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Merlino F, Marzano S, Zizza P, D'Aria F, Grasso N, Carachino A, Iachettini S, Biroccio A, Fonzo SD, Grieco P, Randazzo A, Amato J, Pagano B. Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity. Nucleic Acids Res 2024:gkae471. [PMID: 38828773 DOI: 10.1093/nar/gkae471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Noncanonical nucleic acid structures, particularly G-quadruplexes, have garnered significant attention as potential therapeutic targets in cancer treatment. Here, the recognition of G-quadruplex DNA by peptides derived from the Rap1 protein is explored, with the aim of developing novel peptide-based G-quadruplex ligands with enhanced selectivity and anticancer activity. Biophysical techniques were employed to assess the interaction of a peptide derived from the G-quadruplex-binding domain of the protein with various biologically relevant G-quadruplex structures. Through alanine scanning mutagenesis, key amino acids crucial for G-quadruplex recognition were identified, leading to the discovery of two peptides with improved G-quadruplex-binding properties. However, despite their in vitro efficacy, these peptides showed limited cell penetration and anticancer activity. To overcome this challenge, cell-penetrating peptide (CPP)-conjugated derivatives were designed, some of which exhibited significant cytotoxic effects on cancer cells. Interestingly, selected CPP-conjugated peptides exerted potent anticancer activity across various tumour types via a G-quadruplex-dependent mechanism. These findings underscore the potential of peptide-based G-quadruplex ligands in cancer therapy and pave the way for the development of novel therapeutic strategies targeting these DNA structures.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Alice Carachino
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Sara Iachettini
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste 34149, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
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Klose JW, Begbie AJ, Toronjo-Urquiza L, Pukala TL. Native Mass Spectrometric Insights into the Formation and Stability of DNA Triplexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:613-621. [PMID: 38393825 DOI: 10.1021/jasms.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Deoxyribonucleic acid is a genetic biomacromolecule that contains the inherited information required to build and maintain a living organism. While the canonical duplex DNA structure is rigorously characterized, the structure and function of higher order DNA structures such as DNA triplexes are comparatively poorly understood. Previous literature has shown that these triplexes can form under physiological conditions, and native mass spectrometry offers a useful platform to study their formation and stability. However, experimental conditions including buffer salt concentration, pH, and instrumentation parameters such as ion mode can confound analysis by impacting the amount of triplex observed by mass spectrometry. Using model 30mer Y-type triplex sequences, we demonstrate the influence a range of experimental variables have on the detection of DNA triplex structures, informing suitable conditions for the study. When carefully considered conditions are used, mass spectrometry offers a powerful complementary tool for the analysis of higher order DNA assemblies.
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Affiliation(s)
- Jack W Klose
- Discipline of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alexander J Begbie
- Discipline of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Luis Toronjo-Urquiza
- School of Chemical Engineering, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Georgiou K, Konstantinidi A, Hutterer J, Freudenberger K, Kolarov F, Lambrinidis G, Stylianakis I, Stampelou M, Gauglitz G, Kolocouris A. Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184258. [PMID: 37995846 DOI: 10.1016/j.bbamem.2023.184258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Experimental binding free energies of 27 adamantyl amines against the influenza M2(22-46) WT tetramer, in its closed form at pH 8, were measured by ITC in DPC micelles. The measured Kd's range is ~44 while the antiviral potencies (IC50) range is ~750 with a good correlation between binding free energies computed with Kd and IC50 values (r = 0.76). We explored with MD simulations (ff19sb, CHARMM36m) the binding profile of complexes with strong, moderate and weak binders embedded in DMPC, DPPC, POPC or a viral mimetic membrane and using different experimental starting structures of M2. To predict accurately differences in binding free energy in response to subtle changes in the structure of the ligands, we performed 18 alchemical perturbative single topology FEP/MD NPT simulations (OPLS2005) using the BAR estimator (Desmond software) and 20 dual topology calculations TI/MD NVT simulations (ff19sb) using the MBAR estimator (Amber software) for adamantyl amines in complex with M2(22-46) WT in DMPC, DPPC, POPC. We observed that both methods with all lipids show a very good correlation between the experimental and calculated relative binding free energies (r = 0.77-0.87, mue = 0.36-0.92 kcal mol-1) with the highest performance achieved with TI/MBAR and lowest performance with FEP/BAR in DMPC bilayers. When antiviral potencies are used instead of the Kd values for computing the experimental binding free energies we obtained also good performance with both FEP/BAR (r = 0.83, mue = 0.75 kcal mol-1) and TI/MBAR (r = 0.69, mue = 0.77 kcal mol-1).
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Affiliation(s)
- Kyriakos Georgiou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Athina Konstantinidi
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Johanna Hutterer
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Kathrin Freudenberger
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Felix Kolarov
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany; Roche, Penzberg, Bavaria, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Ioannis Stylianakis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Margarita Stampelou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Günter Gauglitz
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece.
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Yan S, Li M, Jiang Q, Li M, Hu M, Shi X, Liang P, Yin M, Gao X, Shen J, Zhang L. Self-assembled co-delivery nanoplatform for increasing the broad-spectrum susceptibility of fall armyworm toward insecticides. J Adv Res 2024:S2090-1232(24)00044-4. [PMID: 38286302 DOI: 10.1016/j.jare.2024.01.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024] Open
Abstract
INTRODUCTION Unscientific application of insecticides has led to severe resistance of pests to almost all classes of insecticides. Enhanced detoxification is the most common mechanism for this kind of resistance. OBJECT Fall armyworm (FAW) has developed insecticide resistance, which is often linked to the overexpression of detoxification genes. Herein, a multicomponent nano-pesticide is designed to increase its broad-spectrum susceptibility toward insecticides. METHOD Regulatory function of nuclear factor erythroid 2-related factor 2 (Nrf2) in detoxification was confirmed using transcriptome sequencing, quantitative real-time PCR and enzyme activity measurement. A star polycation (SPc) was adopted to construct the pesticide/SPc/complex, whose self-assembly mechanism and characterization were examined using isothermal titration calorimetry, dynamic light scattering and transmission electron microscope. The delivery efficiency of SPc-loaded dsRNA was examined in vitro and in vivo using fluorescent tracer technique. A multicomponent nano-pesticide was created through the integration of bacterial expression system and nano-delivery system, and its bioactivity was tested in laboratory and field. RESULTS We confirmed the crucial role of Nrf2 in regulating the detoxification in FAW, and silencing Nrf2 could decrease detoxification gene expression and increase insecticide susceptibility. We then applied the SPc to self-assemble a nanoplatform for delivering Nrf2 double-stranded RNA (dsRNA) and pesticide simultaneously. Nano-sized pesticide/SPc/dsRNA complex exhibited high delivery efficiency in vitro and in vivo. Excitingly, the insecticidal activities of pesticide/SPc/dsNrf2 complexes were remarkably improved with the normalized synergistic ratios of 5.43-6.25 for chlorantraniliprole, 4.45-15.00 for emamectin benzoate, and 6.75-15.00 for spinetoram. Finally, we developed a multicomponent nano-pesticide (pesticide/SPc/dsNrf2 complex) using a bacterial expression system and nano-delivery system. This approach exhibited excellent leaf protection and pest control efficacy. CONCLUSION The integration between the pesticide nanometerization and insecticide susceptibility improvement offers a promising strategy to increase insecticidal activity. Our study provides a revolutionary and universal strategy to increase insecticidal activity and decease application doses.
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Affiliation(s)
- Shuo Yan
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China.
| | - Mingjian Li
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Qinhong Jiang
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Mingshan Li
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Mengfan Hu
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Xueyan Shi
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Pei Liang
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, 100029 Beijing, PR China
| | - Xiwu Gao
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China
| | - Jie Shen
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China.
| | - Lei Zhang
- College of Plant Protection, China Agricultural University, 100193 Beijing, PR China.
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Yang Y, Wei Y, Yin M, Liu E, Du X, Shen J, Dong M, Yan S. Efficient Polyamine-Based Nanodelivery System for Proline: Enhanced Uptake Improves the Drought Tolerance of Tobacco. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:1550-1560. [PMID: 38207102 DOI: 10.1021/acs.jafc.3c05636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Drought stress is one of the most unfavorable factors affecting plant growth and productivity among various environmental stresses. Nanotechnology is expected to enhance the effectiveness of conventional biostimulants. Herein, the current study constructed an efficient proline (Pro) nanodelivery system based on a star polyamine (SPc). The hydroxyl groups of Pro could assemble with carbonyl groups of SPc, and the self-assembly of Pro with SPc formed the nanoscale particles of the Pro/SPc complex. Compared to Pro alone, the contact angle of SPc-loaded Pro decreased, and its retentivity and plant uptake increased. Importantly, the tobacco (Nicotiana benthamiana) seeds and seedlings treated with Pro/SPc complex exhibited stronger drought tolerance. RNA-Seq analysis indicated that the SPc-loaded Pro could further upregulate photosynthesis-related genes and endocytosis-related genes. The current study constructed an efficient nanodelivery system for improving the bioactivity of biostimulants, which has broad application prospects in the agricultural field.
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Affiliation(s)
- Yanxiao Yang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Ying Wei
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China
| | - Enliang Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China
| | - Xiangge Du
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
| | - Min Dong
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
| | - Shuo Yan
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, P. R. China
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6
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Ballal S. A brief account of evolution of assays to study carbohydrate-protein interaction. J Mol Recognit 2024; 37:e3065. [PMID: 37864321 DOI: 10.1002/jmr.3065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/02/2023] [Accepted: 10/07/2023] [Indexed: 10/22/2023]
Abstract
Molecular recognition remains one of the most desirable means of cellular communication. Each cell offers a unique surface pattern of biomolecules that makes it very specific about the nature of molecules that interact with the cell. Protein-glycan interaction has been one of the most common forms of cell signaling. Glycans expressed on the cell surface interact with an exogenous protein, and in many cases lead to a physiological response. These carbohydrate-binding proteins, commonly known as lectins, are very specific to the glycan they bind to. An exogenous lectin interacting with an animal cell surface glycan is generally studied using the classical hemagglutination assay. However, this method presents certain challenges that make it imperative to design and develop novel methods that are more specific and efficient in their interaction. In the last decade, a few methods have been developed to analyze more diverse reactions and use a lesser amount of sample. In some cases, the processing of the sample is also reduced. This review discusses how the methods have evolved over the decades and how they have reduced error while becoming more efficient.
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Affiliation(s)
- Suhas Ballal
- Department of Chemistry and Biochemistry, Jain (Deemed to be) University, Bengaluru, India
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7
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Holowinski P, Dybowski MP. Determination of 3- and 4-chloromethcathinone interactions with plasma proteins: study involving analytical and theoretical methods. Forensic Toxicol 2023:10.1007/s11419-023-00677-7. [PMID: 38108940 DOI: 10.1007/s11419-023-00677-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/27/2023] [Indexed: 12/19/2023]
Abstract
PURPOSE The purpose of this paper was to determine 3- and 4-chloromethcathinone (3- and 4-CMC) binding degree and possible binding interaction modes with human serum albumin (HSA) using analytical and theoretical methods. METHODS Experimental determination of 3- and 4-CMC binding degree with HSA was performed using gas chromatography-tandem mass spectrometry preceded by the equilibrium dialysis (ED) and ultrafiltration (UF). Nuclear magnetic resonance (NMR) spectroscopy was used to determine 3- and 4-CMC epitope-binding maps and possible binding sites in HSA. The molecular docking and molecular dynamics were employed to obtain detailed information about binding modes of 3- and 4-CMC enantiomers in HSA. RESULTS As follows from the presented data, the degree of binding of 3- and 4-CMC is at a similar level of approx. 80%. This indicates a relatively strong binding of CMC to plasma proteins. The model studies employing the NMR spectroscopy and molecular simulations indicate that both CMCs bind to HSA. The whole 3- and 4-CMC molecules are embedded in the binding sites, with aromatic moieties being in the closest contact with the HSA residues. Moreover, conducted experiments show that Sudlow site II is the main binding center for 3- and 4-CMC and Sudlow site I acts as the secondary binding site. CONCLUSIONS Although many studies describe pharmacological and toxicological properties of synthetic cathinones (SC), the data taking SCs binding in plasma into consideration are scarce. To our knowledge, this is the first report presenting comprehensive experimental and theoretical characterization of 3- and 4-CMC binding with plasma proteins.
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Affiliation(s)
- Piotr Holowinski
- Faculty of Chemistry, Department of Chromatography, Institute of Chemical Sciences, Maria Curie Sklodowska University in Lublin, 20-031, Lublin, Poland
| | - Michal P Dybowski
- Faculty of Chemistry, Department of Chromatography, Institute of Chemical Sciences, Maria Curie Sklodowska University in Lublin, 20-031, Lublin, Poland.
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Deng L, Fu Q, Zhang Y, Shui F, Tang J, Wu J, Zeng J. Study of molecular interactions by nonequilibrium capillary electrophoresis of equilibrium mixtures: Originations, developments, and applications. Electrophoresis 2023; 44:1664-1673. [PMID: 37621032 DOI: 10.1002/elps.202300166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023]
Abstract
Molecular interactions play a vital role in regulating various physiological and biochemical processes in vivo. Kinetic capillary electrophoresis (KCE) is an analytical platform that offers significant advantages in studying the thermodynamic and kinetic parameters of molecular interactions. It enables the simultaneous analysis of these parameters within an interaction pattern and facilitates the screening of binding ligands with predetermined kinetic parameters. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was the first proposed KCE method, and it has found widespread use in studying molecular interactions involving proteins/aptamers, proteins/small molecules, and peptides/small molecules. The successful applications of NECEEM have demonstrated its promising potential for further development and broader application. However, there has been a dearth of recent reviews on NECEEM. To address this gap, our study provides a comprehensive description of NECEEM, encompassing its origins, development, and applications from 2015 to 2022. The primary focus of the applications section is on aptamer selection and screening of small-molecule ligands. Furthermore, we discuss important considerations in NECEEM experimental design, such as buffer suitability, detector selection, and protein adsorption. By offering this thorough review, we aim to contribute to the understanding, advancement, and wider utilization of NECEEM as a valuable tool for studying molecular interactions and facilitating the identification of potential ligands and targets.
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Affiliation(s)
- Li Deng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Qifeng Fu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Yujie Zhang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Fan Shui
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jia Tang
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jianming Wu
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
- School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, P. R. China
| | - Jing Zeng
- School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, P. R. China
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Wang Y, Li M, Ying J, Shen J, Dou D, Yin M, Whisson SC, Birch PRJ, Yan S, Wang X. High-efficiency green management of potato late blight by a self-assembled multicomponent nano-bioprotectant. Nat Commun 2023; 14:5622. [PMID: 37699893 PMCID: PMC10497615 DOI: 10.1038/s41467-023-41447-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 09/02/2023] [Indexed: 09/14/2023] Open
Abstract
Potato late blight caused by Phytophthora infestans is a devastating disease worldwide. Unlike other plant pathogens, double-stranded RNA (dsRNA) is poorly taken up by P. infestans, which is a key obstacle in using dsRNA for disease control. Here, a self-assembled multicomponent nano-bioprotectant for potato late blight management is designed based on dsRNA and a plant elicitor. Nanotechnology overcomes the dsRNA delivery bottleneck for P. infestans and extends the RNAi protective window. The protective effect of nano-enabled dsRNA against infection arises from a synergistic mechanism that bolsters the stability of dsRNA and optimizes its effective intracellular delivery. Additionally, the nano-enabled elicitor enhances endocytosis and amplifies the systemic defense response of the plants. Co-delivery of dsRNA and an elicitor provides a protective effect via the two aspects of pathogen inhibition and elevated plant defense mechanisms. The multicomponent nano-bioprotectant exhibits superior control efficacy compared to a commercial synthetic pesticide in field conditions. This work proposes an eco-friendly strategy to manage devastating plant diseases and pests.
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Affiliation(s)
- Yuxi Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Mingshan Li
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jiahan Ying
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jie Shen
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Daolong Dou
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
- College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Stephen C Whisson
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul R J Birch
- Cell and Molecular Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, School of Life Science, University of Dundee (at James Hutton Institute), Invergowrie, Dundee, DD2 5DA, UK
| | - Shuo Yan
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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10
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Zhao J, Yan S, Li M, Sun L, Dong M, Yin M, Shen J, Zhao Z. NPFR regulates the synthesis and metabolism of lipids and glycogen via AMPK: Novel targets for efficient corn borer management. Int J Biol Macromol 2023; 247:125816. [PMID: 37451386 DOI: 10.1016/j.ijbiomac.2023.125816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
RNA biopesticides are regarded as "the third revolution in the history of pesticides" due to their extensive advantages such as precision, high efficiency, green, pollution-free, etc. In the current study, two target genes encoding neuropeptide F receptor (NPFR) and AMP-activated protein kinase (AMPK), which are essential for insect feeding, cellular energy homeostasis and nutrient availability, were selected to design RNA pesticides. We achieved high RNA interference (RNAi) efficiency of npfr via a star polycation nanocarrier-based double-stranded RNA (dsRNA) delivery system. The food consumption of Ostrinia furnacalis is largely suppressed, which leads to a good protective effect on corn leaves. We determined the mechanism of the above genes. NPFR binds to the Gα protein and activates the intracellular second messengers cAMP and Ca2+, which in turn phosphorylate AMPK to regulate the synthesis and metabolism of lipids and glycogen. We then adopted a highly efficient bacteria-based expression system for the production of large amounts of dsRNA segments targeting npfr and ampk simultaneously and subsequently complexed them with nanocarriers to develop a novel dual-target RNA pesticide. Our RNA nanopesticide dramatically inhibits larval feeding, growth and development, and its controlling effect is even better than that of the widely used anti-feedant azadirachtin.
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Affiliation(s)
- Jiajia Zhao
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Shuo Yan
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Mingshan Li
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Lina Sun
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Min Dong
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Meizhen Yin
- State Key Lab of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Shen
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
| | - Zhangwu Zhao
- Department of Entomology and MARA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
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Su X, Yan S, Zhao W, Liu H, Jiang Q, Wei Y, Guo H, Yin M, Shen J, Cheng H. Self-assembled thiophanate-methyl/star polycation complex prevents plant cell-wall penetration and fungal carbon utilization during cotton infection by Verticillium dahliae. Int J Biol Macromol 2023; 239:124354. [PMID: 37028625 DOI: 10.1016/j.ijbiomac.2023.124354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/23/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
No effective fungicides are available for the management of Verticillium dahliae, which causes vascular wilt disease. In this study, a star polycation (SPc)-based nanodelivery system was used for the first time to develop a thiophanate-methyl (TM) nanoagent for the management of V. dahliae. SPc spontaneously assembled with TM through hydrogen bonding and Van der Waals forces to decrease the particle size of TM from 834 to 86 nm. Compared to TM alone, the SPc-loaded TM further reduced the colony diameter of V. dahliae to 1.12 and 0.64 cm, and the spore number to 1.13 × 108 and 0.72 × 108 cfu/mL at the concentrations of 3.77 and 4.71 mg/L, respectively. The TM nanoagents disturbed the expression of various crucial genes in V. dahliae, and contributed to preventing plant cell-wall degradation and carbon utilization by V. dahliae, which mainly impaired the infective interaction between pathogens and plants. TM nanoagents remarkably decreased the plant disease index and the fungal biomass in the root compared to TM alone, and its control efficacy was the best (61.20 %) among the various formulations tested in the field. Furthermore, SPc showed negligible acute toxicity toward cotton seeds. To the best of our knowledge, this study is the first to design a self-assembled nanofungicide that efficiently inhibits V. dahliae growth and protects cotton from the destructive Verticillium wilt.
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Affiliation(s)
- Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, PR China
| | - Shuo Yan
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
| | - Weisong Zhao
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Baoding 071000, PR China
| | - Haiyang Liu
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, PR China
| | - Qinhong Jiang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Ying Wei
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, PR China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, PR China.
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, PR China.
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12
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Faerch O, Worth R, Achilonu I, Dirr H. Nuclear localisation sequences of chloride intracellular channels 1 and 4 facilitate nuclear import via interactions with import mediator importin-α: An empirical and theoretical perspective. J Mol Recognit 2023; 36:e2996. [PMID: 36175369 PMCID: PMC10078197 DOI: 10.1002/jmr.2996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 01/14/2023]
Abstract
Chloride intracellular channel proteins (CLICs) display ubiquitous expression, with each member exhibiting specific subcellular localisation. While all CLICs, except CLIC3, exhibit a highly conserved putative nuclear localisation sequence (NLS), only CLIC1, CLIC3 and CLIC4 exist within the nucleus. The CLIC4 NLS, 199-KVVAKKYR-206, appears crucial for nuclear entry and interacts with mouse nuclear import mediator Impα isoform 1, omitting the IBB domain (mImpα1ΔIBB). The essential nature of the basic residues in the CLIC4 NLS has been established by the fact that mutating out these residues inhibits nuclear import, which in turn is linked to cutaneous squamous cell cancer. Given the conservation of the CLIC NLS, CLIC1 likely follows a similar import pathway to CLIC4. Peptides of the CLIC1 (Pep1; Pep1_S C/S mutant) and CLIC4 (Pep4) NLSs were designed to examine binding to human Impα isoform 1, omitting the IBB domain (hImpα1ΔIBB). Molecular docking indicated that the core CLIC NLS region (KKYR) forms a similar binding pattern to both mImpα1ΔIBB and hImpα1ΔIBB. Fluorescence quenching demonstrated that Pep1_S (Kd ≈ 237 μM) and Pep4 (Kd ≈ 317 μM) bind hImpα1ΔIBB weakly. Isothermal titration calorimetry confirmed the weak binding interaction between Pep4 and hImpα1ΔIBB (Kd ≈ 130 μM) and the presence of a proton-linked effect. This weak interaction may be due to regions distal from the CLIC NLS needed to stabilise and strengthen hImpα1ΔIBB binding. Additionally, this NLS may preferentially bind another hImpα isoform with different flexibility properties.
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Affiliation(s)
- Olga Faerch
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Roland Worth
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Heini Dirr
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
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13
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Zhang L, Yan S, Li M, Wang Y, Shi X, Liang P, Yin M, Shen J, Gao X. Nanodelivery System Alters an Insect Growth Regulator's Action Mode: From Oral Feeding to Topical Application. ACS APPLIED MATERIALS & INTERFACES 2022; 14:35105-35113. [PMID: 35867633 DOI: 10.1021/acsami.2c08239] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Insect growth regulators (IGRs) guide animal development through injection, oral feeding, or topical application. Among them, lufenuron is a widely used insect cuticle inhibitor but only shows a gastric toxic effect. Lacking contact toxicity limits the effective utilization when spraying the lufenuron pesticide. To overcome this shortcoming, a nanocarrier (star polycation, SPc)-based transdermal delivery system was applied to improve the penetrability and contact toxicity of lufenuron. The fluoride groups in lufenuron could interact with the tertiary amines in the branch-chain of the SPc through electrostatic interaction to form a lufenuron/SPc complex. The above interaction reduced the particle size of lufenuron from 933 to 70 nm. Interestingly, the contact toxicity of SPc-loaded lufenuron was remarkably improved with effects of higher larval mortality and lower egg hatching rate of the devastating pest fall armyworm. The physiological and molecular toxic mechanism was revealed by RNA-Seq analysis. The SPc-loaded lufenuron apparently down-regulated cuticle-related genes and thus inhibited insect cuticle formation. Such contact toxicity was achieved by the transdermal nanodelivery of lufenuron, which up-regulated endocytosis-related genes for drug uptake. This study is the first successful application of a nanoparticle-mediated transdermal delivery system to explore the contact toxicity of an IGR, which alters the IRG's action mode from oral feeding to topical application.
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Affiliation(s)
- Lei Zhang
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Shuo Yan
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Mingjian Li
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Ye Wang
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Xueyan Shi
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Pei Liang
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, No. 15, North Third Ring East Road, Chaoyang District, Beijing 100029, P. R. China
| | - Jie Shen
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
| | - Xiwu Gao
- College of Plant Protection, China Agricultural University, No. 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, P. R. China
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14
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Yan S, Gu N, Peng M, Jiang Q, Liu E, Li Z, Yin M, Shen J, Du X, Dong M. A Preparation Method of Nano-Pesticide Improves the Selective Toxicity toward Natural Enemies. NANOMATERIALS 2022; 12:nano12142419. [PMID: 35889640 PMCID: PMC9323491 DOI: 10.3390/nano12142419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/23/2022]
Abstract
Various nano-delivery systems have been designed to deliver synthetic/botanical pesticides for improved bioactivity. However, the enhanced toxicity of nanocarrier-loaded pesticides may injure the natural enemies, and their selective toxicity should be evaluated before the large-scale application. In this context, a star polymer (SPc)-based cyantraniliprole (CNAP) nano-delivery system was constructed, and its selective toxicity was evaluated using pest Frankliniella occidentalis (WFT) and predator Orius sauteri. The amide NH of CNAP could assemble with carbonyl groups or tertiary amines of SPc through hydrogen bonds to form CNAP/SPc complex spontaneously. The above self-assembly decreased the particle size of CNAP from 808 to 299 nm. With the help of SPc, the lethal concentration 50 (LC50) values of CNAP decreased from 99 to 54 mg/L and 230 to 173 mg/L toward WFTs and O. sauteri due to the enhancement of broad-spectrum bioactivity. Interestingly, the toxicity selective ratio (TSR) of CNAP increased from 2.33 to 3.23 with the help of SPc, revealing the higher selectivity of SPc-loaded CNAP. To our knowledge, it was the first successful exploration of the selective toxicity of nanocarrier-loaded pesticides, and the higher selective toxicity of SPc-loaded CNAP was beneficial for alleviating the negative impacts on predators.
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Affiliation(s)
- Shuo Yan
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
| | - Na Gu
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
| | - Min Peng
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China; (M.P.); (M.Y.)
| | - Qinhong Jiang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
| | - Enliang Liu
- Research Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi 830022, China;
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China; (M.P.); (M.Y.)
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
| | - Xiangge Du
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
| | - Min Dong
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China; (S.Y.); (N.G.); (Q.J.); (J.S.); (X.D.)
- Correspondence:
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15
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Jiang Q, Peng M, Yin M, Shen J, Yan S. Nanocarrier-Loaded Imidaclothiz Promotes Plant Uptake and Decreases Pesticide Residue. Int J Mol Sci 2022; 23:ijms23126651. [PMID: 35743094 PMCID: PMC9224201 DOI: 10.3390/ijms23126651] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
There is a great demand for improving the effective utilization of pesticides and reducing their application for sustainable agriculture, and polymeric nanoparticles have provided strong technical support for the efficient delivery of pesticides. To this context, we tried to construct a relatively safe imidaclothiz nano-delivery system for enhanced plant uptake, reduced pesticide residue and improved bioactivity toward green peach aphids. The imidaclothiz could be assembled with the hydrophobic core of SPc through hydrophobic association, which led to the self-assembly of nanoscale imidaclothiz/SPc complex consisting of nearly spherical particles. The SPc decreased the contact angle of imidaclothiz drops and remarkably increased the plant uptake. Furthermore, the bioactivity and control efficacy of imidaclothiz were significantly improved with the help of SPc in both laboratory and field. Excitingly, the residue of imidaclothiz decreased with the help of SPc 7 d after the treatment due to the faster degradation of nanoscale imidaclothiz/SPc complex, which exhibited no negative effects on agronomic traits of tobacco plants. The current study successfully constructed a nano-delivery system for imidaclothiz, which can not only increase the effective utilization of pesticides, but also decrease the pesticide residue.
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Affiliation(s)
- Qinhong Jiang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Min Peng
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shuo Yan
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing 100193, China
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16
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A Star Polyamine-Based Nanocarrier Delivery System for Enhanced Avermectin Contact and Stomach Toxicity against Green Peach Aphids. NANOMATERIALS 2022; 12:nano12091445. [PMID: 35564154 PMCID: PMC9100206 DOI: 10.3390/nano12091445] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/18/2022]
Abstract
The unscientific application of synthesized/botanical pesticides has not only brought the resistance of plant pathogens and pests, but also led to serious environmental pollution. In recent years, various nano-delivery systems have been used for the development of environmental-friendly pesticides with improved efficacy. Herein, the current study constructed an efficient avermectin B1a (AVM) nano-delivery system based on a star polyamine (SPc) and focused on the characterization and bioactivity of SPc-loaded AVM at various mass ratios. The hydroxyl groups of AVM could assemble with carbonyl groups of SPc through hydrogen bond and van der Waals forces, and the self-assembly of AVM and SPc formed nearly spherical particles of AVM/SPc complex with nanoscale size. The contact angle of SPc-loaded AVM decreased with the increasing mass ratio of SPc, revealing the easier distribution and spreading of the AVM/SPc complex. Furthermore, the stomach and contact toxicity of AVM/SPc complex also increased along with the increasing SPc mass ratio, which could be attributed to the enhanced systemic transportation in plants, enlarged contact area to insect pests and stronger permeability across the insect cuticle. The current study provides an efficient nano-delivery system for increasing stomach and contact toxicity of pesticides with wide applications in the agricultural field.
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17
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Feng X, Liao D, Sun L, Feng S, Wu S, Lan P, Wang Z, Lan X. Exploration of interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide from Wakame (Undaria pinnatifida). Int J Biol Macromol 2022; 204:193-203. [PMID: 35090938 DOI: 10.1016/j.ijbiomac.2022.01.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/18/2022]
Abstract
The interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide KNFL from Wakame was explored using isothermal titration calorimetry, multiple spectroscopic techniques and molecular dynamics simulations, and an inhibition model was established based on free energy binding theory. The experiments revealed that the binding of KNFL to ACE was a spontaneous exothermic process driven by enthalpy and entropy and occurred via multiple binding sites to form stable complexes. The complexes may be formed through multiple steps of inducing fit and conformational selection. The peptide KNFL had a fluorescence quenching effect on ACE and its addition not only affected the microenvironment around the ACE Trp and Tyr residues, but also increased the diameter and altered the conformation of ACE. This study should prove useful for improving our understanding of the mechanism of ACE inhibitory peptides.
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Affiliation(s)
- Xuezhen Feng
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China; Medical College, Guangxi University of Science and Technology, Liuzhou, Guangxi 545006, People's Republic of China
| | - Dankui Liao
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China.
| | - Lixia Sun
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Shuzhen Feng
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Shanguang Wu
- Medical College, Guangxi University of Science and Technology, Liuzhou, Guangxi 545006, People's Republic of China
| | - Ping Lan
- Guangxi Key Laboratory of Polysaccharide Materials and Modifications, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, People's Republic of China
| | - Zefen Wang
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Xiongdiao Lan
- Guangxi Key Laboratory of Polysaccharide Materials and Modifications, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, People's Republic of China
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18
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Ma Z, Zheng Y, Chao Z, Chen H, Zhang Y, Yin M, Shen J, Yan S. Visualization of the process of a nanocarrier-mediated gene delivery: stabilization, endocytosis and endosomal escape of genes for intracellular spreading. J Nanobiotechnology 2022; 20:124. [PMID: 35264206 PMCID: PMC8905852 DOI: 10.1186/s12951-022-01336-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/26/2022] [Indexed: 12/20/2022] Open
Abstract
Nanoparticles have been widely applied as gene carrier for improving RNA interference (RNAi) efficiency in medical and agricultural fields. However, the mechanism and delivery process of nanoparticle-mediated RNAi is not directly visualized and elucidated. Here we synthesized a star polymer (SPc) consisted of a hydrophilic shell with positively-charged tertiary amine in the side chain, which was taken as an example to investigate the mechanism in gene delivery. The SPc could assemble with dsRNA spontaneously through electrostatic force, hydrogen bond and van der Waals force. Interestingly, the SPc could protect dsRNA from degradation by RNase A and insect hemolymph, thus remarkably increasing the stability of dsRNA. Meanwhile, the SPc could efficiently promote the cellular uptake and endosomal escape for intracellular spreading of dsRNA. Transcriptome analysis revealed that the SPc could up-regulate some key genes such as Chc, AP2S1 and Arf1 for activating clathrin-mediated endocytosis. Furthermore, the suppression of endocytosis hindered the cellular uptake of SPc-delivered dsRNA in vitro, and the subsequent RNAi effect was also disappeared in vivo. To our knowledge, our study is the first direct visualization of the detailed cellular delivery process and mechanism of nanocarrier-mediated gene delivery. Above mechanism supports the application of nanocarrier-based RNAi in gene therapy and pest management.
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Affiliation(s)
- Zhongzheng Ma
- Department of Plant Biosecurity and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China.,Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Yang Zheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225002, Jiangsu, People's Republic of China
| | - Zijian Chao
- Department of Plant Biosecurity and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Hongtao Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yunhui Zhang
- Department of Plant Biosecurity and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Lab of Biomedical Materials, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Jie Shen
- Department of Plant Biosecurity and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shuo Yan
- Department of Plant Biosecurity and MOA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China.
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19
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Yang Z, Muccio DD, Melo N, Atigadda VR, Renfrow MB. Stability of the Retinoid X Receptor-α Homodimer in the Presence and Absence of Rexinoid and Coactivator Peptide. Biochemistry 2021; 60:1165-1177. [PMID: 33792309 PMCID: PMC9949482 DOI: 10.1021/acs.biochem.0c00865] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-α ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. The apo-RXRα LBD homodimer displayed a single thermal unfolding transition with a Tm of 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to the apo-homodimer increased Tm by 5 to 9 °C and increased the ΔG of the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. GRIP-1 binding to holo-homodimers containing rexinoid resulted in additional increases in ΔG of 14 kJ/mol, a value that was the same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. The complexes of UAB110 and UAB111 are each more stable than the UAB30 complex by 8 kJ/mol due to enhanced hydrophobic interactions in the binding pocket because of their larger end groups. This increase in thermodynamic stability positively correlates with their improved RXR activation potency. Thermodynamic measurements are thus valuable in predicting agonist potency.
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Affiliation(s)
- Zhengrong Yang
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Donald D. Muccio
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Nathalia Melo
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Venkatram R. Atigadda
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Matthew B. Renfrow
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
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20
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Jiang Y, Liu HF, Liu R. Systematic comparison and prediction of the effects of missense mutations on protein-DNA and protein-RNA interactions. PLoS Comput Biol 2021; 17:e1008951. [PMID: 33872313 PMCID: PMC8084330 DOI: 10.1371/journal.pcbi.1008951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/29/2021] [Accepted: 04/08/2021] [Indexed: 12/30/2022] Open
Abstract
The binding affinities of protein-nucleic acid interactions could be altered due to missense mutations occurring in DNA- or RNA-binding proteins, therefore resulting in various diseases. Unfortunately, a systematic comparison and prediction of the effects of mutations on protein-DNA and protein-RNA interactions (these two mutation classes are termed MPDs and MPRs, respectively) is still lacking. Here, we demonstrated that these two classes of mutations could generate similar or different tendencies for binding free energy changes in terms of the properties of mutated residues. We then developed regression algorithms separately for MPDs and MPRs by introducing novel geometric partition-based energy features and interface-based structural features. Through feature selection and ensemble learning, similar computational frameworks that integrated energy- and nonenergy-based models were established to estimate the binding affinity changes resulting from MPDs and MPRs, but the selected features for the final models were different and therefore reflected the specificity of these two mutation classes. Furthermore, the proposed methodology was extended to the identification of mutations that significantly decreased the binding affinities. Extensive validations indicated that our algorithm generally performed better than the state-of-the-art methods on both the regression and classification tasks. The webserver and software are freely available at http://liulab.hzau.edu.cn/PEMPNI and https://github.com/hzau-liulab/PEMPNI. Protein-nucleic acid interactions play important roles in various cellular processes. Missense mutations occurring in DNA- or RNA-binding proteins (termed MPDs and MPRs, respectively) could change the binding affinities of these interactions. Previous studies have compared protein-DNA and protein-RNA interactions from multifaceted viewpoints, but less attention has been given to the similarities and specific differences between the effects of MPDs and MPRs and between the methodologies for predicting the affinity changes induced by the two mutation classes. Therefore, we systematically compared their impacts and demonstrated that MPDs and MPRs could have specific preferences for binding affinity changes. These observations motivated us to construct regression models separately for MPDs and MPRs by introducing novel energy and nonenergy descriptors. Although similar frameworks were developed to estimate these two categories of mutation effects, different descriptors were selected in the regression models and further revealed the specificity of mutation classes. The interplay between the energy and nonenergy modules effectively improved prediction performance. Our algorithm can also be adopted to disentangle mutations significantly decreasing binding affinities from other mutations.
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Affiliation(s)
- Yao Jiang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hui-Fang Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rong Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, P. R. China
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21
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Zhang S, Chen KY, Zou X. Carbohydrate-Protein Interactions: Advances and Challenges. COMMUNICATIONS IN INFORMATION AND SYSTEMS 2021; 21:147-163. [PMID: 34366717 DOI: 10.4310/cis.2021.v21.n1.a7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A carbohydrate, also called saccharide in biochemistry, is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms. For example, sugars are low molecular-weight carbohydrates, and starches are high molecular-weight carbohydrates. Carbohydrates are the most abundant organic substances in nature and essential constituents of all living things. Protein-carbohydrate interactions play important roles in many biological processes, such as cell growth, differentiation, and aggregation. They also have broad applications in pharmaceutical drug design. In this review, we will summarize the characteristic features of protein-carbohydrate interactions and review the computational methods for structure prediction, energy calculations, and kinetic studies of protein-carbohydrate complexes. Finally, we will discuss the challenges in this field.
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Affiliation(s)
- Shuang Zhang
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Kyle Yu Chen
- Rock Bridge High School, 4303 South Providence Rd, Columbia, MO 65203, USA
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
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22
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Liyanage SH, Yan M. Quantification of binding affinity of glyconanomaterials with lectins. Chem Commun (Camb) 2020; 56:13491-13505. [PMID: 33057503 PMCID: PMC7644678 DOI: 10.1039/d0cc05899h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Carbohydrate-mediated interactions are involved in many cellular activities including immune responses and infections. These interactions are relatively weak, and as such, cells employ multivalency, i.e., the presentation of multiple monovalent carbohydrate ligands within a close proximity, for cooperative binding thus drastically enhanced binding affinity. In the past two decades, the field of glyconanomaterials has emerged where nanomaterials are used as multivalent scaffolds to present multiple copies of carbohydrate ligands on the nanomaterial surface. At the core of glyconanomaterial research is the ability to control and modulate multivalency through ligand display. For the quantitative evaluation of multivalency, the binding affinity must be determined. Quantification of the binding parameters provides insights for not only the fundamental glyconanomaterial-lectin interactions, but also the rational design of effective diagnostics and therapeutics. Several methods have been developed to determine the binding affinity of glyconanomaterials with lectins, including fluorescence competitive assays in solution or on microarrays, Förster resonance energy transfer, fluorescence quenching, isothermal titration calorimetry, surface plasmon resonance spectroscopy, quartz crystal microbalance and dynamic light scattering. This Feature Article discusses each of these techniques, as well as how each technique is applied to determine the binding affinity of glyconanomaterials with lectins, and the data analysis. Although the results differed depending on the specific method used, collectively, they showed that nanomaterials as multivalent scaffolds could amplify the binding affinity of carbohydrate-lectin interactions by several orders of magnitude, the extent of which depending on the structure of the carbohydrate ligand, the ligand density, the linker length and the particle size.
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Affiliation(s)
- Sajani H Liyanage
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, Massachusetts 01854, USA.
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23
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Cotrina EY, Oliveira Â, Leite JP, Llop J, Gales L, Quintana J, Cardoso I, Arsequell G. Repurposing Benzbromarone for Familial Amyloid Polyneuropathy: A New Transthyretin Tetramer Stabilizer. Int J Mol Sci 2020; 21:E7166. [PMID: 32998442 PMCID: PMC7583827 DOI: 10.3390/ijms21197166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022] Open
Abstract
Transthyretin (TTR) is a homotetrameric protein involved in human amyloidosis, including familial amyloid polyneuropathy (FAP). Discovering small-molecule stabilizers of the TTR tetramer is a therapeutic strategy for these diseases. Tafamidis, the only approved drug for FAP treatment, is not effective for all patients. Herein, we discovered that benzbromarone (BBM), a uricosuric drug, is an effective TTR stabilizer and inhibitor against TTR amyloid fibril formation. BBM rendered TTR more resistant to urea denaturation, similarly to iododiflunisal (IDIF), a very potent TTR stabilizer. BBM competes with thyroxine for binding in the TTR central channel, with an IC50 similar to IDIF and tafamidis. Results obtained by isothermal titration calorimetry (ITC) demonstrated that BBM binds TTR with an affinity similar to IDIF, tolcapone and tafamidis, confirming BBM as a potent binder of TTR. The crystal structure of the BBM-TTR complex shows two molecules binding deeply in the thyroxine binding channel, forming strong intermonomer hydrogen bonds and increasing the stability of the TTR tetramer. Finally, kinetic analysis of the ability of BBM to inhibit TTR fibrillogenesis at acidic pH and comparison with other stabilizers revealed that benzbromarone is a potent inhibitor of TTR amyloidogenesis, adding a new interesting scaffold for drug design of TTR stabilizers.
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Affiliation(s)
- Ellen Y. Cotrina
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain;
| | - Ângela Oliveira
- IBMC—Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal; (Â.O.); (J.P.L.); (L.G.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - José Pedro Leite
- IBMC—Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal; (Â.O.); (J.P.L.); (L.G.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 4050-013 Porto, Portugal
| | - Jordi Llop
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 San Sebastian, Spain;
| | - Luis Gales
- IBMC—Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal; (Â.O.); (J.P.L.); (L.G.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 4050-013 Porto, Portugal
| | - Jordi Quintana
- Research Programme on Biomedical Informatics, Universitat Pompeu Fabra (UPF-IMIM), 08003 Barcelona, Spain;
| | - Isabel Cardoso
- IBMC—Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal; (Â.O.); (J.P.L.); (L.G.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 4050-013 Porto, Portugal
| | - Gemma Arsequell
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain;
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24
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Parray Z, Ahmad F, Hassan MI, Hasan I, Islam A. Effects of Ethylene Glycol on the Structure and Stability of Myoglobin Using Spectroscopic, Interaction, and In Silico Approaches: Monomer Is Different from Those of Its Polymers. ACS OMEGA 2020; 5:13840-13850. [PMID: 32566850 PMCID: PMC7301589 DOI: 10.1021/acsomega.0c01185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
Investigation of changes in thermal stabilities and structures of proteins in the presence of different co-solutes (ligands) is an integral part in the basic research, discovery, and development of drugs. Ethylene glycol (EG) is known to be toxic and causes teratogenic, inducing primarily skeletal and external malformations and other diseases. The effect of EG on the structure and thermal stability of myoglobin (Mb) was studied using various spectroscopic techniques at pH 7.0 and two different temperatures. As revealed by circular dichroism, Trp fluorescence, nano-DSF, and absorption (UV and visible) measurements, EG (i) has no significant effect on secondary and tertiary structures of Mb at 25 °C, and (ii) it decreases the thermal stability of the protein, which increases with increasing concentration of EG. As revealed by ANS (8-anilino-1-naphthalene sulfonic acid) fluorescence measurements, heat-induced denatured protein has newly exposed hydrophobic patches that bind to ANS. Isothermal titration calorimetry revealed that the interaction between EG and Mb is temperature dependent; the preferential interaction of EG is entropy driven at low temperature, 298 K (25 °C), and it is enthalpy driven at higher temperature, 343 K (70 °C). Molecular docking study showed that EG interacts with side chains of amino acid residues of Mb through van der Waals interactions and hydrogen bonding.
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Affiliation(s)
- Zahoor
Ahmad Parray
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Faizan Ahmad
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Md Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ikramul Hasan
- Department
of Basic Medical Science, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 110025, KSA
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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25
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Hu J, Xiao Y, Shao SA, Gu R, Shi QM, Liu ZH, Yin J. Construction and application of carbohydrate microarrays to detect foodborne bacteria. Chin J Nat Med 2020; 18:219-225. [PMID: 32245592 DOI: 10.1016/s1875-5364(20)30024-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Indexed: 02/02/2023]
Abstract
The rapid detection of pathogenic bacteria is vital for the prevention of outbreaks of infectious diseases, including infections by the common foodborne bacteria E.coli and Salmonella Carbohydrate microarrays have been developed as a powerful method to investigate carbohydrate-protein interaction with only very small amounts of glycans, which show great potential for detect the carbohydrate mediated interaction with pathogens. Here, different mannose-coated microarrays were constructed and tested with E.coli (K-12 and BL-21) and Salmonella enterica strains (ATCC9184 and ATCC31685) exhibiting different mannose binding affinities. The optimized carbohydrate microarray was then applied to test the binding of 12 Salmonella enterica and 9 E.coli isolates from local patients for the first time and showed strong binding with certain serovars or subtypes. The results showed that microarray probed with the single mannose structure is not enough for the detection of bacteria with various serovars or subtypes, which contain a high degree of allelic variation in adhesin. We suggest that a complex carbohydrate microarray containing different glycan conformation may be needed for detection of different bacteria isolates.
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Affiliation(s)
- Jing Hu
- Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China
| | - Yong Xiao
- Microbiology Laboratory, Wuxi Center for Disease Control and Prevention, Wuxi 214122, China
| | - Shu-An Shao
- Wuxi School of Medicine, Jiangnan University, Wuxi 214000, China
| | - Rui Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Qi-Min Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhong-Hua Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Yin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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26
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Biswas S, Adhikari A, Mukherjee A, Das S, Adak S. Regulation of Leishmania major PAS domain-containing phosphoglycerate kinase by cofactor Mg 2+ ion at neutral pH. FEBS J 2020; 287:5183-5195. [PMID: 32196942 DOI: 10.1111/febs.15305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/12/2020] [Accepted: 03/18/2020] [Indexed: 11/26/2022]
Abstract
Recently, we described the PAS domain-containing phosphoglycerate kinase (PGK) from Leishmania major (LmPAS-PGK) that shows acidic pH (5.5)-dependent optimum catalytic activity. The PAS domain of LmPAS-PGK is expected to regulate PGK activity during catalysis, but the mechanism of regulation by PAS domain at the molecular level is uncharacterized. In this work, we have utilized the full-length, PAS domain-deleted, and mutant enzymes to measure the enzymatic activity in the presence of divalent cation at various pH values. Catalytic activity measurement indicates that Mg2+ binding through PAS domain inhibits the PGK activity at pH 7.5, and this inhibition is withdrawn at pH 5.5. To identify the Mg2+ binding residues of the PAS domain, we exploited a systematic mutational analysis of all (four) His residues in the PAS domain for potential divalent cation binding. Replacement of His-57 with alanine resulted in depression in the presence of Mg2+ at pH 7.5, but H71A, H89A, and H111A showed similar characteristics with respect to the wild-type protein. Fluorescence and isothermal titration calorimetry studies revealed that H57 is responsible for Mg2+ binding in the absence of substrates. Thus, the protonated form of His57 at acidic pH 5.5 destabilizes the Mg2+ binding in the PAS domain, which is an essential requirement in the wild-type LmPAS-PGK for a conformational alteration in the sensor domain that, sequentially, activates the PGK domain, resulting in the synthesis of higher amounts of ATP.
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Affiliation(s)
- Saroj Biswas
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Ayan Adhikari
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aditi Mukherjee
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sumit Das
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subrata Adak
- Division of Structural Biology & Bio-informatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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27
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Cotrina EY, Gimeno A, Llop J, Jiménez-Barbero J, Quintana J, Valencia G, Cardoso I, Prohens R, Arsequell G. Calorimetric Studies of Binary and Ternary Molecular Interactions between Transthyretin, Aβ Peptides, and Small-Molecule Chaperones toward an Alternative Strategy for Alzheimer's Disease Drug Discovery. J Med Chem 2020; 63:3205-3214. [PMID: 32124607 PMCID: PMC7115756 DOI: 10.1021/acs.jmedchem.9b01970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Transthyretin
(TTR) modulates the deposition, processing, and toxicity
of Abeta (Aβ) peptides. We have shown that this effect is enhanced
in mice by treatment with small molecules such as iododiflunisal (IDIF, 4), a good TTR stabilizer. Here, we describe the thermodynamics
of the formation of binary and ternary complexes among TTR, Aβ(1–42)
peptide, and TTR stabilizers using isothermal titration calorimetry
(ITC). A TTR/Aβ(1–42) (1:1)
complex with a dissociation constant of Kd = 0.94 μM is formed; with IDIF
(4), this constant improves up to Kd = 0.32 μM, indicating
the presence of a ternary complex TTR/IDIF/Aβ(1–42).
However, with the drugs diflunisal (1) or Tafamidis (2), an analogous chaperoning effect could not be observed.
Similar phenomena could be recorded with the shorter peptide Aβ(12–28)
(7). We propose the design of a simple assay system for
the search of other chaperones that behave like IDIF and may become
potential candidate drugs for Alzheimer’s disease (AD).
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Affiliation(s)
- Ellen Y Cotrina
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Ana Gimeno
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Jordi Llop
- CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 San Sebastian, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940 Leioa, Bizkaia, Spain
| | - Jordi Quintana
- Research Programme on Biomedical Informatics, Universitat Pompeu Fabra (UPF-IMIM), 08003 Barcelona, Spain
| | - Gregorio Valencia
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
| | - Isabel Cardoso
- IBMC-Instituto de Biologia Molecular e Celular, 4200-135 Porto, Portugal.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Rafel Prohens
- Unitat de Polimorfisme i Calorimetria, Centres Cientı́fics i Tecnològics, Universitat de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Gemma Arsequell
- Institut de Quı́mica Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034 Barcelona, Spain
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28
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Interaction of a bile salt (sodium taurocholate) with cationic (ε-polylysine) and anionic (pectin) biopolymers under simulated gastrointestinal conditions. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2018.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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29
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Diaz-Parga P, de Alba E. Protein interactions of the inflammasome adapter ASC by solution NMR. Methods Enzymol 2019; 625:223-252. [PMID: 31455529 PMCID: PMC8455076 DOI: 10.1016/bs.mie.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ASC (apoptosis-associated speck-like protein containing a CARD) is a modular protein that functions as an adapter of the inflammasome, a multi-protein complex that triggers the inflammatory response in the presence of infection or cell damage. ASC bridges the inflammasome components (PYD-containing sensors and procaspase 1) via homotypic interactions mediated by its two death domains, PYD and CARD. The self-assembly and oligomerization of multiple copies of these three proteins result in the activation of procaspase 1, in turn rendering different cytokines functional. An in-depth understanding of ASC binding capabilities is crucial to decipher the molecular mechanisms of its role in inflammasome formation. In this chapter, we discuss the use of solution NMR to identify specific interacting surfaces of the inflammasome adapter ASC, and describe detailed protocols to perform NMR titrations with Death Domains to obtain apparent dissociation constants of the resulting complexes. The incorporation of NMR restraints in molecular docking to obtain models of these protein assemblies is presented.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Quantitative Systems Biology Graduate Program, University of California, Merced, CA, United States
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Corresponding author:
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30
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Lan X, Sun L, Muhammad Y, Wang Z, Liu H, Sun J, Zhou L, Feng X, Liao D, Wang S. Studies on the Interaction between Angiotensin-Converting Enzyme (ACE) and ACE Inhibitory Peptide from Saurida elongata. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13414-13422. [PMID: 30511571 DOI: 10.1021/acs.jafc.8b04303] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Angiotensin-converting enzyme (ACE) inhibitory peptides derived from food protein exhibited antihypertensive effects by inhibiting ACE activity. In this work, the interaction between ACE inhibitory peptide GMKCAF (GF-6) and ACE was studied by isothermal titration calorimetry (ITC), molecular docking, ultraviolet absorption spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy. Experimental results revealed that the binding of GF-6 to ACE was a spontaneous exothermic process driven by both enthalpy and entropy. The interaction occurred via a static quenching mechanism and involved the alteration of the conformation of ACE. In addition, ITC and molecular docking results indicated binding of GF-6 to ACE via multiple binding sites on the protein surface. This study could be deemed helpful for the better understanding of the inhibitory mechanism of ACE inhibitory peptides.
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Affiliation(s)
- Xiongdiao Lan
- School of Chemistry and Chemical Engineering , Guangxi University for Nationalities , Nanning , Guangxi 530008 , People's Republic of China
| | | | - Yaseen Muhammad
- Institute of Chemical Sciences , University of Peshawar , Peshawar , Khyber Pakhtunkhwa 25120 , Pakistan
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31
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Avci FG, Akbulut BS, Ozkirimli E. Membrane Active Peptides and Their Biophysical Characterization. Biomolecules 2018; 8:biom8030077. [PMID: 30135402 PMCID: PMC6164437 DOI: 10.3390/biom8030077] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022] Open
Abstract
In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Marmara University, Kadikoy, 34722 Istanbul, Turkey.
| | | | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey.
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32
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Meekrathok P, Stubbs KA, Suginta W. Potent inhibition of a GH20 exo-β-N-acetylglucosaminidase from marine Vibrio bacteria by reaction intermediate analogues. Int J Biol Macromol 2018; 115:1165-1173. [DOI: 10.1016/j.ijbiomac.2018.04.193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/14/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
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33
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Paul S, Samanta A. Ground- and Excited-State Interactions of a Psoralen Derivative with Human Telomeric G-Quadruplex DNA. J Phys Chem B 2018; 122:2277-2286. [PMID: 29376354 DOI: 10.1021/acs.jpcb.7b12475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
G-quadruplex DNA has been a recent target for anticancer agents, and its binding interactions with small molecules, often used as anticancer drugs, have become an important area of research. Considering that psoralens have long been studied in the context of duplex DNA but that very little is known about their potential as G-quadruplex binders and their excited-state interaction with the latter has not been explored, we have studied herein the binding of a planar water-soluble psoralen derivative, 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), with the 22-mer human telomeric G-quadruplex-forming sequence, AGGG(TTAGGG)3, labeled here as (hTel22), and investigated the consequences of photoexcitation of AMT by calorimetric and spectroscopic techniques. The results show an enthalpy-driven 1:1 binding of AMT with hTel22 via end-stacking mode. Fluorescence quenching experiments on 6-fluorescein amidite-labeled oligomers indicate that the binding site is nearer to the 3' end of hTel22 in the diagonal loop region. Femtosecond time-resolved transient absorption measurements indicate electron transfer from the guanine moiety of hTel22 to photoexcited AMT, leading to the formation of a radical pair species (AMT•-G•+), which survives for 30 ps and is favored by a parallel/quasi-parallel orientation between the two. The findings reveal psoralens as a prospective class of compounds for the development of anticancer therapeutics by targeting the G-quadruplex DNA.
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Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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Tzitzoglaki C, Wright A, Freudenberger K, Hoffmann A, Tietjen I, Stylianakis I, Kolarov F, Fedida D, Schmidtke M, Gauglitz G, Cross TA, Kolocouris A. Binding and Proton Blockage by Amantadine Variants of the Influenza M2WT and M2S31N Explained. J Med Chem 2017; 60:1716-1733. [DOI: 10.1021/acs.jmedchem.6b01115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christina Tzitzoglaki
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Anna Wright
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Anja Hoffmann
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Ian Tietjen
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ioannis Stylianakis
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - David Fedida
- Department
of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Michaela Schmidtke
- Department
of Virology and Antiviral Therapy, Jena University Hospital, Hans Knoell Strasse 2, D-07745 Jena, Germany
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls Universität, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Timothy A. Cross
- Institute
of Molecular Biophysics and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, United States
- Department
of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Antonios Kolocouris
- Section
of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens 157 71, Greece
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Abstract
Isothermal titration calorimetry (ITC) has emerged as a leading approach in the characterization of protein/ligand interactions. This technique measures the heat change of a system upon binding of a ligand to a biomolecule, and thereby requires no immobilization, intrinsic fluorescence, or labeling of any kind of either species. If properly designed, a single experiment can not only measure the binding affinity, but also determine additional binding and thermodynamic parameters, including the enthalpy, entropy, and the stoichiometry of the interaction. Here, we describe the protocol for the collection of calorimetric data for the binding of peptides to SH2 protein domains.
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Affiliation(s)
- Marissa A McKercher
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO, 80309, USA
| | - Deborah S Wuttke
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO, 80309, USA.
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Bhatia S, Camacho LC, Haag R. Pathogen Inhibition by Multivalent Ligand Architectures. J Am Chem Soc 2016; 138:8654-66. [DOI: 10.1021/jacs.5b12950] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sumati Bhatia
- Institut
für Chemie
und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Luis Cuellar Camacho
- Institut
für Chemie
und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Rainer Haag
- Institut
für Chemie
und Biochemie, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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37
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Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z, Gohlke H, Kolocouris A. Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J Chem Inf Model 2016; 56:862-76. [DOI: 10.1021/acs.jcim.6b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Harris Ioannidis
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Drakopoulos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Christina Tzitzoglaki
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Nadine Homeyer
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Felix Kolarov
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Paraskevi Gkeka
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Kathrin Freudenberger
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Christos Liolios
- Demokritos, National Center for Scientific Research, 15310 Athens, Greece
| | - Günter Gauglitz
- Institut
für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Antonios Kolocouris
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
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Gurung AB, Bhattacharjee A, Ajmal Ali M, Al-Hemaid F, Lee J. Binding of small molecules at interface of protein-protein complex - A newer approach to rational drug design. Saudi J Biol Sci 2016; 24:379-388. [PMID: 28149177 PMCID: PMC5272936 DOI: 10.1016/j.sjbs.2016.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/03/2015] [Accepted: 01/03/2016] [Indexed: 01/07/2023] Open
Abstract
Protein–protein interaction is a vital process which drives many important physiological processes in the cell and has also been implicated in several diseases. Though the protein–protein interaction network is quite complex but understanding its interacting partners using both in silico as well as molecular biology techniques can provide better insights for targeting such interactions. Targeting protein–protein interaction with small molecules is a challenging task because of druggability issues. Nevertheless, several studies on the kinetics as well as thermodynamic properties of protein–protein interactions have immensely contributed toward better understanding of the affinity of these complexes. But, more recent studies on hot spots and interface residues have opened up new avenues in the drug discovery process. This approach has been used in the design of hot spot based modulators targeting protein–protein interaction with the objective of normalizing such interactions.
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Affiliation(s)
- A B Gurung
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong 793022, Meghalaya, India
| | - A Bhattacharjee
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong 793022, Meghalaya, India
| | - M Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - F Al-Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Loosli F, Vitorazi L, Berret JF, Stoll S. Towards a better understanding on agglomeration mechanisms and thermodynamic properties of TiO₂ nanoparticles interacting with natural organic matter. WATER RESEARCH 2015; 80:139-48. [PMID: 26001280 DOI: 10.1016/j.watres.2015.05.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/01/2015] [Accepted: 05/03/2015] [Indexed: 05/19/2023]
Abstract
Interaction between engineered nanoparticles and natural organic matter is investigated by measuring the exchanged heat during binding process with isothermal titration calorimetry. TiO2 anatase nanoparticles and alginate are used as engineered nanoparticles and natural organic matter to get an insight into the thermodynamic association properties and mechanisms of adsorption and agglomeration. Changes of enthalpy, entropy and total free energy, reaction stoichiometry and affinity binding constant are determined or calculated at a pH value where the TiO2 nanoparticles surface charge is positive and the alginate exhibits a negative structural charge. Our results indicate that strong TiO2-alginate interactions are essentially entropy driven and enthalpically favorable with exothermic binding reactions. The reaction stoichiometry and entropy gain are also found dependent on the mixing order. Finally correlation is established between the binding enthalpy, the reaction stoichiometry and the zeta potential values determined by electrophoretic mobility measurements. From these results two types of agglomeration mechanisms are proposed depending on the mixing order. Addition of alginate in TiO2 dispersions is found to form agglomerates due to polymer bridging whereas addition of TiO2 in alginate promotes a more individually coating of the nanoparticles.
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Affiliation(s)
- Frédéric Loosli
- Group of Environmental Physical Chemistry, University of Geneva, F.-A. Forel Institute Section des Sciences de la Terre et de l'Environnement, 10 route de Suisse, 1290 Versoix, Switzerland
| | - Letícia Vitorazi
- Laboratoire Matière et Systèmes Complexes, UMR 7057 Université Paris-Diderot/CNRS, Bâtiment Condorcet, 10 rue Alice Domon et Léonie Duquet, F-75205 Paris Cedex 13, France
| | - Jean-François Berret
- Laboratoire Matière et Systèmes Complexes, UMR 7057 Université Paris-Diderot/CNRS, Bâtiment Condorcet, 10 rue Alice Domon et Léonie Duquet, F-75205 Paris Cedex 13, France
| | - Serge Stoll
- Group of Environmental Physical Chemistry, University of Geneva, F.-A. Forel Institute Section des Sciences de la Terre et de l'Environnement, 10 route de Suisse, 1290 Versoix, Switzerland.
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40
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Arijaje EO, Jayanthi S, Kumar TKS, Wang Y. Linear starch and hexanoic acid complexation evaluated by isothermal titration calorimetry. STARCH-STARKE 2015. [DOI: 10.1002/star.201500030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Srinivas Jayanthi
- Department of Chemistry and BiochemistryUniversity of ArkansasFayettevilleARUSA
| | | | - Ya‐Jane Wang
- Department of Food ScienceUniversity of ArkansasFayettevilleARUSA
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41
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Amaya-González S, López-López L, Miranda-Castro R, de-los-Santos-Álvarez N, Miranda-Ordieres AJ, Lobo-Castañón MJ. Affinity of aptamers binding 33-mer gliadin peptide and gluten proteins: Influence of immobilization and labeling tags. Anal Chim Acta 2015; 873:63-70. [PMID: 25911431 DOI: 10.1016/j.aca.2015.02.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 10/24/2022]
Abstract
Aptamers are starting to increase the reagents tool box to develop more sensitive and reliable methods for food allergens. In most of these assays, aptamers have to be modified for detection and/or immobilization purposes. To take full advantage of their affinity, which decisively influence the detectability, these modifications must be faced rationally. In this work, a recently developed aptamer for an immunotoxic peptide of gliadin associated to celiac disease is used in different configurations and modified with various markers and anchored groups to evaluate the influence of such modifications on the real affinity. The interaction in solution with the peptide is strong for a relatively small molecule (Kd = 45 ± 10 nM, 17 °C) and slightly stronger than that for the immobilized intact protein due to a cooperative binding effect. Comparatively, while only minor differences were found when the peptide or the aptamer were immobilized, labeling with a biotin resulted preferable over fluorescein (Kd = 102 ± 11 vs 208 ± 54 nM, 25 °C). These findings are of prime importance for the design of an aptamer-based analytical method for gluten quantification.
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Affiliation(s)
- Sonia Amaya-González
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
| | - Laura López-López
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
| | - Rebeca Miranda-Castro
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
| | | | | | - María Jesús Lobo-Castañón
- Dpto. Química Física y Analítica, Universidad de Oviedo, Av. Julián Clavería 8, 33006 Oviedo, Spain.
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42
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Sultana A, Lee JE. Measuring Protein‐Protein and Protein‐Nucleic Acid Interactions by Biolayer Interferometry. ACTA ACUST UNITED AC 2015; 79:19.25.1-19.25.26. [DOI: 10.1002/0471140864.ps1925s79] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Azmiri Sultana
- Department of Laboratory Medicine and Pathobiology, University of Toronto Toronto Ontario Canada
| | - Jeffrey E. Lee
- Department of Laboratory Medicine and Pathobiology, University of Toronto Toronto Ontario Canada
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43
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Velazquez-Campoy A, Leavitt SA, Freire E. Characterization of protein-protein interactions by isothermal titration calorimetry. Methods Mol Biol 2015; 1278:183-204. [PMID: 25859950 DOI: 10.1007/978-1-4939-2425-7_11] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The analysis of protein-protein interactions has attracted the attention of many researchers from both a fundamental point of view and a practical point of view. From a fundamental point of view, the development of an understanding of the signaling events triggered by the interaction of two or more proteins provides key information to elucidate the functioning of many cell processes. From a practical point of view, understanding protein-protein interactions at a quantitative level provides the foundation for the development of antagonists or agonists of those interactions. Isothermal Titration Calorimetry (ITC) is the only technique with the capability of measuring not only binding affinity but the enthalpic and entropic components that define affinity. Over the years, isothermal titration calorimeters have evolved in sensitivity and accuracy. Today, TA Instruments and MicroCal market instruments with the performance required to evaluate protein-protein interactions. In this methods paper, we describe general procedures to analyze heterodimeric (porcine pancreatic trypsin binding to soybean trypsin inhibitor) and homodimeric (bovine pancreatic α-chymotrypsin) protein associations by ITC.
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Affiliation(s)
- Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain,
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Espinal-Ruiz M, Parada-Alfonso F, Restrepo-Sánchez LP, Narváez-Cuenca CE, McClements DJ. Interaction of a dietary fiber (pectin) with gastrointestinal components (bile salts, calcium, and lipase): a calorimetry, electrophoresis, and turbidity study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12620-12630. [PMID: 25479310 DOI: 10.1021/jf504829h] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An in vitro gastrointestinal model consisting of oral, gastric, and intestinal phases was used to elucidate the impact of pectin on the digestion of emulsified lipids. Pectin reduced the extent of lipid digestion, which was attributed to its binding interactions with specific gastrointestinal components. The interaction of pectin with bile salts, lipase, CaCl2, and NaCl was therefore investigated by turbidity, microstructure, electrophoresis, and isothermal titration calorimetry (ITC) at pH 7.0 and 37 °C. ITC showed that the interaction of pectin was endothermic with bile salts, but exothermic with CaCl2, NaCl, and lipase. Electrophoresis, microstructure, and turbidity measurements showed that anionic pectin formed electrostatic complexes with calcium ions, which may have decreased lipid digestion due to increased lipid flocculation or microgel formation because this would reduce the surface area of lipid exposed to the lipase. This research provides valuable insights into the physicochemical and molecular mechanisms of the interaction of pectin with gastrointestinal components that may affect the rate and extent of lipid digestion.
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Affiliation(s)
- Mauricio Espinal-Ruiz
- Departamento de Quı́mica, Facultad de Ciencias, Universidad Nacional de Colombia , AA 14490 Bogotá, Colombia
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Ranok A, Wongsantichon J, Robinson RC, Suginta W. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39). J Biol Chem 2014; 290:2617-29. [PMID: 25477513 DOI: 10.1074/jbc.m114.588905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.
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Affiliation(s)
- Araya Ranok
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jantana Wongsantichon
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and
| | - Robert C Robinson
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and the Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
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Mitchell T, Chao G, Sitkoff D, Lo F, Monshizadegan H, Meyers D, Low S, Russo K, DiBella R, Denhez F, Gao M, Myers J, Duke G, Witmer M, Miao B, Ho SP, Khan J, Parker RA. Pharmacologic profile of the Adnectin BMS-962476, a small protein biologic alternative to PCSK9 antibodies for low-density lipoprotein lowering. J Pharmacol Exp Ther 2014; 350:412-24. [PMID: 24917546 DOI: 10.1124/jpet.114.214221] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Proprotein convertase subtilisin kexin-9 (PCSK9) is an important pharmacological target for decreasing low-density lipoprotein (LDL) in cardiovascular disease, although seemingly inaccessible to small molecule approaches. Compared with therapeutic IgG antibodies currently in development, targeting circulating PCSK9 with smaller molecular scaffolds could offer different profiles and reduced dose burdens. This inspired genesis of PCSK9-binding Adnectins, a protein family derived from human fibronectin-10th-type III-domain and engineered for high-affinity target binding. BMS-962476, an ∼11-kDa polypeptide conjugated to polyethylene glycol to enhance pharmacokinetics, binds with subnanomolar affinity to human. The X-ray cocrystal structure of PCSK9 with a progenitor Adnectin shows ∼910 Å(2) of PCSK9 surface covered next to the LDL receptor binding site, largely by residues of a single loop of the Adnectin. In hypercholesterolemic, overexpressing human PCSK9 transgenic mice, BMS-962476 rapidly lowered cholesterol and free PCSK9 levels. In genomic transgenic mice, BMS-962476 potently reduced free human PCSK9 (ED50 ∼0.01 mg/kg) followed by ∼2-fold increases in total PCSK9 before return to baseline. Treatment of cynomolgus monkeys with BMS-962476 rapidly suppressed free PCSK9 >99% and LDL-cholesterol ∼55% with subsequent 6-fold increase in total PCSK9, suggesting reduced clearance of circulating complex. Liver sterol response genes were consequently downregulated, following which LDL and total PCSK9 returned to baseline. These studies highlight the rapid dynamics of PCSK9 control over LDL and liver cholesterol metabolism and characterize BMS-962476 as a potent and efficacious PCSK9 inhibitor.
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Affiliation(s)
- Tracy Mitchell
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Ginger Chao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Doree Sitkoff
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fred Lo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Hossain Monshizadegan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Daniel Meyers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Simon Low
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Katie Russo
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rose DiBella
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Fabienne Denhez
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mian Gao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Joseph Myers
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Gerald Duke
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Mark Witmer
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Bowman Miao
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Siew P Ho
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Javed Khan
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
| | - Rex A Parker
- Molecular Discovery Technologies (T.M., G.C., D.S., S.L., K.R., R.D., F.D., M.G., J.M., G.D., M.W., J.K.), Applied Genomics (S.P.H.), and Cardiovascular Discovery Biology (F.L., H.M., D.M., B.M., R.A.P.), Bristol-Myers Squibb Research and Development, Princeton, New Jersey
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Liu J, Liu W, Ge H, Gao J, He Q, Su L, Xu J, Gu LQ, Huang ZS, Li D. Syntheses and characterization of non-bisphosphonate quinoline derivatives as new FPPS inhibitors. Biochim Biophys Acta Gen Subj 2013; 1840:1051-62. [PMID: 24246954 DOI: 10.1016/j.bbagen.2013.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/11/2013] [Accepted: 11/08/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND Farnesyl pyrophosphate synthase (FPPS) is a key regulatory enzyme in the biosynthesis of cholesterol and in the post-translational modification of signaling proteins. It has been reported that non-bisphosphonate FPPS inhibitors targeting its allosteric binding pocket are potentially important for the development of promising anti-cancer drugs. METHODS The following methods were used: organic syntheses of non-bisphosphonate quinoline derivatives, enzyme inhibition studies, fluorescence titration assays, synergistic effect studies of quinoline derivatives with zoledronate, ITC studies for the binding of FPPS with quinoline derivatives, NMR-based HAP binding assays, molecular modeling studies, fluorescence imaging assay and MTT assays. RESULTS We report our syntheses of a series of quinoline derivatives as new FPPS inhibitors possibly targeting the allosteric site of the enzyme. Compound 6b showed potent inhibition to FPPS without significant hydroxyapatite binding affinity. The compound showed synergistic inhibitory effect with active-site inhibitor zoledronate. ITC experiment confirmed the good binding effect of compound 6b to FPPS, and further indicated the binding ratio of 1:1. Molecular modeling studies showed that 6b could possibly bind to the allosteric binding pocket of the enzyme. The fluorescence microscopy indicated that these compounds could get into cancer cells. CONCLUSIONS Our results showed that quinoline derivative 6b could become a new lead compound for further optimization for cancer treatment. GENERAL SIGNIFICANCE The traditional FPPS active-site inhibitors bisphosphonates show poor membrane permeability to tumor cells, due to their strong polarity. The development of new non-bisphosphonate FPPS inhibitors with good cell membrane permeability is potentially important.
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Protein mechanics: how force regulates molecular function. Biochim Biophys Acta Gen Subj 2013; 1830:4762-8. [PMID: 23791949 DOI: 10.1016/j.bbagen.2013.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 05/26/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Regulation of proteins is ubiquitous and vital for any organism. Protein activity can be altered chemically, by covalent modifications or non-covalent binding of co-factors. Mechanical forces are emerging as an additional way of regulating proteins, by inducing a conformational change or by partial unfolding. SCOPE We review some advances in experimental and theoretical techniques to study protein allostery driven by mechanical forces, as opposed to the more conventional ligand driven allostery. In this respect, we discuss recent single molecule pulling experiments as they have substantially augmented our view on the protein allostery by mechanical signals in recent years. Finally, we present a computational analysis technique, Force Distribution Analysis, that we developed to reveal allosteric pathways in proteins. MAJOR CONCLUSIONS Any kind of external perturbation, being it ligand binding or mechanical stretching, can be viewed as an external force acting on the macromolecule, rendering force-based experimental or computational techniques, a very general approach to the mechanics involved in protein allostery. GENERAL SIGNIFICANCE This unifying view might aid to decipher how complex allosteric protein machineries are regulated on the single molecular level.
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Glycosylated aniline polymer sensor: amine to imine conversion on protein-carbohydrate binding. Biosens Bioelectron 2013; 46:183-9. [PMID: 23563436 DOI: 10.1016/j.bios.2013.02.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 02/07/2013] [Accepted: 02/18/2013] [Indexed: 12/30/2022]
Abstract
In this report, functionalized mannosylated aniline polymer (manno-PANI) was investigated as an electrochemical platform to study carbohydrate-protein interactions by exploiting the conductivity change of manno-PANI when the specific lectin binding occurs. A systematic study was performed to characterize the interconversion of polyaniline content (from amine to imine) in manno-PANI by UV-vis spectroscopy during its binding with concanavalin A (Con A). Both X-ray photoelectron spectrometry (XPS) and UV-vis results suggest that Con A binding with the manno-PANI film triggers the switching of amine functionalities in the polyaniline backbone, converting them to imine forms. Electrochemical impedance spectroscopy (EIS) was used to quantify the specific interactions between Con A and mannose by measuring the impedance change of manno-PANI film for the detection of Con A. A linear relationship between the impedance and Con A concentration was obtained, and the detection limit reaches to 0.12 nM Con A in a buffer solution (pH=7.4), whereas the addition of nonspecific control lectins to the same manno-PANI film gave very little impedance variations. Stability characterization of the manno-PANI film over 20 weeks shows a maximum drift of only 3% from the original signal. Thus, the uniquely constructed carbohydrate-PANI hybrid is a promising new carbohydrate recognition moiety for studying carbohydrate-protein interactions, presumably leading to a new electrochemical method for characterization of carbohydrate-protein interactions and carbohydrate-mediated intercellular recognitions.
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Abstract
Formation of high-affinity complexes is critical for the majority of enzymatic reactions involving proteins. The creation of the family of Michaelis and other intermediate complexes during catalysis clearly involves a complicated manifold of interactions that are diverse and complex. Indeed, computing the energetics of interactions between proteins and small molecule ligands using molecular structure alone remains a great challenge. One of the most difficult contributions to the free energy of protein-ligand complexes to access experimentally is that due to changes in protein conformational entropy. Fortunately, recent advances in solution nuclear magnetic resonance (NMR) relaxation methods have enabled the use of measures-of-motion between conformational states of a protein as a proxy for conformational entropy. This review briefly summarizes the experimental approaches currently employed to characterize fast internal motion in proteins, how this information is used to gain insight into conformational entropy, what has been learned, and what the future may hold for this emerging view of protein function.
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