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Ma Z, Kong K, Yin Y, Guo Z, Ma X, Lin Q, Wang J, Shen Y, Lu X, Xu X, Kong X, Liu Z, Tang R. High Mechanical Strength Alloy-like Minerals Prepared by Inorganic Ionic Co-cross-linking. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308017. [PMID: 38009645 DOI: 10.1002/adma.202308017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Alloys often combine different metals to generate superior mechanical properties. However, it is challenging to prepare high mechanical strength minerals with similar strategies. Using calcium carbonate (CaC) and calcium phosphate (CaP) as examples, this work synthesizes a group of compounds with the chemical formulas Ca(CO3 )x (PO4 )2(1- x )/3 (0 < x < 1, CaCPs) by cross-linking ionic oligomers. Unlike mixtures, these CaCPs exhibit a single temperature for the phase transition from amorphous to crystallized CaC (calcite) and CaP (hydroxyapatite). By heat-induced synchronous crystallization, dual-phase CaC/CaP with continuous crystallized boundaries are resembled to alloy-like minerals (ALMs). The mechanical properties of the ALMs are adjusted by tailoring their chemical compositions to reach a hardness of 5.6 GPa, which exceed those of control calcite and hydroxyapatite samples by 430% and 260%, respectively. This strategy expands the chemical scope of inorganic materials and holds promise for preparing high-performance minerals.
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Affiliation(s)
- Zaiqiang Ma
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Kangren Kong
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Yu Yin
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Zhengxi Guo
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoming Ma
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Qingyun Lin
- Center of Electron Microscopy, School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jie Wang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Yinlin Shen
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
| | - Xingyu Lu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Instrumentation and Service Centre for Molecular Sciences, Westlake University, Hangzhou, 310024, China
| | - Xurong Xu
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, 310027, China
| | - Xueqian Kong
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhaoming Liu
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, Zhejiang University, Hangzhou, 310027, China
| | - Ruikang Tang
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Silicon and Advanced Semiconductor Materials, Zhejiang University, Hangzhou, 310027, China
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2
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Umegawa Y, Yamamoto T, Dixit M, Funahashi K, Seo S, Nakagawa Y, Suzuki T, Matsuoka S, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Shinoda W, Murata M. Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. SCIENCE ADVANCES 2022; 8:eabo2658. [PMID: 35714188 PMCID: PMC9205587 DOI: 10.1126/sciadv.abo2658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/04/2022] [Indexed: 05/30/2023]
Abstract
Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.
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Affiliation(s)
- Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tomoya Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Mayank Dixit
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Kosuke Funahashi
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Sangjae Seo
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Yasuo Nakagawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Taiga Suzuki
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigeru Matsuoka
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Department of Chemistry, Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Project Research Center for Fundamental Sciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Osaka University, Toyonaka, Osaka 560-0043, Japan
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3
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Koshiyama T, Inoue Y, Asada S, Kawahara K, Ide S, Yasuhara K, Ohba M. pH-Dependent ion permeability control of a modified amphotericin B channel through metal complexation. Chem Commun (Camb) 2021; 57:2895-2898. [PMID: 33606865 DOI: 10.1039/d0cc08368b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Amphotericin B incorporating 2,2'-bipyridine (bpy-AmB) forms a membrane channel exhibiting pH-dependent Ca2+ ion permeability with a selective response to Cu2+ ions. The coordination structure at bpy sites depends on the pH and metal ions can control the association state of bpy-AmB in the membrane.
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Affiliation(s)
- Tomomi Koshiyama
- Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University, 1-1-1, Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
| | - Yuki Inoue
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Sana Asada
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Koki Kawahara
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Shogo Ide
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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4
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Chen J, Hope MA, Lin Z, Wang M, Liu T, Halat DM, Wen Y, Chen T, Ke X, Magusin PCMM, Ding W, Xia X, Wu XP, Gong XQ, Grey CP, Peng L. Interactions of Oxide Surfaces with Water Revealed with Solid-State NMR Spectroscopy. J Am Chem Soc 2020; 142:11173-11182. [PMID: 32459963 DOI: 10.1021/jacs.0c03760] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrous materials are ubiquitous in the natural environment and efforts have previously been made to investigate the structures and dynamics of hydrated surfaces for their key roles in various chemical and physical applications, with the help of theoretical modeling and microscopy techniques. However, an overall atomic-scale understanding of the water-solid interface, including the effect of water on surface ions, is still lacking. Herein, we employ ceria nanorods with different amounts of water as an example and demonstrate a new approach to explore the water-surface interactions by using solid-state NMR in combination with density functional theory. NMR shifts and relaxation time analysis provide detailed information on the local structure of oxygen ions and the nature of water motion on the surface: the amount of molecularly adsorbed water decreases rapidly with increasing temperature (from room temperature to 150 °C), whereas hydroxyl groups are stable up to 150 °C, and dynamic water molecules are found to instantaneously coordinate to the surface oxygen ions. The applicability of dynamic nuclear polarization for selective detection of surface oxygen species is also compared to conventional NMR with surface selective isotopic-labeling: the optimal method depends on the feasibility of enrichment and the concentration of protons in the sample. These results provide new insight into the interfacial structure of hydrated oxide nanostructures, which is important to improve performance for various applications.
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Affiliation(s)
- Junchao Chen
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Michael A Hope
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Zhiye Lin
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Meng Wang
- College of Chemistry and Molecular Engineering (CCME), Peking University, Beijing 100871, China
| | - Tao Liu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David M Halat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Yujie Wen
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Teng Chen
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Xiaokang Ke
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Pieter C M M Magusin
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Weiping Ding
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
| | - Xifeng Xia
- Analysis and Testing Center, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xin-Ping Wu
- Key Laboratory for Advanced Materials, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xue-Qing Gong
- Key Laboratory for Advanced Materials, Centre for Computational Chemistry and Research Institute of Industrial Catalysis, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Clare P Grey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Luming Peng
- Key Laboratory of Mesoscopic Chemistry of MOE and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing 210023, China
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5
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Panche AN, Chandra S, Diwan AD. Multi-Target β-Protease Inhibitors from Andrographis paniculata: In Silico and In Vitro Studies. PLANTS 2019; 8:plants8070231. [PMID: 31319560 PMCID: PMC6681301 DOI: 10.3390/plants8070231] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 12/29/2022]
Abstract
Natural products derived from plants play a vital role in the discovery of new drug candidates, and these are used for novel therapeutic drug development. Andrographis paniculata and Spilanthes paniculata are used extensively as medicinal herbs for the treatment of various ailments, and are reported to have neuroprotective properties. β-amyloid is a microscopic brain protein whose significant aggregation is detected in mild cognitive impairment and Alzheimer’s disease (AD) brains. The accumulation of β-amyloid disrupts cell communication and triggers inflammation by activating immune cells, leading to neuronal cell death and cognitive disabilities. The proteases acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and beta secretase-1 (BACE-1) have been reported to be correlated with the synthesis and growth of β-amyloid plaques in the brains of AD patients. In the present study, the phenolic compounds from A. paniculata and S. paniculata that have been reported in the literature were selected for the current investigation. Furthermore, we employed molecular docking and molecular dynamics studies of the phenolic compounds with the proteins AChE, BChE, and BACE-1 in order to evaluate the binding characteristics and identify potent anti-amyloid agents against the neurodegenerative diseases such as AD. In this investigation, we predicted three compounds from A. paniculata with maximum binding affinities with cholinesterases and BACE-1. The computational investigations predicted that these compounds follow the rule of five. We further evaluated these molecules for in vitro inhibition activity against all the enzymes. In the in vitro investigations, 3,4-di-o-caffeoylquinic acid (5281780), apigenin (5280443), and 7-o-methylwogonin (188316) were found to be strong inhibitors of AChE, BChE, and BACE-1. These findings suggest that these compounds can be potent multi-target inhibitors of the proteases that might cumulatively work and inhibit the initiation and formation of β-amyloid plaques, which is a prime cause of neurotoxicity and dementia. According to our knowledge, these findings are the first report on natural compounds isolated from A. paniculata as multi-target potent inhibitors and anti-amyloid agents.
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Affiliation(s)
- Archana N Panche
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India
- MGM's Institute of Biosciences & Technology, Mahatma Gandhi Mission, N-6, CIDCO, Aurangabad 431003, India
| | - Sheela Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India.
| | - A D Diwan
- MGM's Institute of Biosciences & Technology, Mahatma Gandhi Mission, N-6, CIDCO, Aurangabad 431003, India
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6
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Kristanc L, Božič B, Jokhadar ŠZ, Dolenc MS, Gomišček G. The pore-forming action of polyenes: From model membranes to living organisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:418-430. [DOI: 10.1016/j.bbamem.2018.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/04/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023]
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7
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Khan H, Marya, Amin S, Kamal MA, Patel S. Flavonoids as acetylcholinesterase inhibitors: Current therapeutic standing and future prospects. Biomed Pharmacother 2018; 101:860-870. [PMID: 29635895 DOI: 10.1016/j.biopha.2018.03.007] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acetylcholinesterase (AChE), a serine hydrolase, is primarily responsible for the termination of signal transmission in the cholinergic system, owing to its outstanding hydrolyzing potential. Its substrate acetylcholine (ACh), is a neurotransmitter of the cholinergic system, with a predominant effect on motor neurons involved in memory formation. So, by decreasing the activity of this enzyme by employment of specific inhibitors, a number of motor neuron disorders such as myasthenia gravis, glaucoma, Lewy body dementia, and Alzheimer's disease, among others, can be treated. However, the current-available AChE inhibitors have several limitations in terms of efficacy, therapeutic range, and safety. SCOPE AND APPROACH Primarily due to the non-compliance of current therapies, new, effective and safe inhibitors are being searched for, especially those which act through multiple receptor sites, but do not elicit undesirable effects. In this regard, the evaluation of phytochemicals such as flavonoids, can be a rational approach. The therapeutic potential of flavonoids has already been recognized agaisnt several ailments. This review deals with various plant-derived flavonoids, their preclinical potential as AChE inhibitors, in established assays, possible mechanisms of action, and structural activity relationship (SAR). RESULTS AND CONCLUSIONS Subsequently, a number of plant-derived flavonoids with outstanding efficacy and potency as AChE inhibitors, the mechanistic, their safety profiles, and pharmacokinetic attributes have been discussed. Through derivatization of these reported flavonoids, some limitation in efficacy or pharmacokinetic parameters can be addressed. The selected flavonoids ought to be tested in clinical studies to discover new neuro-therapeutic candidates.
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Affiliation(s)
- Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan.
| | - Marya
- Department of Pharmacy, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Surriya Amin
- Department of Botany, Islamia College Peshawar, Pakistan
| | - Mohammad Amjad Kamal
- King Fahd Medical Research Center, King Abdulaziz University, Saudi Arabia; Enzymoics, 7 Peterlee Place, Hebersham, NSW, 2770, Australia; Novel Global Community Educational Foundation, Australia
| | - Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA, 92182, USA.
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8
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Yang H, Staveness D, Ryckbosch SM, Axtman AD, Loy BA, Barnes AB, Pande VS, Schaefer J, Wender PA, Cegelski L. REDOR NMR Reveals Multiple Conformers for a Protein Kinase C Ligand in a Membrane Environment. ACS CENTRAL SCIENCE 2018; 4:89-96. [PMID: 29392180 PMCID: PMC5785774 DOI: 10.1021/acscentsci.7b00475] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Indexed: 05/05/2023]
Abstract
Bryostatin 1 (henceforth bryostatin) is in clinical trials for the treatment of Alzheimer's disease and for HIV/AIDS eradication. It is also a preclinical lead for cancer immunotherapy and other therapeutic indications. Yet nothing is known about the conformation of bryostatin bound to its protein kinase C (PKC) target in a membrane microenvironment. As a result, efforts to design more efficacious, better tolerated, or more synthetically accessible ligands have been limited to structures that do not include PKC or membrane effects known to influence PKC-ligand binding. This problem extends more generally to many membrane-associated proteins in the human proteome. Here, we use rotational-echo double-resonance (REDOR) solid-state NMR to determine the conformations of PKC modulators bound to the PKCδ-C1b domain in the presence of phospholipid vesicles. The conformationally limited PKC modulator phorbol diacetate (PDAc) is used as an initial test substrate. While unanticipated partitioning of PDAc between an immobilized protein-bound state and a mobile state in the phospholipid assembly was observed, a single conformation in the bound state was identified. In striking contrast, a bryostatin analogue (bryolog) was found to exist exclusively in a protein-bound state, but adopts a distribution of conformations as defined by three independent distance measurements. The detection of multiple PKCδ-C1b-bound bryolog conformers in a functionally relevant phospholipid complex reveals the inherent dynamic nature of cellular systems that is not captured with single-conformation static structures. These results indicate that binding, selectivity, and function of PKC modulators, as well as the design of new modulators, are best addressed using a dynamic multistate model, an analysis potentially applicable to other membrane-associated proteins.
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Affiliation(s)
- Hao Yang
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Daryl Staveness
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Steven M. Ryckbosch
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alison D. Axtman
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Brian A. Loy
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Alexander B. Barnes
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Vijay S. Pande
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jacob Schaefer
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United
States
| | - Paul A. Wender
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Department
of Chemical and Systems Biology, Stanford
University, Stanford, California 94305, United States
| | - Lynette Cegelski
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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9
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Lee JH, Kim MS, Lee HW, Lee IYC, Kim HK, Kim ND, Lee S, Seo H, Paik Y. The Application of REDOR NMR to Understand the Conformation of Epothilone B. Int J Mol Sci 2017; 18:E1472. [PMID: 28698492 PMCID: PMC5535963 DOI: 10.3390/ijms18071472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022] Open
Abstract
The structural information of small therapeutic compounds complexed in biological matrices is important for drug developments. However, structural studies on ligands bound to such a large and dynamic system as microtubules are still challenging. This article reports an application of the solid-state NMR technique to investigating the bioactive conformation of epothilone B, a microtubule stabilizing agent, whose analog ixabepilone was approved by the U.S. Food and Drug Administration (FDA) as an anticancer drug. First, an analog of epothilone B was designed and successfully synthesized with deuterium and fluorine labels while keeping the high potency of the drug; Second, a lyophilization protocol was developed to enhance the low sensitivity of solid-state NMR; Third, molecular dynamics information of microtubule-bound epothilone B was revealed by high-resolution NMR spectra in comparison to the non-bound epothilone B; Last, information for the macrolide conformation of microtubule-bound epothilone B was obtained from rotational-echo double-resonance (REDOR) NMR data, suggesting the X-ray crystal structure of the ligand in the P450epoK complex as a possible candidate for the conformation. Our results are important as the first demonstration of using REDOR for studying epothilones.
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Affiliation(s)
- Jae-Ho Lee
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Moon-Su Kim
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Hyo Won Lee
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Ihl-Young C Lee
- Drug Discovery Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea.
| | - Hyun Kyoung Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, 88 Dongnae-ro, Dong-gu, Daegu 41061, Korea.
| | - Nam Doo Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, 88 Dongnae-ro, Dong-gu, Daegu 41061, Korea.
| | - SangGap Lee
- Spin Physics & Engineering Team, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Korea.
| | - Hwajeong Seo
- Daegu Center, Korea Basic Science Institute, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea.
| | - Younkee Paik
- Spin Physics & Engineering Team, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Korea.
- Daegu Center, Korea Basic Science Institute, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea.
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10
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Fillion M, Goudreault M, Voyer N, Bechinger B, Auger M. Amphiphilicity Is a Key Determinant in the Membrane Interactions of Synthetic 14-mer Cationic Peptide Analogues. Biochemistry 2016; 55:6919-6930. [DOI: 10.1021/acs.biochem.6b00961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | - Burkhard Bechinger
- Université de Strasbourg, CNRS, UMR7177, Institut de
Chimie, 4, Rue Blaise
Pascal, 67070 Strasbourg, France
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11
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Nakagawa Y, Umegawa Y, Matsushita N, Yamamoto T, Tsuchikawa H, Hanashima S, Oishi T, Matsumori N, Murata M. The Structure of the Bimolecular Complex between Amphotericin B and Ergosterol in Membranes Is Stabilized by Face-to-Face van der Waals Interaction with Their Rigid Cyclic Cores. Biochemistry 2016; 55:3392-402. [DOI: 10.1021/acs.biochem.6b00193] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Yasuo Nakagawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Naohiro Matsushita
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomoya Yamamoto
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hiroshi Tsuchikawa
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tohru Oishi
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department
of Chemistry,
Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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12
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Pourpoint F, Yehl J, Li M, Gupta R, Trébosc J, Lafon O, Amoureux JP, Polenova T. NMR Crystallography of an Oxovanadium(V) Complex by an Approach Combining Multinuclear Magic Angle Spinning NMR, DFT, and Spin Dynamics Simulations. Chemphyschem 2015; 16:1619-26. [DOI: 10.1002/cphc.201500033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Indexed: 11/08/2022]
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13
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Loy BA, Lesser AB, Staveness D, Billingsley KL, Cegelski L, Wender PA. Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy. J Am Chem Soc 2015; 137:3678-85. [PMID: 25710634 DOI: 10.1021/jacs.5b00886] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein kinase C (PKC) modulators are currently of great importance in preclinical and clinical studies directed at cancer, immunotherapy, HIV eradication, and Alzheimer's disease. However, the bound conformation of PKC modulators in a membrane environment is not known. Rotational echo double resonance (REDOR) NMR spectroscopy could uniquely address this challenge. However, REDOR NMR requires strategically labeled, high affinity ligands to determine interlabel distances from which the conformation of the bound ligand in the PKC-ligand complex could be identified. Here we report the first computer-guided design and syntheses of three bryostatin analogues strategically labeled for REDOR NMR analysis. Extensive computer analyses of energetically accessible analogue conformations suggested preferred labeling sites for the identification of the PKC-bound conformers. Significantly, three labeled analogues were synthesized, and, as required for REDOR analysis, all proved highly potent with PKC affinities (∼1 nM) on par with bryostatin. These potent and strategically labeled bryostatin analogues are new structural leads and provide the necessary starting point for projected efforts to determine the PKC-bound conformation of such analogues in a membrane environment, as needed to design new PKC modulators and understand PKC-ligand-membrane structure and dynamics.
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Affiliation(s)
- Brian A Loy
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Adam B Lesser
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Daryl Staveness
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Kelvin L Billingsley
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Lynette Cegelski
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
| | - Paul A Wender
- †Department of Chemistry and ‡Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, United States
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14
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Cegelski L. REDOR NMR for drug discovery. Bioorg Med Chem Lett 2013; 23:5767-75. [PMID: 24035486 PMCID: PMC4038398 DOI: 10.1016/j.bmcl.2013.08.064] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 08/12/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022]
Abstract
Rotational-echo double-resonance (REDOR) NMR is a powerful and versatile solid-state NMR measurement that has been recruited to elucidate drug modes of action and to drive the design of new therapeutics. REDOR has been implemented to examine composition, structure, and dynamics in diverse macromolecular and whole-cell systems, including taxol-bound microtubules, enzyme-cofactor-inhibitor ternary complexes, and antibiotic-whole-cell complexes. The REDOR approach involves the integrated design of specific isotopic labeling strategies and the selection of appropriate REDOR experiments. By way of example, this digest illustrates the versatility of the REDOR approach, with an emphasis on the practical considerations of experimental design and data interpretation.
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Affiliation(s)
- Lynette Cegelski
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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15
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Gutmann T, Bonnefille E, Breitzke H, Debouttière PJ, Philippot K, Poteau R, Buntkowsky G, Chaudret B. Investigation of the surface chemistry of phosphine-stabilized ruthenium nanoparticles – an advanced solid-state NMR study. Phys Chem Chem Phys 2013; 15:17383-94. [DOI: 10.1039/c3cp52927d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Matsuoka S. [Structural study on small molecules in biological solid samples by using solid state NMR]. YAKUGAKU ZASSHI 2012; 132:969-78. [PMID: 23023412 DOI: 10.1248/yakushi.132.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many small molecule drugs have molecular targets that are non-crystalline and insoluble biological matrices, such as proteins embedded in lipid membrane, cell membranes, and cell walls. To understand the action mechanisms, it is essential to determine the binding structure with atomic-level resolution. Although solution nuclear magnetic resonance (NMR) and X-ray crystallography have been used to determine molecular structures of cell membrane and membrane proteins, these methods are unable to reproduce the complexity of biological systems because either solubilization or crystallization of target molecules is requisite. For structural studies of insoluble non-crystalline biological samples, so-called "biological solids", high resolution distance measurements using solid-state NMR are indispensable techniques, of which rotational-echo double-resonance (REDOR) is one of the most widely used methods. In this paper, a brief introduction to REDOR NMR and its applications to structural studies on the antifungal amphotericin B-membrane phospholipid complex and a structural elucidation of photorespiration metabolites in plant cells without extraction or isolation is provided.
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Affiliation(s)
- Shigeru Matsuoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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17
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Matsuoka S, Murai M, Yamazaki T, Inoue M. Short polyglutamine peptide forms a high-affinity binding site for thioflavin-T at the N-terminus. Org Biomol Chem 2012; 10:5787-90. [DOI: 10.1039/c2ob07157f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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18
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Durand N, Boutevin B, Silly G, Améduri B. “Grafting From” Polymerization of Vinylidene Fluoride (VDF) from Silica to Achieve Original Silica–PVDF Core–Shells. Macromolecules 2011. [DOI: 10.1021/ma2018167] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nelly Durand
- Ingénierie et Architectures Macromoléculaires, Ecole Nationale Supérieure de Chimie de Montpellier (UMR 5253-CNRS), 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 1, France
| | - Bernard Boutevin
- Ingénierie et Architectures Macromoléculaires, Ecole Nationale Supérieure de Chimie de Montpellier (UMR 5253-CNRS), 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 1, France
| | - Gilles Silly
- Chalcogénures et Verres, Institut Charles Gerhardt (UMR 5253-CNRS), CC1503, Université de Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Bruno Améduri
- Ingénierie et Architectures Macromoléculaires, Ecole Nationale Supérieure de Chimie de Montpellier (UMR 5253-CNRS), 8, rue de l’Ecole Normale, 34296 Montpellier Cedex 1, France
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19
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Shintani M, Yoshida K, Sakuraba S, Nakahara M, Matubayasi N. NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics. J Phys Chem B 2011; 115:9106-15. [PMID: 21728286 DOI: 10.1021/jp204051f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Motional correlation times between the hydrophilic and hydrophobic terminal groups in lipid membranes are studied over a wide range of curvatures using the solution-state (1)H NMR-nuclear Overhauser effect (NOE) and molecular dynamics (MD) simulation. To enable (1)H NMR-NOE measurements for large vesicles, the transient NOE method is combined with the spin-echo method, and is successfully applied to a micelle of 1-palmitoyl-lysophosphatidylcholine (PaLPC) with diameter of 5 nm and to vesicles of dipalmitoylphosphatidylcholine (DPPC) with diameters ranging from 30 to 800 nm. It is found that the NOE intensity increases with the diameter up to ∼100 nm, and the model membrane is considered planar on the molecular level beyond ∼100 nm. While the NOE between the hydrophilic terminal and hydrophobic terminal methyl groups is absent for the micelle, its intensity is comparable to that for the neighboring group for vesicles with larger diameters. The origin of NOE signals between distant sites is analyzed by MD simulations of PaLPC micelles and DPPC planar bilayers. The slow relaxation is shown to yield an observable NOE signal even for the hydrophilic and hydrophobic terminal sites. Since the information on distance and dynamics cannot be separated in the experimental NOE alone, the correlation time in large vesicles is determined by combining the experimental NOE intensity and MD-based distance distribution. For large vesicles, the correlation time is found to vary by 2 orders of magnitude over the proton sites. This study shows that NOE provides dynamic information on large vesicles when combined with MD, which provides structural information.
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Affiliation(s)
- Megumi Shintani
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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