canine paroxysmal atrial fibrillation model. Poyendarone hydrochloride (n = 4) and dronedarone hydrochloride (n = 4) in intravenous doses of 0.3 and 3 mg/kg/30 s were cumulatively administered. Poyendarone hardly altered sinoatrial rate, but dronedarone decreased it in a dose-related manner, whereas both drugs slightly but significantly reduced idioventricular rate. Poyendarone shortened duration of burst pacing-induced atrial fibrillation, whereas such abbreviation was not observed by dronedarone. Poyendarone and dronedarone similarly prolonged IACT in a frequency-dependent manner, indicating that their INa inhibitory actions may be similar. The high dose of poyendarone prolonged AERP in a reverse frequency-dependent manner, extent of which at basic pacing cycle lengths of 300 and 400 ms was comparable to that of dronedarone. However, the extent at a basic pacing cycle length of 200 ms was tended to be greater in poyendarone than in dronedarone, suggesting greater IKs inhibitory action of poyendarone. The deuteration of dronedarone attenuated the inhibition of sinus automaticity and prolonged the AERP with keeping the blood pressure and ventricular rate stable. Thus, poyendarone may have both more potent anti-atrial fibrillatory action and wider cardiovascular safety margin than dronedarone.
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Affiliation(s)
- Ryuichi Kambayashi
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Ai Goto
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Yoshio Nunoi
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Mihoko Hagiwara-Nagasawa
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Hiroko Izumi-Nakaseko
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Gopalakrishnan Venkatesan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yoshinori Takei
- Department of Translational Research & Cellular Therapeutics, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Akio Matsumoto
- Department of Aging Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore.
| | - Atsushi Sugiyama
- Department of Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
- Department of Translational Research & Cellular Therapeutics, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
- Department of Aging Pharmacology, Faculty of Medicine, Toho University, 5-21-16 Omori-nishi, Ota-ku, Tokyo, 143-8540, Japan.
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24
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Romanov RS, Mariasina SS, Efimov SV, Klochkov VV, Rodina EV, Polshakov VI. Backbone resonance assignment and dynamics of 110 kDa hexameric inorganic pyrophosphatase from Mycobacterium tuberculosis. Biomol NMR Assign 2020; 14:281-287. [PMID: 32562252 DOI: 10.1007/s12104-020-09962-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Family I soluble inorganic pyrophosphatases (PPases; EC 3.6.1.1) are enzymes essential for all organisms. They hydrolyze inorganic pyrophosphate, thus providing the driving force for numerous biosynthetic reactions. Soluble PPases retain enzymatic activity only in multimeric forms. PPases from various organisms are extensively studied by X-ray crystallography but until now there was no information on their structure and dynamics in solution. Hexameric 110 kDa (6 × 18.3 kDa) PPase from Mycobacterium tuberculosis (Mt-PPase) is a promising target for the rational design of potential anti-tuberculosis agents. In order to use NMR techniques in functional studies of Mt-PPase and rational design of the inhibitors for this enzyme, it is necessary to have information on the backbone 1H, 13C and 15N resonance assignments. Samples of Mt-PPase enriched with 99% of 13C and 15N isotopes, and 95% of 2H were obtained using recombinant protein expression in an isotopically-labeled medium and effective heat-shock protocol for the deuterium-to-hydrogen exchange of the amide groups. Backbone resonance assignment was achieved for more than 95% of the residues. It was found that the secondary structure of Mt-PPase in solution corresponds well to the crystal structure of this protein. Protein backbone dynamics were studied using 15N NMR relaxation experiments. Determined resonance assignments and dynamic properties provide the basis for the subsequent structure-based design of novel inhibitors of Mt-PPase-potential anti-tuberculosis drugs.
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Affiliation(s)
- Roman S Romanov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sofia S Mariasina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sergey V Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya St., Kazan, Russia, 420008
| | - Vladimir V Klochkov
- NMR Laboratory, Institute of Physics, Kazan Federal University, 18 Kremlevskaya St., Kazan, Russia, 420008
| | - Elena V Rodina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir I Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
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25
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Ranneva SV, Okotrub KA, Amstislavsky SY, Surovtsev NV. Deuterated stearic acid uptake and accumulation in lipid droplets of cat oocytes. Arch Biochem Biophys 2020; 692:108532. [PMID: 32795451 DOI: 10.1016/j.abb.2020.108532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 01/04/2023]
Abstract
Fatty acid uptake and accumulation in lipid droplets are essential processes of lipid metabolism. Oocyte in vitro culture in media enriched with fatty acid is used to modify the lipid content and composition, aiming to study the consequences of obesity and enhance cell cryotolerance. We applied Raman spectroscopy and deuterium labeling approach to quantify stearic acid uptake and investigate its incorporation within oocytes. Our data suggest that deuterium labeling does not affect oocyte maturation rates. The efficiency of deuterated stearic acid (dSA) uptake was shown to decrease with the increase of its concentration in culture medium and the duration of in vitro culture. The molar ratio between dSA and bovine serum albumin has no significant effect on the dSA uptake for 200 μM but modifies concentration dependence of the lipid uptake. dSA accumulates in all the lipid droplets inside oocytes. Different lipid droplets within the same oocyte exhibit different concentrations of dSA. The scatter in the dSA concentration in lipid droplets decreases with the culture time. Using dSA as an example, we provide a comprehensive description of how fatty acid concentration, its molar ratio versus bovine serum albumin, and culture time affect the uptake of the fatty acids in oocytes. Raman microspectroscopy of deuterium-labeled fatty acids is a nondestructive tool providing information about fatty acid uptake and heterogeneity of their accumulation between lipid droplets within the single oocyte.
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26
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Liu X, Gao Z, Fu Q, Song L, Zhang P, Zhang X, Hendrickson H, Crooks PA, Zhou D, Zheng G. Deuteration of the farnesyl terminal methyl groups of δ-tocotrienol and its effects on the metabolic stability and ability of inducing G-CSF production. Bioorg Med Chem 2020; 28:115498. [PMID: 32291146 DOI: 10.1016/j.bmc.2020.115498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/05/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 01/22/2023]
Abstract
δ-tocotrienol (DT3), a member of vitamin E family, has been shown to have a potent radio-protective effect. However, its application as a radioprotectant is limited, at least in part, by its short plasma elimination half-life and low bioavailability. In an effort to increase the metabolic stability of DT3, a deuterium substituted DT3 derivative, d6-DT3, was designed and synthesized. d6-DT3 showed improved in vitro and in vivo metabolic stability compared to DT3. The unexpected lower potency of d6-DT3 in inducing granulocyte-colony stimulating factor (G-CSF) production in mouse revealed that the metabolite(s) of DT3 might play a major role in inducing G-CSF induction.
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Affiliation(s)
- Xingui Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Zhengya Gao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Qiang Fu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Lin Song
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Peiyi Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Xuan Zhang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Howard Hendrickson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Pharmaceutical, Social and Administrative Sciences, School of Pharmacy, Samford University, Birmingham, AL 35229, United States
| | - Peter A Crooks
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Daohong Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Guangrong Zheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States.
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27
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Kambayashi R, Hagiwara-Nagasawa M, Kondo Y, Yeo ZJ, Goto A, Chiba K, Nunoi Y, Izumi-Nakaseko H, Leow JWH, Venkatesan G, Matsumoto A, Chan ECY, Sugiyama A. How the Deuteration of Dronedarone Can Modify Its Cardiovascular Profile: In Vivo Characterization of Electropharmacological Effects of Poyendarone, a Deuterated Analogue of Dronedarone. Cardiovasc Toxicol 2020; 20:339-50. [PMID: 31898152 DOI: 10.1007/s12012-019-09559-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Since deuterium replacement has a potential to modulate pharmacodynamics, pharmacokinetics and toxicity, we developed deuterated dronedarone; poyendarone, and assessed its cardiovascular effects. Poyendarone hydrochloride in doses of 0.3 and 3 mg/kg over 30 s was intravenously administered to the halothane-anesthetized dogs (n = 4), which provided peak plasma concentrations of 108 ± 10 and 1120 ± 285 ng/mL, respectively. The 0.3 mg/kg shortened the ventricular repolarization period. The 3 mg/kg transiently increased the heart rate at 5 min but decreased at 45 min, and elevated the total peripheral vascular resistance and left ventricular preload, whereas it reduced the mean blood pressure at 5 min, left ventricular contractility and cardiac output. The transient tachycardic action is considered to be induced by the hypotension-induced, reflex-mediated increase of sympathetic tone. The 3 mg/kg delayed both intra-atrial and intra-ventricular conductions, indicating Na+ channel inhibitory action. Moreover, the 3 mg/kg transiently shortened the ventricular repolarization period at 5 min. No significant change was detected in the late repolarization by poyendarone, indicating it might not hardly significantly alter rapidly activating delayed-rectifier K+ current (IKr). Poyendarone prolonged the atrial effective refractory period greater than the ventricular parameter. When compared with dronedarone, poyendarone showed similar pharmacokinetics of dronedarone, but reduced β-adrenoceptor blocking activity as well as the cardio-suppressive effect. Poyendarone failed to inhibit IKr and showed higher atrial selectivity in prolonging the effective refractory period of atrium versus ventricle. Thus, the deuteration may be an effective way to improve the cardiovascular profile of dronedarone. Poyendarone is a promising anti-atrial fibrillatory drug candidate.
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28
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Ali R, Clark LD, Zahm JA, Lemoff A, Ramesh K, Rosenbaum DM, Rosen MK. Improved strategy for isoleucine 1H/ 13C methyl labeling in Pichia pastoris. J Biomol NMR 2019; 73:687-697. [PMID: 31541396 PMCID: PMC6875547 DOI: 10.1007/s10858-019-00281-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Site specific methyl labeling combined with methyl TROSY offers a powerful NMR approach to study structure and dynamics of proteins and protein complexes of high molecular weight. Robust and cost-effective methods have been developed for site specific protein 1H/13C methyl labeling in an otherwise deuterated background in bacteria. However, bacterial systems are not suitable for expression and isotope labeling of many eukaryotic and membrane proteins. The yeast Pichia pastoris (P. pastoris) is a commonly used host for expression of eukaryotic proteins, and site-specific methyl labeling of perdeuterated eukaryotic proteins has recently been achieved with this system. However, the practical utility of methyl labeling and deuteration in P. pastoris is limited by high costs. Here, we describe an improved method for 1H/13C-labeling of the δ-methyl group of isoleucine residues in a perdeuterated background, which reduces the cost by ≥ 50% without compromising the efficiency of isotope enrichment. We have successfully implemented this method to label actin and a G-protein coupled receptor. Our approach will facilitate studies of the structure and dynamics of eukaryotic proteins by NMR spectroscopy.
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Affiliation(s)
- Rustam Ali
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Lindsay D Clark
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Jacob A Zahm
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 130 Longwood Avenue, Boston, MA, 02115, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karthik Ramesh
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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29
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Kaiser M, Hacker C, Duchardt-Ferner E, Wöhnert J. 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii. Biomol NMR Assign 2019; 13:309-314. [PMID: 31069720 DOI: 10.1007/s12104-019-09897-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/03/2019] [Indexed: 06/09/2023]
Abstract
The protein dimethyladenosine transferase 1 (Dim1) is a highly conserved protein occurring in organisms ranging from bacteria such as E. coli where it is named KsgA to humans. Since Dim1 is involved in the biogenesis of the small ribosomal subunit it is an essential protein. During ribosome biogenesis Dim1 acts as an rRNA modification enzyme and dimethylates two adjacent adenosine residues of the small ribosomal subunit rRNA. In eukaryotes it is also required to ensure the proper endonucleolytic processing of the small ribosomal subunit rRNA precursor. Recently, a third function was proposed for eukaryotic Dim1. Karbstein and coworkers suggested that Dim1 interacts with the essential ribosome assembly factor Fap7 and that Fap7 is responsible for the dissociation of Dim1 from the nascent small ribosomal subunit. Here, we report the backbone 1H, 13C and 15N NMR resonance assignments for the 30.9 kDa Dim1 homologue from the hyperthermophilic archaeon Pyrococcus horikoshii (PhDim1) as a prerequisite for a detailed structural investigation of the PhDim1/PhFap7 interaction.
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Affiliation(s)
- Marco Kaiser
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
| | - Carolin Hacker
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt/M, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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30
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Linnik IV, Rayner PJ, Stow RA, Duckett SB, Cheetham GMT. Pharmacokinetics of the SABRE agent 4,6-d 2-nicotinamide and also nicotinamide in rats following oral and intravenous administration. Eur J Pharm Sci 2019; 135:32-37. [PMID: 31077749 PMCID: PMC6556870 DOI: 10.1016/j.ejps.2019.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 03/18/2019] [Revised: 05/01/2019] [Accepted: 05/04/2019] [Indexed: 01/14/2023]
Abstract
To prepare the way for using the isotopically labelled SABRE hyperpolarized 4,6-d2-nicotinamide as an MRI agent in humans we have performed an in-vivo study to measure its pharmacokinetics in the plasma of healthy rats after intravenous and oral administration. Male Han Wistar rats were dosed with either 4,6-d2-nicotinamide or the corresponding control, non-labelled nicotinamide, and plasma samples were obtained at eight time points for up to 24 h after administration. Pharmacokinetic parameters were determined from agent concentration-versus-time data for both 4,6-d2-nicotinamide and nicotinamide. 4,6-d2-Nicotinamide proved to be well tolerated regardless of route of administration at the concentrations used (20, 80 and 120 mg/kg). Pharmacokinetic parameters were similar after oral and intravenous administration and similar to those obtained for nicotinamide. Analysis of nicotinamide plasma concentrations after dosing 4,6-d2-nicotinamide intravenously demonstrates a reversible exchange of endogenous nicotinamide by this labelled agent over the time-course of our assays. Supported by a large body of evidence for the safety of nicotinamide when dosed orally in humans, we conclude that 4,6-d2-nicotinamide can also be safely administered intravenously, which will provide significant benefit when using this agent for planned imaging studies in humans.
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Affiliation(s)
- Inna V Linnik
- Centre for Hyperpolarisation in Magnetic Resonance (CHyM), Department of Chemistry, University of York, Heslington YO10 5DD, UK
| | - Peter J Rayner
- Centre for Hyperpolarisation in Magnetic Resonance (CHyM), Department of Chemistry, University of York, Heslington YO10 5DD, UK
| | - Ruth A Stow
- Covance Laboratories, Harrogate, North Yorkshire HG3 1PY, UK
| | - Simon B Duckett
- Centre for Hyperpolarisation in Magnetic Resonance (CHyM), Department of Chemistry, University of York, Heslington YO10 5DD, UK
| | - Graham M T Cheetham
- Centre for Hyperpolarisation in Magnetic Resonance (CHyM), Department of Chemistry, University of York, Heslington YO10 5DD, UK.
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31
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Evans BR, Foston M, O'Neill HM, Reeves D, Rempe C, McGrath K, Ragauskas AJ, Davison BH. Production of deuterated biomass by cultivation of Lemna minor (duckweed) in D 2O. Planta 2019; 249:1465-1475. [PMID: 30697645 DOI: 10.1007/s00425-019-03097-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
Common duckweed Lemna minor was cultivated in 50% D2O to produce biomass with 50-60% deuterium incorporation containing cellulose with degree of polymerization close (85%) to that of H2O-grown controls. The small aquatic plant duckweed, particularly the genus Lemna, widely used for toxicity testing, has been proposed as a potential source of biomass for conversion into biofuels as well as a platform for production of pharmaceuticals and specialty chemicals. Ability to produce deuterium-substituted duckweed can potentially extend the range of useful products as well as assist process improvement. Cultivation of these plants under deuterating conditions was previously been reported to require addition of kinetin to induce growth and was hampered by anomalies in cellular morphology and protein metabolism. Here, we report the production of biomass with 50-60% deuterium incorporation by long-term photoheterotrophic growth of common duckweed Lemna minor in 50% D2O with 0.5% glucose. L. minor grown in 50% D2O without addition of kinetin exhibited a lag phase twice that of H2O-grown controls, before start of log phase growth at 40% of control rates. Compared to continuous white fluorescent light, growth rates increased fivefold for H2O and twofold for 50% D2O when plants were illuminated at higher intensity with a metal halide lamp and a diurnal cycle of 12-h light/12-h dark. Deuterium incorporation was determined by a combination of 1H and 2H nuclear magnetic resonance (NMR) to be 40-60%. The cellulose from the deuterated plants had an average-number degree of polymerization (DPn) and polydispersity index (PDI) close to that of H2O-grown controls, while Klason lignin content was reduced. The only major gross morphological change noted was root inhibition.
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Affiliation(s)
- Barbara R Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Marcus Foston
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Hugh M O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - David Reeves
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Caroline Rempe
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- School of Genome Science and Technology, F337 Walters Life Science, University of Tennessee, Knoxville, 37996, TN, USA
| | - Kathi McGrath
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Sierra Vista High School, Las Vegas, NV, USA
| | - Arthur J Ragauskas
- Institute of Paper Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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Funk AM, Wen X, Hever T, Maptue NR, Khemtong C, Sherry AD, Malloy CR. Effects of deuteration on transamination and oxidation of hyperpolarized 13C-Pyruvate in the isolated heart. J Magn Reson 2019; 301:102-108. [PMID: 30861456 PMCID: PMC6666394 DOI: 10.1016/j.jmr.2019.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/01/2019] [Accepted: 03/03/2019] [Indexed: 06/04/2023]
Abstract
This study was designed to determine the effects of deuteration in pyruvate on exchange reactions in alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and flux through pyruvate dehydrogenase (PDH). Although deuteration of a 13C enriched substrate is commonly used to increase the lifetime of a probe for hyperpolarization experiments, the potential impact of kinetic isotope effects on such substitutions has not been studied in detail. Metabolism of deuterated pyruvate was investigated in isolated rat hearts. Hearts were perfused with a 1:1 mixture of [U-13C3]pyruvate and [2-13C1]pyruvate or a 1:1 mixture of [U-13C3]pyruvate plus [2-13C1, U-2H3]pyruvate for 30 min before being freeze clamped. Another set of hearts received [2-13C1, U-2H3]pyruvate and was freeze-clamped at 3 min or 6 min. Tissue extracts were analyzed by 1H and 13C{1H} NMR spectroscopy. The chemical shift isotope effect of 2H was monitored in the 13C NMR spectra of the C2 resonance of lactate and alanine plus the C5 of glutamate. There was little kinetic isotope effect of 2H in pyruvate on flux through PDH, LDH or ALT as detected by the distribution of 13C, but the distribution of 2H differed markedly between alanine and lactate. At steady-state, alanine was a mixture of deuterated species, while lactate was largely perdeuterated. Consistent with results at steady-state, hearts freeze-clamped at 3 min or 6 min showed rapid removal of deuterium in alanine but not in lactate. Metabolism of hyperpolarized [1-13C1]pyruvate was compared to [1-13C1,U-2H3]pyruvate in isolated hearts. Consistent with the results from tissue extracts, there was little effect of deuteration on the kinetics of appearance of lactate, alanine or bicarbonate, but there was a small, time-dependent upfield chemical shift in the HP[1-13C1]alanine signal reflecting exchange of methyl deuterons with water protons. Together, these results demonstrate that (1) the kinetics of pyruvate metabolism in hearts detected by 13C NMR are not affected by replacement of the pyruvate methyl protons with deuterons and (2) that the loss of deuterium from the methyl position occurs rapidly during the conversion of pyruvate to alanine. The majority of the deuterium atoms are lost on the time-scale of a hyperpolarization experiment.
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Affiliation(s)
- Alexander M Funk
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Xiaodong Wen
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Thomas Hever
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Nesmine R Maptue
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chalermchai Khemtong
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - A D Sherry
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Chemistry, University of Texas at Dallas, Richardson, TX, United States
| | - Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Radiology, University of Texas Southwestern Medical Center, Dallas, TX, United States; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, United States; Veterans Affairs North Texas Healthcare System, Dallas, TX, United States.
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Bryant G, Taylor MB, Darwish TA, Krause-Heuer AM, Kent B, Garvey CJ. Effect of deuteration on the phase behaviour and structure of lamellar phases of phosphatidylcholines - Deuterated lipids as proxies for the physical properties of native bilayers. Colloids Surf B Biointerfaces 2019; 177:196-203. [PMID: 30743066 DOI: 10.1016/j.colsurfb.2019.01.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 12/20/2018] [Accepted: 01/19/2019] [Indexed: 12/29/2022]
Abstract
Deuteration of phospholipids is a common practice to elucidate membrane structure, dynamics and function, by providing selective visualisation in neutron scattering, nuclear magnetic resonance and vibrational spectroscopy. It is generally assumed that the properties of the deuterated lipids are identical to those of the protiated lipids, and while a number of papers have compared the properties of different forms, to date this has been no systematic study of the effects over a range of conditions. Here we present a study of the effects of deuteration on the organisation and phase behaviour of four common phospholipids (DSPC, DPPC, DMPC, DOPC), observing the effect of chain deuteration and headgroup deuteration on lipid structure and phase behaviour. For saturated lipids in excess water the gel-fluid phase transition temperature is 4.3 ± 0.1 °C lower for lipids with deuterated chains compared to protiated chains, consistent with previous work. Despite this significant change, well away from the transition structural changes as measured by powder small angle X-ray scattering are small and within errors. To investigate this further, measurements were carried out on oriented multilamellar stacks of DOPC in the fluid phase at reduced hydration. Neutrons are used in conjunction with contrast variation to elucidate the role of the deuteration explicitly. It is found that deuterated chains cause a reduction in the lamellar repeat spacing and bilayer thickness, but deuterated headgroups cause an increase. Consequences for the interpretation of Neutron Scattering data with deuterated lipids are discussed.
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Affiliation(s)
- Gary Bryant
- Centre for Molecular and Nanoscale Physics, School of Science, RMIT University, Melbourne, Australia.
| | - Matthew B Taylor
- Centre for Molecular and Nanoscale Physics, School of Science, RMIT University, Melbourne, Australia
| | - Tamim A Darwish
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia.
| | - Anwen M Krause-Heuer
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia
| | - Ben Kent
- Institute for Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, Berlin, Germany.
| | - Christopher J Garvey
- Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, Australia.
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Abstract
Neutron scattering has significant benefits for examining the structure of protein-lipid complexes. Cold (slow) neutrons are nondamaging and predominantly interact with the atomic nucleus, meaning that neutron beams can penetrate deeply into samples, which allows for flexibility in the design of samples studied. Most importantly, there is a strong difference in neutron scattering length (i.e., scattering power) between protium ([Formula: see text], 99.98% natural abundance) and deuterium ([Formula: see text] or D, 0.015%). Through the mixing of H2O and D2O in the samples and in some cases the deuterium labeling of the biomolecules, components within a complex can be hidden or enhanced in the scattering signal. This enables both the overall structure and the relative distribution of components within a complex to be resolved. Lipid-protein complexes are most commonly studied using neutron reflectometry (NR) and small angle neutron scattering (SANS). In this review the methodologies to produce and examine a variety of model biological membrane systems using SANS and NR are detailed. These systems include supported lipid bilayers derived from vesicle dispersions or Langmuir-Blodgett deposition, tethered bilayer systems, membrane protein-lipid complexes and polymer wrapped lipid nanodiscs. The three key stages of any SANS/NR study on model membrane systems-sample preparation, data collection, and analysis-are described together with some background on the techniques themselves.
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Affiliation(s)
- Luke A Clifton
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK.
| | - Stephen C L Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Najet Mahmoudi
- Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot, Oxfordshire, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
- National Institute of Standards and Technology Centre for Neutron Research, Gaithersburg, MD, USA
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK.
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35
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Vugmeyster L, Griffin A, Ostrovsky D, Bhattacharya S, Nichols PJ, McKnight CJ, Vögeli B. Correlated motions of C'-N and C α-C β pairs in protonated and per-deuterated GB3. J Biomol NMR 2018; 72:39-54. [PMID: 30121872 PMCID: PMC6218248 DOI: 10.1007/s10858-018-0205-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
We investigated correlated µs-ms time scale motions of neighboring 13C'-15N and 13Cα-13Cβ nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange. The time scale of motions falls into the intermediate to fast regime (with respect to the chemical shift time scale, 100-400 s-1 range) for the 13C'-15N pairs and into the slow to intermediate regime for the 13Cα-13Cβ pairs (about 150 s-1). Comparison of the results obtained for protonated and deuterated GB3 suggests that deuteration has a tendency to reduce these slow scale correlated motions, especially for the 13Cα-13Cβ pairs.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, 1201 Larimer Street, Denver, CO, 80204, USA.
| | - Aaron Griffin
- Department of Chemistry, University of Colorado at Denver, 1201 Larimer Street, Denver, CO, 80204, USA
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, CO, 80204, USA
| | | | - Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - C James McKnight
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, CO, 80045, USA
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36
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Clark L, Dikiy I, Rosenbaum DM, Gardner KH. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. J Biomol NMR 2018; 71:203-211. [PMID: 30121871 PMCID: PMC7282444 DOI: 10.1007/s10858-018-0204-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 05/21/2023]
Abstract
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY, 10016, USA.
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37
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Franke B, Opitz C, Isogai S, Grahl A, Delgado L, Gossert AD, Grzesiek S. Production of isotope-labeled proteins in insect cells for NMR. J Biomol NMR 2018; 71:173-184. [PMID: 29687312 DOI: 10.1007/s10858-018-0172-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/28/2018] [Indexed: 06/08/2023]
Abstract
Baculovirus-infected insect cells have become a powerful tool to express recombinant proteins for structural and functional studies by NMR spectroscopy. This article provides an introduction into the insect cell/baculovirus expression system and its use for the production of recombinant isotope-labeled proteins. We discuss recent advances in inexpensive isotope-labeling methods using labeled algal or yeast extracts as the amino acid source and give examples of advanced NMR applications for proteins, which have become accessible by this eukaryotic expression host.
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Affiliation(s)
- Bastian Franke
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Christian Opitz
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Leonildo Delgado
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Department of Biology, ETH Zürich, 8093, Zürich, Switzerland.
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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38
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Persons JD, Khan SN, Ishima R. An NMR strategy to detect conformational differences in a protein complexed with highly analogous inhibitors in solution. Methods 2018; 148:9-18. [PMID: 29656080 DOI: 10.1016/j.ymeth.2018.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/06/2018] [Accepted: 04/08/2018] [Indexed: 11/17/2022] Open
Abstract
This manuscript presents an NMR strategy to investigate conformational differences in protein-inhibitor complexes, when the inhibitors tightly bind to a protein at sub-nanomolar dissociation constants and are highly analogous to each other. Using HIV-1 protease (PR), we previously evaluated amide chemical shift differences, ΔCSPs, of PR bound to darunavir (DRV) compared to PR bound to several DRV analogue inhibitors, to investigate subtle but significant long-distance conformation changes caused by the inhibitor's chemical moiety variation [Khan, S. N., Persons, J. D. Paulsen, J. L., Guerrero, M., Schiffer, C. A., Kurt-Yilmaz, N., and Ishima, R., Biochemistry, (2018), 57, 1652-1662]. However, ΔCSPs are not ideal for investigating subtle PR-inhibitor interface differences because intrinsic differences in the electron shielding of the inhibitors affect protein ΔCSPs. NMR relaxation is also not suitable as it is not sensitive enough to detect small conformational differences in rigid regions among similar PR-inhibitor complexes. Thus, to gain insight into conformational differences at the inhibitor-protein interface, we recorded 15N-half filtered NOESY spectra of PR bound to two highly analogous inhibitors and assessed NOEs between PR amide protons and inhibitor protons, between PR amide protons and hydroxyl side chains, and between PR amide protons and water protons. We also verified the PR amide-water NOEs using 2D water-NOE/ROE experiments. Differences in water-amide proton NOE peaks, possibly due to amide-protein hydrogen bonds, were observed between subunit A and subunit B, and between the DRV-bound form and an analogous inhibitor-bound form, which may contribute to remote conformational changes.
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Affiliation(s)
- John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shahid N Khan
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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39
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Luchini A, Delhom R, Demé B, Laux V, Moulin M, Haertlein M, Pichler H, Strohmeier GA, Wacklin H, Fragneto G. The impact of deuteration on natural and synthetic lipids: A neutron diffraction study. Colloids Surf B Biointerfaces 2018; 168:126-33. [PMID: 29433911 DOI: 10.1016/j.colsurfb.2018.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/09/2018] [Accepted: 02/03/2018] [Indexed: 12/19/2022]
Abstract
The structural investigation of cellular membranes requires access to model systems where the molecular complexity is representative of the cellular environment and that allow for the exploitation of structural techniques. Neutron scattering, and in particular neutron diffraction can provide unique and detailed information on the structure of lipid membranes. However, deuterated samples are desirable to fully exploit this powerful method. Recently, the extraction of lipids from microorganisms grown in deuterated media was demonstrated to be both an attracting route to obtain complex lipid mixtures resembling the composition of natural membranes, and to producing deuterated molecules in a very convenient way. A full characterization of these deuterated extracts is hence pivotal for their use in building up model membrane systems. Here we report the structural characterization of lipid extracts obtained from Pichia pastoris by means of neutron diffraction measurements. In particular, we compare the structure of membranes extracted from yeast cells grown in a standard culture medium and in a corresponding deuterated culture medium. The results show that the different molecular composition of the deuterated and protiated lipid extracts induce different structural organization of the lipid membranes. In addition, we compare these membranes composed of extracted yeast lipids with stacked bilayers prepared from synthetic lipid mixtures.
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40
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Schubeis T, Le Marchand T, Andreas LB, Pintacuda G. 1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins. J Magn Reson 2018; 287:140-152. [PMID: 29413327 DOI: 10.1016/j.jmr.2017.11.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 06/08/2023]
Abstract
Building on a decade of continuous advances of the community, the recent development of very fast (60 kHz and above) magic-angle spinning (MAS) probes has revolutionised the field of solid-state NMR. This new spinning regime reduces the 1H-1H dipolar couplings, so that direct detection of the larger magnetic moment available from 1H is now possible at high resolution, not only in deuterated molecules but also in fully-protonated substrates. Such capabilities allow rapid "fingerprinting" of samples with a ten-fold reduction of the required sample amounts with respect to conventional approaches, and permit extensive, robust and expeditious assignment of small-to-medium sized proteins (up to ca. 300 residues), and the determination of inter-nuclear proximities, relative orientations of secondary structural elements, protein-cofactor interactions, local and global dynamics. Fast MAS and 1H detection techniques have nowadays been shown to be applicable to membrane-bound systems. This paper reviews the strategies underlying this recent leap forward in sensitivity and resolution, describing its potential for the detailed characterization of membrane proteins.
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Affiliation(s)
- Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Tanguy Le Marchand
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
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41
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Abstract
Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) can provide valuable information about binding, allostery, and other conformational effects of interaction in protein complexes. For protein-ligand complexes, where the ligand may be a small molecule, peptide, nucleotide, or another protein(s), a typical experiment measures HDX in the protein alone and then compares that with HDX for the protein when part of the complex. Multiple factors are critical in the design and implementation of such experiments, including thoughtful consideration of the percent protein bound, the effects of the labeling protocol on the protein complex, and the dynamic range of the analysis method. With careful planning and techniques, HDX MS analysis of protein complexes can be very informative.
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Affiliation(s)
- Brent A Kochert
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.,Center for Drug Discovery, Northeastern University, Boston, MA, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Alexandros Makriyannis
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.,Center for Drug Discovery, Northeastern University, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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42
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Bernadó P, Shimizu N, Zaccai G, Kamikubo H, Sugiyama M. Solution scattering approaches to dynamical ordering in biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:253-274. [PMID: 29107147 DOI: 10.1016/j.bbagen.2017.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 05/15/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 01/09/2023]
Abstract
Clarification of solution structure and its modulation in proteins and protein complexes is crucially important to understand dynamical ordering in macromolecular systems. Small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are among the most powerful techniques to derive structural information. Recent progress in sample preparation, instruments and software analysis is opening up a new era for small-angle scattering. In this review, recent progress and trends of SAXS and SANS are introduced from the point of view of instrumentation and analysis, touching on general features and standard methods of small-angle scattering. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Giuseppe Zaccai
- Institut Laue Langevin, Institut de Biologie Structurale, CNRS, CNRS, UGA, Grenoble, France
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan..
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43
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Chevelkov V, Giller K, Becker S, Lange A. Measurement of backbone hydrogen-deuterium exchange in the type III secretion system needle protein PrgI by solid-state NMR. J Magn Reson 2017; 283:110-116. [PMID: 28985499 DOI: 10.1016/j.jmr.2017.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/15/2017] [Accepted: 08/27/2017] [Indexed: 06/07/2023]
Abstract
In this report we present site-specific measurements of amide hydrogen-deuterium exchange rates in a protein in the solid state phase by MAS NMR. Employing perdeuteration, proton detection and a high external magnetic field we could adopt the highly efficient Relax-EXSY protocol previously developed for liquid state NMR. According to this method, we measured the contribution of hydrogen exchange on apparent 15N longitudinal relaxation rates in samples with differing D2O buffer content. Differences in the apparent T1 times allowed us to derive exchange rates for multiple residues in the type III secretion system needle protein.
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Affiliation(s)
- Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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44
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Abstract
INTRODUCTION The pharmacokinetics and/or toxicity of many known drugs can be modified by selective deuteration, an area of significant commercial interest and scientific and regulatory progress. Areas covered: This review firstly discusses recent developments in deuterated drugs including the FDA approval of deutetrabenazine. Secondly, it discusses 35 U.S.C. §103 'obviousness' as it relates to recent patent prosecution, and also to Inter Partes Review (IPR). IPR is a new post-award review of patentability under §102 or §103, two IPR petitions upon deuterated drugs have been instituted and included §103 arguments. Finally, an extended analysis of §103 obviousness based upon the practices of major pharmaceutical companies is provided, that supports rather late priority dates, while §102 is also discussed. Expert opinion: The total value of transactions involving deuterated drugs is close to $5 billion. While the importance of §103 'obviousness' rejections remains in patent applications under current prosecution, IPR of issued patents is developing and will affect likely affect §103 interpretations in this area. However, patents are still issuing with later priority dates, and further litigation will likely occur.
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Affiliation(s)
- Graham S Timmins
- a College of Pharmacy , University of New Mexico Health Sciences Center , Albuquerque , NM , USA.,b Department of Pharmaceutical Science , SpinCeutica , Santa Fe , NM , USA
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45
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Abstract
Methyl groups are very useful probes of structure, dynamics, and interactions in protein NMR spectroscopy. In particular, methyl-directed experiments provide high sensitivity even in very large proteins, such as membrane proteins in a membrane-mimicking environment. In this chapter, we discuss the approach for labeling methyl groups in E. coli-based protein expression, as exemplified with the mitochondrial carrier GGC.
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Takeuchi K, Arthanari H, Shimada I, Wagner G. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. J Biomol NMR 2015; 63:323-331. [PMID: 26497830 PMCID: PMC4749451 DOI: 10.1007/s10858-015-9991-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/01/2015] [Indexed: 05/18/2023]
Abstract
Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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Massink A, Holzheimer M, Hölscher A, Louvel J, Guo D, Spijksma G, Hankemeier T, IJzerman AP. Mass spectrometry-based ligand binding assays on adenosine A1 and A2A receptors. Purinergic Signal 2015; 11:581-94. [PMID: 26482925 PMCID: PMC4648803 DOI: 10.1007/s11302-015-9477-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 09/02/2015] [Accepted: 10/02/2015] [Indexed: 12/01/2022] Open
Abstract
Conventional methods to measure ligand-receptor binding parameters typically require radiolabeled ligands as probes. Despite the robustness of radioligand binding assays, they carry inherent disadvantages in terms of safety precautions, expensive synthesis, special lab requirements, and waste disposal. Mass spectrometry (MS) is a method that can selectively detect ligands without the need of a label. The sensitivity of MS equipment increases progressively, and currently, it is possible to detect low ligand quantities that are usually found in ligand binding assays. We developed a label-free MS ligand binding (MS binding) assay on the adenosine A1 and A2A receptors (A1AR and A2AAR), which are well-characterized members of the class A G protein-coupled receptor (GPCR) family. Radioligand binding assays for both receptors are well established, and ample data is available to compare and evaluate the performance of an MS binding assay. 1,3-Dipropyl-8-cyclopentyl-xanthine (DPCPX) and 4-(2-((7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a]-[1,3,5]triazin-5-yl)amino)ethyl)phenol (ZM-241,385) are high-affinity ligands selective for the A1AR and A2AAR, respectively. To proof the feasibility of MS binding on the A1AR and A2AAR, we first developed an MS detection method for unlabeled DPCPX and ZM-241,385. To serve as internal standards, both compounds were also deuterium-labeled. Subsequently, we investigated whether the two unlabeled compounds could substitute for their radiolabeled counterparts as marker ligands in binding experiments, including saturation, displacement, dissociation, and competition association assays. Furthermore, we investigated the accuracy of these assays if the use of internal standards was excluded. The results demonstrate the feasibility of the MS binding assay, even in the absence of a deuterium-labeled internal standard, and provide great promise for the further development of label-free assays based on MS for other GPCRs.
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Affiliation(s)
- A Massink
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - M Holzheimer
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - A Hölscher
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - J Louvel
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - D Guo
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands
| | - G Spijksma
- Division of Analytical Biosciences, LACDR, Leiden University, Leiden, The Netherlands
| | - T Hankemeier
- Division of Analytical Biosciences, LACDR, Leiden University, Leiden, The Netherlands
| | - A P IJzerman
- Division of Medicinal Chemistry, LACDR, Leiden University, Leiden, The Netherlands. .,Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands.
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Abstract
Soon after the discovery of deuterium, efforts to utilize this stable isotope of hydrogen for labeling of plants began and have proven successful for natural abundance to 20% enrichment. However, isotopic labeling with deuterium ((2)H) in higher plants at the level of 40% and higher is complicated by both physiological responses, particularly water exchange through transpiration, and inhibitory effects of D2O on germination, rooting, and growth. The highest incorporation of 40-50% had been reported for photoheterotrophic cultivation of the duckweed Lemna. Higher substitution is desirable for certain applications using neutron scattering and nuclear magnetic resonance (NMR) techniques. (1)H(2)H NMR and mass spectroscopy are standard methods frequently used for determination of location and amount of deuterium substitution. The changes in infrared (IR) absorption observed for H to D substitution in hydroxyl and alkyl groups provide rapid initial evaluation of incorporation. Short-term experiments with cold-tolerant annual grasses can be carried out in enclosed growth containers to evaluate incorporation. Growth in individual chambers under continuous air perfusion with dried sterile-filtered air enables long-term cultivation of multiple plants at different D2O concentrations. Vegetative propagation from cuttings extends capabilities to species with low germination rates. Cultivation in 50% D2O of annual ryegrass and switchgrass following establishment of roots by growth in H2O produces samples with normal morphology and 30-40% deuterium incorporation in the biomass. Winter grain rye (Secale cereale) was found to efficiently incorporate deuterium by photosynthetic fixation from 50% D2O but did not incorporate deuterated phenylalanine-d8 from the growth medium.
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Affiliation(s)
- Barbara R Evans
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
| | - Riddhi Shah
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Abstract
The particular advantage of the cell-free reaction is that it allows a plethora of supplementation during protein expression and offers complete control over the available amino acid pool in view of concentration and composition. In combination with the fast and reliable production efficiencies of cell-free systems, the labeling and subsequent structural evaluation of very challenging targets, such as membrane proteins, comes into focus. We describe current methods for the isotopic labeling of cell-free synthesized membrane proteins and we review techniques available to the practitioner pursuing structural studies by nuclear magnetic resonance spectroscopy. Though isotopic labeling of individual amino acid types appears to be relatively straightforward, an ongoing critical issue in most labeling schemes for structural approaches is the selective substitution of deuterons for protons. While few options are available, the continuous refinement of labeling schemes in combination with improved pulse sequences and optimized instrumentation gives promising perspectives for extended applications in the structural evaluation of cell-free synthesized membrane.
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Affiliation(s)
- Aisha LaGuerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
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Le Brun AP, Clifton LA, Holt SA, Holden PJ, Lakey JH. Deuterium Labeling Strategies for Creating Contrast in Structure-Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry. Methods Enzymol 2015; 566:231-52. [PMID: 26791981 DOI: 10.1016/bs.mie.2015.05.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Studying the outer membrane of Gram-negative bacteria is challenging due to the complex nature of its structure. Therefore, simplified models are required to undertake structure-function studies of processes that occur at the outer membrane/fluid interface. Model membranes can be created by immobilizing bilayers to solid supports such as gold or silicon surfaces, or as monolayers on a liquid support where the surface pressure and fluidity of the lipids can be controlled. Both model systems are amenable to having their structure probed by neutron reflectometry, a technique that provides a one-dimensional depth profile through a membrane detailing its thickness and composition. One of the strengths of neutron scattering is the ability to use contrast matching, allowing molecules containing hydrogen and those enriched with deuterium to be highlighted or matched out against the bulk isotopic composition of the solvent. Lipopolysaccharides, a major component of the outer membrane, can be isolated for incorporation into model membranes. Here, we describe the deuteration of lipopolysaccharides from rough strains of Escherichia coli for incorporation into model outer membranes, and how the use of deuterated materials enhances structural analysis of model membranes by neutron reflectometry.
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Affiliation(s)
- Anton P Le Brun
- National Deuteration Facility, Bragg Institute, Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia.
| | - Luke A Clifton
- ISIS Neutron Facility, STFC Rutherford Appleton Laboratory, Didcot, Oxfordshire, United Kingdom
| | - Stephen A Holt
- Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, New South Wales Australia
| | - Peter J Holden
- National Deuteration Facility, Bragg Institute, Australian Nuclear Science and Technology Organization, Lucas Heights, New South Wales, Australia
| | - Jeremy H Lakey
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
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