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Jabbari S, Dabirmanesh B, Daneshjou S, Khajeh K. The potential of a novel enzyme-based surface plasmon resonance biosensor for direct detection of dopamine. Sci Rep 2024; 14:14303. [PMID: 38906902 PMCID: PMC11192927 DOI: 10.1038/s41598-024-64796-w] [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: 01/24/2023] [Accepted: 06/13/2024] [Indexed: 06/23/2024] Open
Abstract
Dopamine is one of the significant neurotransmitters and its monitoring in biological fluids is a critical issue in healthcare and modern biomedical technology. Here, we have developed a dopamine biosensor based on surface plasmon resonance (SPR). For this purpose, the carboxymethyl dextran SPR chip was used as a surface to immobilize laccase as a bioaffinity recognition element. Data analysis exhibited that the acidic pH value is the optimal condition for dopamine interaction. Calculated kinetic affinity (KD) (48,545 nM), obtained from a molecular docking study, showed strong association of dopamine with the active site of laccase. The biosensor exhibited a linearity from 0.01 to 189 μg/ml and a lower detection limit of 0.1 ng/ml (signal-to-noise ratio (S/N) = 3) that is significantly higher than the most direct dopamine detecting sensors reported so far. Experiments for specificity in the presence of compounds that can co-exist with dopamine detection such as ascorbic acid, urea and L-dopa showed no significant interference. The current dopamine biosensor with high sensitivity and specificity, represent a novel detection tool that offers a label-free, simple procedure and cost effective monitoring system.
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Affiliation(s)
- Safoura Jabbari
- Department of Biochemistry and Biophysics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Sara Daneshjou
- Department of Nanobiotechnology, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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2
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Tongkanarak K, Loupiac C, Neiers F, Chambin O, Srichana T. Evaluating the biomolecular interaction between delamanid/formulations and human serum albumin by fluorescence, CD spectroscopy and SPR: Effects on protein conformation, kinetic and thermodynamic parameters. Colloids Surf B Biointerfaces 2024; 239:113964. [PMID: 38761495 DOI: 10.1016/j.colsurfb.2024.113964] [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: 03/22/2024] [Revised: 04/27/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Delamanid is an anti-tuberculosis drug used for the treatment of drug-resistant tuberculosis. Since delamanid has a high protein bound potential, even patients with low albumin levels should experience high and rapid delamanid clearance. However, the interaction between delamanid and albumin should be better controlled to optimize drug efficacy. This study was designed to evaluate the binding characteristics of delamanid to human serum albumin (HSA) using various methods: fluorescence spectroscopy, circular dichroism (CD), surface plasmon resonance (SPR), and molecular docking simulation. The fluorescence emission band without any shift indicated the interaction was not affected by the polarity of the fluorophore microenvironment. The reduction of fluorescence intensity at 344 nm was proportional to the increment of delamanid concentration as a fluorescence quencher. UV-absorbance measurement at the maximum wavelength (λmax, 280 nm) was evaluated using inner filter effect correction. The HSA conformation change was explained by the intermolecular energy transfer between delamanid and HSA during complex formation. The study, which was conducted at temperatures of 298 K, 303 K, and 310 K, revealed a static quenching mechanism that correlated with a decreased of bimolecular quenching rate constant (kq) and binding constant (Ka) at increased temperatures. The Ka was 1.75-3.16 × 104 M-1 with a specific binding site with stoichiometry 1:1. The negative enthalpy change, negative entropy change, and negative Gibbs free energy change demonstrated an exothermic-spontaneous reaction while van der Waals forces and hydrogen bonds played a vital role in the binding. The molecular displacement approach and molecular docking confirmed that the binding occurred mainly in subdomain IIA, which is a hydrophobic pocket of HSA, with a theoretical binding free energy of -9.33 kcal/mol. SPR exhibited a real time negative sensorgram that resulted from deviation of the reflex angle due to ligand delamanid-HSA complex forming. The binding occurred spontaneously after delamanid was presented to the HSA surface. The SPR mathematical fitting model revealed that the association rate constant (kon) was 2.62 × 108 s-1M-1 and the dissociation rate constant (koff) was 5.65 × 10-3 s-1. The complexes were performed with an association constant (KA) of 4.64 × 1010 M-1 and the dissociation constant (KD) of 2.15 × 10-11 M. The binding constant indicated high binding affinity and high stability of the complex in an equilibrium. Modified CD spectra revealed that conformation of the HSA structure was altered by the presence of delamanid during preparation of the proliposomes that led to the reduction of secondary structure stabilization. This was indicated by the percentage decrease of α-helix. These findings are beneficial to understanding delamanid-HSA binding characteristics as well as the drug administration regimen.
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Affiliation(s)
- Krittawan Tongkanarak
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Camille Loupiac
- Univ. Bourgogne Franche - Comté, L'Institut Agro, Université de Bourgogne, INRAE, UMR PAM 1517, Joint Unit Food Processing and Microbiology, Food and Wine Physico-Chemistry Unit, 1 esplanade Erasme, Dijon 21000, France
| | - Fabrice Neiers
- Flavour Perception: Molecular Mechanisms (Flavours), Université de Bourgogne, 7 bd Jeanne d'Arc, Dijon 21000, France
| | - Odile Chambin
- Univ. Bourgogne Franche - Comté, L'Institut Agro, Université de Bourgogne, INRAE, UMR PAM 1517, Joint Unit Food Processing and Microbiology, Food and Wine Physico-Chemistry Unit, 1 esplanade Erasme, Dijon 21000, France; Department of Pharmaceutical Technology, Faculty of Health Sciences, Université de Bourgogne, 7 bd Jeanne d'Arc, Dijon Cedex 21079, France
| | - Teerapol Srichana
- Drug Delivery System Excellence Center, Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.
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3
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Krishna Rao V, Paul S, Gulkis M, Shen Z, Nair H, Singh A, Li C, Sharma AK, Çağlayan M, Das C, Das B, Kundu CN, Narayan S, Guchhait SK. Molecular editing of NSC-666719 enabling discovery of benzodithiazinedioxide-guanidines as anticancer agents. RSC Med Chem 2024; 15:937-962. [PMID: 38516586 PMCID: PMC10953490 DOI: 10.1039/d3md00648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
DNA polymerase β (Polβ) is crucial for the base excision repair (BER) pathway of DNA damage repair and is an attractive target for suppressing tumorigenesis as well as chemotherapeutic intervention of cancer. In this study, a unique strategy of scaffold-hopping-based molecular editing of a bioactive agent NSC-666719 was investigated, which led to the development of new molecular motifs with Polβ inhibitory activity. NSC compound and its analogs (two series) were prepared, focusing on pharmacophore-based molecular diversity. Most compounds showed higher activities than the parent NSC-666719 and exhibited effects on apoptosis. The inhibitory activity of Polβ was evaluated in both in vitro reconstituted and in vivo intact cell systems. Compound 10e demonstrated significant Polβ interaction and inhibition characteristics, including direct, non-covalent, reversible, and comparable binding affinity. The investigated approach is useful, and the discovered novel analogs have a high potential for developing as anticancer therapeutics.
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Affiliation(s)
- Vajja Krishna Rao
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
| | - Subarno Paul
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Zhihang Shen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Haritha Nair
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Amandeep Singh
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Chinmay Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Chanakya N Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Satya Narayan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
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4
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Lawanprasert A, Sloand JN, Vargas MG, Singh H, Eldor T, Miller MA, Pimcharoen S, Wang J, Leighow SM, Pritchard JR, Dokholyan NV, Medina SH. Deciphering the Mechanistic Basis for Perfluoroalkyl-Protein Interactions. Chembiochem 2023; 24:e202300159. [PMID: 36943393 PMCID: PMC10364144 DOI: 10.1002/cbic.202300159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/23/2023]
Abstract
Although rarely used in nature, fluorine has emerged as an important elemental ingredient in the design of proteins with altered folding, stability, oligomerization propensities, and bioactivity. Adding to the molecular modification toolbox, here we report the ability of privileged perfluorinated amphiphiles to noncovalently decorate proteins to alter their conformational plasticity and potentiate their dispersion into fluorous phases. Employing a complementary suite of biophysical, in-silico and in-vitro approaches, we establish structure-activity relationships defining these phenomena and investigate their impact on protein structural dynamics and intracellular trafficking. Notably, we show that the lead compound, perfluorononanoic acid, is 106 times more potent in inducing non-native protein secondary structure in select proteins than is the well-known helix inducer trifluoroethanol, and also significantly enhances the cellular uptake of complexed proteins. These findings could advance the rational design of fluorinated proteins, inform on potential modes of toxicity for perfluoroalkyl substances, and guide the development of fluorine-modified biologics with desirable functional properties for drug discovery and delivery applications.
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Affiliation(s)
- Atip Lawanprasert
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Janna N. Sloand
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Mariangely González Vargas
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Department of Industrial Engineering, University of Puerto Rico, Mayagüez, Puerto Rico 00682
| | - Harminder Singh
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Tomer Eldor
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Michael A. Miller
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Sopida Pimcharoen
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hershey, PA, USA, 17033
| | - Scott M. Leighow
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
| | - Justin R. Pritchard
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
| | - Nikolay V. Dokholyan
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Department of Pharmacology, Penn State College of Medicine, Pennsylvania State University, Hershey, PA, USA, 17033
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA, 17033
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
| | - Scott H. Medina
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA, 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA, 16802
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5
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Feng Z, Feng X, Lu X. Bioinspired N-Oxide-Based Zwitterionic Polymer Brushes for Robust Fouling-Resistant Surfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7298-7308. [PMID: 37116217 DOI: 10.1021/acs.est.3c00128] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Fouling-resistant surfaces are needed for various environmental applications. Inspired by superhydrophilic N-oxide-based osmolytes in saltwater fish, we demonstrate the use of a trimethylamine N-oxide (TMAO) analogue for constructing fouling-resistant surfaces. The readily synthesized N-oxide monomer of methacrylamide is grafted to filtration membrane surfaces by surface-initiated atom transfer radical polymerization (SI-ATRP). Successful grafting of the amine N-oxide brush layer as confirmed by material characterization endows the surface with increased hydrophilicity, reduced charge, and decreased roughness. Notably, the introduction of the N-oxide layer does not compromise transport properties, i.e., water permeability and water-salt selectivity. Moreover, the modified membrane exhibits improved antifouling properties with a lower flux decline (32.1%) and greater fouling reversibility (18.55%) than the control sample (45.4% flux decline and 3.26% fouling reversibility). We further evaluate foulant-membrane interaction using surface plasmon resonance (SPR) to relate the reduced fouling tendency to the synergic effects of surface characteristic changes after amine N-oxide modification. Our results demonstrate the promise and potential of the N-oxide-based polymer brushes for the design of fouling resistance surfaces for a variety of emerging environmental applications.
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Affiliation(s)
- Zimou Feng
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xunda Feng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Center for Advanced Low-Dimension Materials, and College of Materials Sciences and Engineering, Donghua University, Shanghai 201620, China
| | - Xinglin Lu
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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6
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Pons M, Perenon M, Bonnet H, Gillon E, Vallée C, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude. Analyst 2022; 147:4197-4205. [DOI: 10.1039/d2an00824f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The spacer length and immobilization mode impact the Surface plasmon resonance (SPR) signal and affinity measured for small target/aptamer recognition. The signal could be positive, negative or null explained by refractive index increment deviation.
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Affiliation(s)
- Marina Pons
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Marine Perenon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Hugues Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Emilie Gillon
- Univ. Grenoble Alpes, CERMAV-CNRS, 601 rue de la chimie, F-38610 Gières, France
| | - Celio Vallée
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Eric Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - Nicolas Spinelli
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | | | - Jérôme Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, F-25000 Besançon, France
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7
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Vandana , Pandey R, Srinivasan E, Kalia I, Singh AP, Saxena A, Rajaekaran R, Gupta D, Pandey KC. Plasmodium falciparum metacaspase-2 capture its natural substrate in a non-canonical way. J Biochem 2021; 170:639-653. [DOI: 10.1093/jb/mvab086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Programmed cell death (PCD) is a multi-step process initiated by a set of proteases, which interacts and cleaves diverse proteins, thus modulating their biochemical and cellular functions. In metazoans, PCD is mediated by proteolytic enzymes called caspases, which triggered cell death by proteolysis of human Tudor staphylococcus nuclease (TSN). Non-metazoans lack a close homologue of caspases but possess an ancestral family of cysteine proteases termed ‘metacaspases’. Studies supported that metacaspases are involved in PCD, but their natural substrates remain unknown. In this study, we performed the Plasmodium falciparum TSN (PfTSN) cleavage assay using wild and selected mutants of P. falciparum metacaspases-2 (PfMCA-2) in vitro and in vivo. Interestingly, PfMCA-2, cleaved a phylogenetically conserved protein, PfTSN at multiple sites. Deletion or substitution mutation in key interacting residues at the active site, Cys157 and His205 of PfMCA-2, impaired its enzymatic activity with the artificial substrate, z-GRR-AMC. However, the mutant Tyr224A did not affect the activity with z-GRR-AMC but abolished the cleavage of PfTSN. These results indicated that the catalytic dyad, Cys157 and His205 of PfMCA-2 was essential for its enzymatic activity with an artificial substrate, whereas Tyr224 and Cys157 residues were responsible for its interaction with the natural substrate and subsequent degradation of PfTSN. Our results suggested that MCA-2 interacts with TSN substrate in a non-canonical way using non-conserved or conformationally available residues for its binding and cleavage. In future, it would be interesting to explore how this interaction leads to the execution of PCD in the Plasmodium.
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Affiliation(s)
- Vandana
- ICMR-National Institute of Malaria Research (Indian Council of Medical Research), Department of Health Research, Ministry of Health & FW, Govt. of India Sector-8, Dwarka, New Delhi-110077, India
| | - Rajan Pandey
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - E Srinivasan
- Department of Biotechnology, SBST, Vellore Institute of Technology, Tiruvalam Rd, Katpadi, Vellore, Tamil Nadu-632014, India
| | - Inderjeet Kalia
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi-110067, India
| | - Agam P Singh
- Infectious Diseases Laboratory, National Institute of Immunology, New Delhi-110067, India
| | - Ajay Saxena
- School of Life Science (SLS), Jawaharlal Nehru University, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - R Rajaekaran
- Department of Biotechnology, SBST, Vellore Institute of Technology, Tiruvalam Rd, Katpadi, Vellore, Tamil Nadu-632014, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kailash C Pandey
- ICMR-National Institute of Malaria Research (Indian Council of Medical Research), Department of Health Research, Ministry of Health & FW, Govt. of India Sector-8, Dwarka, New Delhi-110077, India
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A Miniature Bio-Photonics Companion Diagnostics Platform for Reliable Cancer Treatment Monitoring in Blood Fluids. SENSORS 2021; 21:s21062230. [PMID: 33806753 PMCID: PMC8005058 DOI: 10.3390/s21062230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022]
Abstract
In this paper, we present the development of a photonic biosensor device for cancer treatment monitoring as a complementary diagnostics tool. The proposed device combines multidisciplinary concepts from the photonic, nano-biochemical, micro-fluidic and reader/packaging platforms aiming to overcome limitations related to detection reliability, sensitivity, specificity, compactness and cost issues. The photonic sensor is based on an array of six asymmetric Mach Zender Interferometer (aMZI) waveguides on silicon nitride substrates and the sensing is performed by measuring the phase shift of the output signal, caused by the binding of the analyte on the functionalized aMZI surface. According to the morphological design of the waveguides, an improved sensitivity is achieved in comparison to the current technologies (<5000 nm/RIU). This platform is combined with a novel biofunctionalization methodology that involves material-selective surface chemistries and the high-resolution laser printing of biomaterials resulting in the development of an integrated photonics biosensor device that employs disposable microfluidics cartridges. The device is tested with cancer patient blood serum samples. The detection of periostin (POSTN) and transforming growth factor beta-induced protein (TGFBI), two circulating biomarkers overexpressed by cancer stem cells, is achieved in cancer patient serum with the use of the device.
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Bonnet H, Coche-Guérente L, Defrancq E, Spinelli N, Van der Heyden A, Dejeu J. Negative SPR Signals during Low Molecular Weight Analyte Recognition. Anal Chem 2021; 93:4134-4140. [PMID: 33577288 DOI: 10.1021/acs.analchem.1c00071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Surface plasmon resonance (SPR) is a powerful technique for studying biomolecular interactions mainly due to its sensitivity and real-time and label free advantages. While SPR signals are usually positive, only a few studies have reported sensorgrams with negative signals. The aim of the present work is to investigate and to explain the observation of negative SPR signals with the hypothesis that it reflects major changes in ligand conformation resulting from target binding. We demonstrated that these negative unconventional signals were due to the negative complex (ligand/analyte) refractive index increment (RII) deviation from the sum of the RII of the individual entities which counterbalanced the theoretical increase of the signal triggered by the target recognition and the ligand folding. We also found that the conformation change of biomolecules can induce a negative or a positive complex RII deviation depending on its sequence and immobilization mode.
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Affiliation(s)
- H Bonnet
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - L Coche-Guérente
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - E Defrancq
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - N Spinelli
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - A Van der Heyden
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
| | - J Dejeu
- Université Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France
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10
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Villemagne B, Machelart A, Tran NC, Flipo M, Moune M, Leroux F, Piveteau C, Wohlkönig A, Wintjens R, Li X, Gref R, Brodin P, Deprez B, Baulard AR, Willand N. Fragment-Based Optimized EthR Inhibitors with in Vivo Ethionamide Boosting Activity. ACS Infect Dis 2020; 6:366-378. [PMID: 32011115 DOI: 10.1021/acsinfecdis.9b00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Killing more than one million people each year, tuberculosis remains the leading cause of death from a single infectious agent. The growing threat of multidrug-resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. EthR, a mycobacterial transcriptional regulator, is involved in the control of the bioactivation of the second-line drug ethionamide. We have previously reported the discovery of in vitro nanomolar boosters of ethionamide through fragment-based approaches. In this study, we have further explored the structure-activity and structure-property relationships in this chemical family. By combining structure-based drug design and in vitro evaluation of the compounds, we identified a new oxadiazole compound as the first fragment-based ethionamide booster which proved to be active in vivo, in an acute model of tuberculosis infection.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Arnaud Machelart
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ngoc Chau Tran
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie bioorganique et Macromoléculaire (CP206/04), Institut de Pharmacie, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Xue Li
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Ruxandra Gref
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
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11
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Ralph EC, Hall J. An SPR-based analysis of cGAS substrate K D and steady-state K M values. Methods Enzymol 2019; 625:61-76. [PMID: 31455537 DOI: 10.1016/bs.mie.2019.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surface plasmon resonance (SPR) is a standard method for evaluating direct protein-small molecule binding. While studying the catalytic mechanism of cyclic GMP-AMP synthase (cGAS), we developed an SPR-based method to measure steady-state KM values that complements traditional SPR affinity measurements. The method relies on refractive changes to detect protein interaction with substrates and products, and takes advantage of stimulator of type 1 interferon genes (STING) binding to the cGAS product, 2',3'-cGAMP. The specific method described here uses co-immobilization of cGAS and double-stranded DNA through a biotin tag; it should be generally applicable to other proteins and protein complexes.
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Affiliation(s)
- Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States.
| | - Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States
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12
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Tatum N, Duarte F, Kamerlin SCL, Pohl E. Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds. J Phys Chem Lett 2019; 10:2244-2249. [PMID: 30965004 PMCID: PMC6503467 DOI: 10.1021/acs.jpclett.9b00741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Transcriptional repressor EthR from Mycobacterium tuberculosis is a valuable target for antibiotic booster drugs. We previously reported a virtual screening campaign to identify EthR inhibitors for development. Two ligand binding orientations were often proposed, though only the top scoring pose was utilized for filtering of the large data set. We obtained biophysically validated hits, some of which yielded complex crystal structures. In some cases, the crystallized binding mode and top scoring mode agree, while for others an alternate ligand binding orientation was found. In this contribution, we combine rigid docking, molecular dynamics simulations, and the linear interaction energy method to calculate binding free energies and derive relative binding energies for a number of EthR inhibitors in both modes. This strategy allowed us to correctly predict the most favorable orientation. Therefore, this widely applicable approach will be suitable to triage multiple binding modes within EthR and other potential drug targets with similar characteristics.
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Affiliation(s)
- Natalie
J. Tatum
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K.
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Shina C. L. Kamerlin
- Department
of Chemistry - BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Ehmke Pohl
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K.
- Department
of Biosciences, Durham University, Durham DH1 3LE, U.K.
- Biophysical
Sciences Institute, Durham University, Durham DH1 3LE, U.K.
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13
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The KN-93 Molecule Inhibits Calcium/Calmodulin-Dependent Protein Kinase II (CaMKII) Activity by Binding to Ca 2+/CaM. J Mol Biol 2019; 431:1440-1459. [PMID: 30753871 DOI: 10.1016/j.jmb.2019.02.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/14/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022]
Abstract
Calcium/calmodulin-dependent protein kinase II (CaMKII) is a multifunctional serine/threonine protein kinase that transmits calcium signals in various cellular processes. CaMKII is activated by calcium-bound calmodulin (Ca2+/CaM) through a direct binding mechanism involving a regulatory C-terminal α-helix in CaMKII. The Ca2+/CaM binding triggers transphosphorylation of critical threonine residues proximal to the CaM-binding site leading to the autoactivated state of CaMKII. The demonstration of its critical roles in pathophysiological processes has elevated CaMKII to a key target in the management of numerous diseases. The molecule KN-93 is the most widely used inhibitor for studying the cellular and in vivo functions of CaMKII. It is widely believed that KN-93 binds directly to CaMKII, thus preventing kinase activation by competing with Ca2+/CaM. Herein, we employed surface plasmon resonance, NMR, and isothermal titration calorimetry to characterize this presumed interaction. Our results revealed that KN-93 binds directly to Ca2+/CaM and not to CaMKII. This binding would disrupt the ability of Ca2+/CaM to interact with CaMKII, effectively inhibiting CaMKII activation. Our findings also indicated that KN-93 can specifically compete with a CaMKIIδ-derived peptide for binding to Ca2+/CaM. As indicated by the surface plasmon resonance and isothermal titration calorimetry data, apparently at least two KN-93 molecules can bind to Ca2+/CaM. Our findings provide new insight into how in vitro and in vivo data obtained with KN-93 should be interpreted. They further suggest that other Ca2+/CaM-dependent, non-CaMKII activities should be considered in KN-93-based mechanism-of-action studies and drug discovery efforts.
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14
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Salehabadi H, Khajeh K, Dabirmanesh B, Biglar M, Amanlou M. Evaluation of angiotensin converting enzyme inhibitors by SPR biosensor and theoretical studies. Enzyme Microb Technol 2018; 120:117-123. [PMID: 30396392 DOI: 10.1016/j.enzmictec.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/13/2018] [Accepted: 10/19/2018] [Indexed: 01/01/2023]
Abstract
Surface plasmon resonance (SPR) biosensor has been utilized for monitoring analyte-ligand interactions in modern drug discovery processes. SPR biosensors measure the change in refractive indexes over the course of analyte molecules' binding to a specific immobilized ligand on sensor chip. This effort highlights a comprehensive SPR study besides enzymatic assay for discovery of new Angiotensin Converting Enzyme (ACE) inhibitors via screening of medicinal plants. At first, five medicinal plants were selected as potential sources for developing new ACE inhibitors through hydrolyzing hippuryl-L-histidyl-L-leucine (HHL) assay. The interaction of selected extracts with immobilized ACE on the sensor chip (500D) confirmed that the Onopordum acanthium L. had the greatest ACE inhibition activity among the set of compounds and its active compound (onopordia) was isolated. SPR biosensor used to evaluate binding affinity of onopordia and ACE. Equilibrium constant (KD), and changes in Gibb's free energy of the binding (ΔGbinding) values for the interaction of onopordia with ACE were found to be 10.24 μM and -28.48 kJ/mol, respectively. Computational analysis supported the binding of onopordia to the ACE active site. Kinetic and thermodynamic parameters of binding revealed that onopordia is an acceptable ACE inhibitor and could treat hypertension. SPR biosensor can be used to improve the drug discovery process for many important classes of drug targets due to its great sensitivity.
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Affiliation(s)
- Hafezeh Salehabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-111, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-111, Iran
| | - Mahmood Biglar
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran; Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, 14176-53955, Iran.
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15
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Quantitative monitoring of two simultaneously binding species using Label-Enhanced surface plasmon resonance. Biochem Biophys Res Commun 2018; 497:133-138. [PMID: 29427666 DOI: 10.1016/j.bbrc.2018.02.040] [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: 01/25/2018] [Accepted: 02/05/2018] [Indexed: 11/21/2022]
Abstract
Surface plasmon resonance (SPR) is a well-established method for biomolecular interaction studies. SPR monitors the binding of molecules to a solid surface, embodied as refractive index changes close to the surface. One limitation of conventional SPR is the universal nature of the detection that results in an inability to qualitatively discriminate between different binding species. Furthermore, it is impossible to directly discriminate two species simultaneously binding to different sites on a protein, which limits the utility of SPR, for example, in the study of allosteric binders or bi-specific molecules. It is also impossible in principle to discriminate protein conformation changes from actual binding events. Here we demonstrate how Label-Enhanced SPR can be utilized to discriminate and quantitatively monitor the simultaneous binding of two different species - one dye-labeled and one unlabeled - on a standard, single-wavelength SPR instrument. This new technique increases the versatility of SPR technology by opening up application areas where the usefulness of the approach has previously been limited.
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16
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Hall J, Ralph EC, Shanker S, Wang H, Byrnes LJ, Horst R, Wong J, Brault A, Dumlao D, Smith JF, Dakin LA, Schmitt DC, Trujillo J, Vincent F, Griffor M, Aulabaugh AE. The catalytic mechanism of cyclic GMP-AMP synthase (cGAS) and implications for innate immunity and inhibition. Protein Sci 2017; 26:2367-2380. [PMID: 28940468 PMCID: PMC5699495 DOI: 10.1002/pro.3304] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/12/2017] [Accepted: 09/18/2017] [Indexed: 01/05/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is activated by ds-DNA binding to produce the secondary messenger 2',3'-cGAMP. cGAS is an important control point in the innate immune response; dysregulation of the cGAS pathway is linked to autoimmune diseases while targeted stimulation may be of benefit in immunoncology. We report here the structure of cGAS with dinucleotides and small molecule inhibitors, and kinetic studies of the cGAS mechanism. Our structural work supports the understanding of how ds-DNA activates cGAS, suggesting a site for small molecule binders that may cause cGAS activation at physiological ATP concentrations, and an apparent hotspot for inhibitor binding. Mechanistic studies of cGAS provide the first kinetic constants for 2',3'-cGAMP formation, and interestingly, describe a catalytic mechanism where 2',3'-cGAMP may be a minor product of cGAS compared with linear nucleotides.
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Affiliation(s)
- Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Suman Shanker
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Hong Wang
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Laura J Byrnes
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Reto Horst
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Jimson Wong
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Amy Brault
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Darren Dumlao
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - James F Smith
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Leslie A Dakin
- Worldwide Medicinal Chemistry, Pfizer, 610 Main St, Cambridge, Massachusetts, 02139
| | - Daniel C Schmitt
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - John Trujillo
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Fabien Vincent
- Hit Discovery and Lead Profiling, Pfizer Centers for Therapeutic Innovation (CTI), Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Matt Griffor
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
| | - Ann E Aulabaugh
- Worldwide Medicinal Chemistry, Pfizer, Eastern Point Road, Groton, Connecticut, 06340
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17
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Cyclic di-GMP regulates Mycobacterium tuberculosis resistance to ethionamide. Sci Rep 2017; 7:5860. [PMID: 28725053 PMCID: PMC5517500 DOI: 10.1038/s41598-017-06289-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/12/2017] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis is still on the top of infectious diseases list on both mobility and mortality, especially due to drug-resistance of Mycobacterium tuberculosis (M.tb). Ethionamide (ETH) is one of effective second line anti-TB drugs, a synthetic compound similar to isoniazid (INH) structurally, with existing severe problem of ETH resistance. ETH is a prodrug, which is activated by Etha inside M.tb, and etha is transcriptionally repressed by Ethr. We found that c-di-GMP could bind Ethr, enhanced the binding of Ethr to the promoter of etha, and then repressed the transcription of etha, thus caused resistance of M.tb to ETH. Through docking analysis and in vitro validation, we identified that c-di-GMP binds 3 amino acids of Ethr, i.e., Q125, R181 and E190, while the first 2 were the major binding sites. Homology analysis showed that Ethr was highly conservative among mycobacteria. Further docking analysis showed that c-di-GMP preferentially bound proteins of TetR family at the junction hole of symmetric dimer or tetramer proteins. Our results suggest a possible drug-resistance mechanism of ETH through the regulation of Ethr by c-di-GMP.
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18
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Duan J, Xiaokaiti Y, Fan S, Pan Y, Li X, Li X. Direct interaction between caffeic acid phenethyl ester and human neutrophil elastase inhibits the growth and migration of PANC-1 cells. Oncol Rep 2017; 37:3019-3025. [PMID: 28339071 DOI: 10.3892/or.2017.5516] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/16/2017] [Indexed: 11/06/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignant tumors of the digestive system, but the mechanisms of its development and progression are unclear. Inflammation is thought to be fundamental to pancreatic cancer development and caffeic acid phenethyl ester (CAPE) is an active component of honey bee resin or propolis with anti-inflammatory and anticancer activities. We investigated the inhibitory effects of CAPE on cell growth and migration induced by human neutrophil elastase (HNE) and report that HNE induced cancer cell migration at low doses and growth at higher doses. In contrast, lower CAPE doses inhibited migration and higher doses of CAPE inhibited the growth induced by HNE. HNE activity was significantly inhibited by CAPE (7.5-120 µM). Using quantitative real-time PCR and western blotting, we observed that CAPE (18-60 µM) did not affect transcription and translation of α1-antitrypsin (α1-AT), an endogenous HNE inhibitor. However, in an in silico drug target docking model, we found that CAPE directly bound to the binding pocket of HNE (25.66 kcal/mol) according to CDOCKER, and the residue of the catalytic site stabilized the interaction between CAPE and HNE as evidenced by molecular dynamic simulation. Response unit (RU) values of surface plasmon resonance (SPR) significantly increased with incremental CAPE doses (7.5-120 µM), indicating that CAPE could directly bind to HNE in a concentration-dependent manner. Thus, CAPE is an effective inhibitor of HNE via direct interaction whereby it inhibits the migration and growth of PANC-1 cells in a dose-dependent manner.
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Affiliation(s)
- Jianhui Duan
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
| | - Yilixiati Xiaokaiti
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
| | - Shengjun Fan
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
| | - Yan Pan
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
| | - Xin Li
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
| | - Xuejun Li
- Department of Pharmacology, School of Basic Medical Sciences, Peking University and State Key Laboratory of Natural and Biomimetic Drugs, Peking University and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, P.R. China
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19
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Lee YY, Crauste C, Wang H, Leung HH, Vercauteren J, Galano JM, Oger C, Durand T, Wan JMF, Lee JCY. Extra Virgin Olive Oil Reduced Polyunsaturated Fatty Acid and Cholesterol Oxidation in Rodent Liver: Is This Accounted for Hydroxytyrosol-Fatty Acid Conjugation? Chem Res Toxicol 2016; 29:1689-1698. [DOI: 10.1021/acs.chemrestox.6b00214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Yiu Yiu Lee
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
| | - Céline Crauste
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université de Montpellier & ENSCM (School of Chemistry), Faculté de Pharmacie, 15 Av. Charles Flahault, 34093 Montpellier cedex 05, France
| | - Hualin Wang
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
| | - Ho Hang Leung
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
| | - Joseph Vercauteren
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université de Montpellier & ENSCM (School of Chemistry), Faculté de Pharmacie, 15 Av. Charles Flahault, 34093 Montpellier cedex 05, France
| | - Jean-Marie Galano
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université de Montpellier & ENSCM (School of Chemistry), Faculté de Pharmacie, 15 Av. Charles Flahault, 34093 Montpellier cedex 05, France
| | - Camille Oger
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université de Montpellier & ENSCM (School of Chemistry), Faculté de Pharmacie, 15 Av. Charles Flahault, 34093 Montpellier cedex 05, France
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université de Montpellier & ENSCM (School of Chemistry), Faculté de Pharmacie, 15 Av. Charles Flahault, 34093 Montpellier cedex 05, France
| | - Jennifer Man-Fan Wan
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
| | - Jetty Chung-Yung Lee
- School
of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR
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20
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Origin and prediction of free-solution interaction studies performed label-free. Proc Natl Acad Sci U S A 2016; 113:E1595-604. [PMID: 26960999 DOI: 10.1073/pnas.1515706113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interaction/reaction assays have led to significant scientific discoveries in the biochemical, medical, and chemical disciplines. Several fundamental driving forces form the basis of intermolecular and intramolecular interactions in chemical and biochemical systems (London dispersion, hydrogen bonding, hydrophobic, and electrostatic), and in the past three decades the sophistication and power of techniques to interrogate these processes has developed at an unprecedented rate. In particular, label-free methods have flourished, such as NMR, mass spectrometry (MS), surface plasmon resonance (SPR), biolayer interferometry (BLI), and backscattering interferometry (BSI), which can facilitate assays without altering the participating components. The shortcoming of most refractive index (RI)-based label-free methods such as BLI and SPR is the requirement to tether one of the interaction entities to a sensor surface. This is not the case for BSI. Here, our hypothesis is that the signal origin for free-solution, label-free determinations can be attributed to conformation and hydration-induced changes in the solution RI. We propose a model for the free-solution response function (FreeSRF) and show that, when quality bound and unbound structural data are available, FreeSRF correlates well with the experiment (R(2)> 0.99, Spearman rank correlation coefficients >0.9) and the model is predictive within ∼15% of the experimental binding signal. It is also demonstrated that a simple mass-weighted dη/dC response function is the incorrect equation to determine that the change in RI is produced by binding or folding event in free solution.
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21
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Surface Plasmon Resonance Sensors: Methods of Surface Functionalization and Sensitivity Enhancement. THEOR EXP CHEM+ 2015. [DOI: 10.1007/s11237-015-9427-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Pechalrieu D, Lopez M. Compounds for use in the treatment of mycobacterial infections: a patent evaluation (WO2014049107A1). Expert Opin Ther Pat 2015; 25:729-35. [PMID: 25752488 DOI: 10.1517/13543776.2015.1021333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Tuberculosis is one of the main causes of mortality with 1.5 million deaths a year worldwide. The growing emergence of multi- and extremely resistant strains highlights the urgent need of novel antibiotic strategies. Ethionamide, interfering with the mycobacterial membrane biosynthesis, is used in second-line treatment. This molecule is a prodrug, which requires activation by EthA. The patent described in this evaluation (WO2014049107A1) claimed a new family of molecules and their use as antibiotic treatment against mycobacteria such as Mycobacterium tuberculosis, M. leprae and atypical mycobacteria, either as a single active agent or in combination with antibiotics activable by EthA pathway.
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Affiliation(s)
- Dany Pechalrieu
- Unité de Service et de Recherche CNRS - Pierre Fabre n°3388 ETaC - Epigenetic Targeting of Cancer , CRDPF, 3 avenue Hubert Curien, 31035 Toulouse Cedex 01 , France
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