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Yu HJ, Jang E, Woo A, Han IW, Jeon HG, Linh VTN, Park SG, Jung HS, Lee MY. Cancer screening through surface-enhanced Raman spectroscopy fingerprinting analysis of urinary metabolites using surface-carbonized silver nanowires on a filter membrane. Anal Chim Acta 2024; 1292:342233. [PMID: 38309850 DOI: 10.1016/j.aca.2024.342233] [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: 08/04/2023] [Revised: 11/05/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
BACKGROUND Label-free surface-enhanced Raman spectroscopy (SERS)-based metabolic profiling has great potential for early cancer diagnosis, but further advancements in analytical methods and clinical evidence studies are required for clinical applications. To improve the cancer diagnostic accuracy of label-free SERS spectral analysis of complex biological fluids, it is necessary to obtain specifically enhanced SERS signals of cancer-related metabolites present at low concentrations. RESULTS This study presents a novel 3D SERS sensor, comprising a surface-carbonized silver nanowire (AgNW)-stacked filter membrane, alongside an optimized urine/methanol/chloroform extraction technique, which specifically changes the molecular adsorption and orientation of aromatic metabolites onto SERS substrates. By analyzing the pretreated urine samples on the surface-carbonized AgNW 3D SERS sensor, distinct and highly enhanced SERS peaks derived from semi-polar aromatic metabolites were observed for pancreatic cancer and prostate cancer samples compared with normal controls. Urine metabolite analysis using SERS fingerprinting successfully differentiated pancreatic cancer and prostate cancer groups from normal control group: normal control (n = 56), pancreatic cancer (n = 40), and prostate cancer (n = 39). SIGNIFICANCE AND NOVELTY We confirmed the clinical feasibility of performing fingerprint analysis of urinary metabolites based on the surface-carbonized AgNW 3D SERS sensor and methanol/chloroform extraction for noninvasive cancer screening. This technology holds potential for large-scale screening owing to its high accuracy, and cost effective, simple and rapid detection method.
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Affiliation(s)
- Ho-Jae Yu
- Medical Device Research Center, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - Eunji Jang
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Ayoung Woo
- Medical Device Research Center, Samsung Medical Center, Seoul, 06351, Republic of Korea
| | - In Woong Han
- Division of Hepato Biliary Pancreatic Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Hwang Gyun Jeon
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Vo Thi Nhat Linh
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Sung-Gyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Ho Sang Jung
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea.
| | - Min-Young Lee
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea.
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Hammond OS, Atri R, Bowron DT, Edler KJ. Neutron Diffraction Study of Indole Solvation in Deep Eutectic Systems of Choline Chloride, Malic Acid, and Water. Chemistry 2022; 28:e202200566. [PMID: 35510678 PMCID: PMC9400976 DOI: 10.1002/chem.202200566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 11/09/2022]
Abstract
Deep eutectic systems are currently under intense investigation to replace traditional organic solvents in a range of syntheses. Here, indole in choline chloride‐malic acid deep eutectic solvent (DES) was studied as a function of water content, to identify solute interactions with the DES which affect heterocycle reactivity and selectivity, and as a proxy for biomolecule solvation. Empirical Potential Structure Refinement models of neutron diffraction data showed [Cholinium]+ cations associate strongly with the indole π‐system due to electrostatics, whereas malic acid is only weakly associated. Trace water is sequestered into the DES and does not interact strongly with indole. When water is added to the DES, it does not interact with the indole π‐system but is exclusively in‐plane with the heterocyclic rings, forming strong H‐bonds with the ‐NH group, and also weak H‐bonds and thus prominent hydrophobic hydration of the indole aromatic region, which could direct selectivity in reactions.
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Affiliation(s)
- Oliver S. Hammond
- Centre for Sustainable Chemical Technologies and Department of Chemistry University of Bath Claverton Down Bath BA2 7AY U.K
- Current address: Department of Materials and Environmental Chemistry Stockholm University Stockholm Sweden
| | - Ria Atri
- Centre for Sustainable Chemical Technologies and Department of Chemical Engineering University of Bath Claverton Down Bath BA2 7AY U.K
| | - Daniel T. Bowron
- ISIS Neutron and Muon Source Science and Technology Facilities Council Rutherford Appleton Laboratory Didcot OX11 0QX U.K
| | - Karen J. Edler
- Centre for Sustainable Chemical Technologies and Department of Chemistry University of Bath Claverton Down Bath BA2 7AY U.K
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3
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Tinjacá DA, Martínez F, Almanza OA, Jouyban A, Acree WE. Solubility, Dissolution Thermodynamics and Preferential Solvation of Meloxicam in (Methanol + Water) Mixtures. J SOLUTION CHEM 2021. [DOI: 10.1007/s10953-021-01084-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Henao A, Ruiz GN, Steinke N, Cerveny S, Macovez R, Guàrdia E, Busch S, McLain SE, Lorenz CD, Pardo LC. On the microscopic origin of the cryoprotective effect in lysine solutions. Phys Chem Chem Phys 2020; 22:6919-6927. [DOI: 10.1039/c9cp06192d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lysine cryoprotective properties are due to the tight bonding of the first hydration Shell to the amino acid. However this effect is only possible for concentration up to 5.4 water molecules per lysine.
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Affiliation(s)
- Andrés Henao
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Guadalupe N. Ruiz
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Nicola Steinke
- Center for Marine Environmental Sciences (MARUM)
- University of Bremen
- 28359 Bremen
- Germany
| | - Silvina Cerveny
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC)
- Donostia International Physics Center (DIPC)
- 20018 San Sebastián
- Spain
| | - Roberto Macovez
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
| | - Elvira Guàrdia
- Grup de Simulació per Ordinador en Matèria Condensada
- Departament de Física
- Universitat Politècnica de Catalunya
- E-08034 Barcelona
- Spain
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ)
- Helmholtz-Zentrum Geesthacht GmbH
- 85747 Garching bei München
- Germany
| | - Sylvia E. McLain
- Department of Chemistry
- School of Life Sciences
- University of Sussex
- Brighton
- UK
| | | | - Luis Carlos Pardo
- Grup de Caracterització de Materials
- Departament de Física
- ETSEIB, Universitat Politècnica de Catalunya
- E-08019 Barcelona
- Spain
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5
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Abstract
The idea that water is a mixture of two distinct states is analyzed in some detail. It is shown that the known compressibility of water is in fact sufficiently small that for a volume of water of size 1 nm3, the density fluctuations are of order 4% of the average density. This is much smaller than the ≈25% density fluctuations that would be required for significant regions of high and low density water to occur on this volume scale. It is also pointed out that the density fluctuations in water are, if anything, smaller than those that occur in other common liquids which do not have the anomalous properties of water. It is shown that if the distribution of density fluctuations is unimodal, the system is in the one-phase region, and if bimodal, it is in the two-phase region. None of the liquid or amorphous phases of water explored in this work give any sign of being in the two-phase region. Existing neutron and X-ray scattering data on water in the amorphous phases, and in the stable liquid phases as a function pressure and temperature, are subject to a new set of empirical potential structure refinement simulations. These simulations are interrogated for their configurational entropy, using a spherical harmonic reconstruction of the full orientational pair correlation function. It is shown that the excess pair entropy derived from this function, plus the known perfect gas contributions, give a reasonable account of the total entropy of water, within the likely errors. This estimated entropy follows the expected declining trend with decreasing temperature. Evidence that higher density water will have higher entropy than lower density water emerges, in accordance with what is expected from the negative thermal expansion coefficient of water at low temperatures. However, this entropy increase is not large and goes through a maximum before declining at yet higher densities and pressures, in a manner reminiscent of what has been previously observed in the diffusion coefficient as a function of pressure. There is no evidence that ambient water can be regarded as patches of high density, high entropy and low density, low entropy liquid, as some have claimed, since high density water has a similar entropy to low density water. There is some evidence that the distinction between these two states will become more pronounced as the temperature is lowered. Extensive discussion of the use of order parameters to describe water structure is given, and it is pointed out that these indices generally cannot be used to infer two-state behavior.
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Affiliation(s)
- A K Soper
- ISIS Facility, UKRI-STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
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6
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Basma NS, Headen TF, Shaffer MSP, Skipper NT, Howard CA. Local Structure and Polar Order in Liquid N-Methyl-2-pyrrolidone (NMP). J Phys Chem B 2018; 122:8963-8971. [DOI: 10.1021/acs.jpcb.8b08020] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nadir S. Basma
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, U.K
- Department of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Thomas F. Headen
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, Oxfordshire, U.K
| | - Milo S. P. Shaffer
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, U.K
| | - Neal T. Skipper
- Department of Physics and Astronomy, University College London, London WC1E 6BT, U.K
| | - Christopher A. Howard
- Department of Physics and Astronomy, University College London, London WC1E 6BT, U.K
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7
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Headen TF, Cullen PL, Patel R, Taylor A, Skipper NT. The structures of liquid pyridine and naphthalene: the effects of heteroatoms and core size on aromatic interactions. Phys Chem Chem Phys 2018; 20:2704-2715. [DOI: 10.1039/c7cp06689a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spatial and orientational structures of liquid naphthalene and pyridine revealed using neutron scattering combined with empirical potential structure refinement.
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Affiliation(s)
- T. F. Headen
- ISIS Neutron Facility, STFC Rutherford Appleton Laboratory, Harwell Campus
- Didcot
- UK
| | - P. L. Cullen
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - R. Patel
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - A. Taylor
- University College London, Dept. Physics and Astronomy
- London
- UK
| | - N. T. Skipper
- University College London, Dept. Physics and Astronomy
- London
- UK
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8
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Graziano G. Comment on “On the positional and orientational order of water and methanol around indole: a study on the microscopic origin of solubility” Phys. Chem. Chem. Phys., 2016, 18, 23006. Phys Chem Chem Phys 2018; 20:2113-2115. [DOI: 10.1039/c7cp03698a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Indole solubility is larger in methanol than in water due to lower magnitude of the cavity creation work.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie
- Università del Sannio
- Via Port’Arsa 11
- 82100 Benevento
- Italy
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9
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Rhys NH, Bruni F, Imberti S, McLain SE, Ricci MA. Glucose and Mannose: A Link between Hydration and Sweetness. J Phys Chem B 2017; 121:7771-7776. [DOI: 10.1021/acs.jpcb.7b03919] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. H. Rhys
- Department
of Biochemistry, University of Oxford, South Park Road, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - F. Bruni
- Dipartimento
di Scienze, Sezione di Nanoscienze, Università degli Studi “Roma Tre”, Via della Vasca Navale 84, 00146 Roma, Italy
| | - S. Imberti
- ISIS
Neutron and Muon source, STFC, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
| | - S. E. McLain
- Department
of Biochemistry, University of Oxford, South Park Road, Oxford, Oxfordshire OX1 3QU, United Kingdom
| | - M. A. Ricci
- Dipartimento
di Scienze, Sezione di Nanoscienze, Università degli Studi “Roma Tre”, Via della Vasca Navale 84, 00146 Roma, Italy
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10
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Duboué-Dijon E, Mason PE, Fischer HE, Jungwirth P. Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations. J Chem Phys 2017. [DOI: 10.1063/1.4982937] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Elise Duboué-Dijon
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Henry E. Fischer
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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11
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Maier JM, Li P, Vik EC, Yehl CJ, Strickland SMS, Shimizu KD. Measurement of Solvent OH−π Interactions Using a Molecular Balance. J Am Chem Soc 2017; 139:6550-6553. [DOI: 10.1021/jacs.7b02349] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Josef M. Maier
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Erik C. Vik
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Christopher J. Yehl
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Sharon M. S. Strickland
- Department
of Biology, Chemistry, and Physics, Converse College, Spartanburg, South Carolina 29302, United States
| | - Ken D. Shimizu
- Department
of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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12
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13
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Sridhar A, Ross GA, Biggin PC. Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin. PLoS One 2017; 12:e0172743. [PMID: 28235019 PMCID: PMC5325533 DOI: 10.1371/journal.pone.0172743] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket and contribute to the free energy of binding. It would thus be extremely useful to be able to accurately predict the position and orientation of water molecules within a binding pocket. Recently, we developed the WaterDock protocol that was able to predict 97% of the water molecules in a test set. However, this approach generated false positives at a rate of over 20% in most cases and whilst this might be acceptable for some applications, in high throughput scenarios this is not desirable. Here we tackle this problem via the inclusion of knowledge regarding the solvation structure of ligand functional groups. We call this new protocol WaterDock2 and demonstrate that this protocol maintains a similar true positive rate to the original implementation but is capable of reducing the false-positive rate by over 50%. To improve the usability of the method, we have also developed a plugin for the popular graphics program PyMOL. The plugin also contains an implementation of the original WaterDock.
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Affiliation(s)
- Akshay Sridhar
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Gregory A. Ross
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Silva-Santisteban A, Steinke N, Johnston AJ, Ruiz GN, Carlos Pardo L, McLain SE. On the structure of prilocaine in aqueous and amphiphilic solutions. Phys Chem Chem Phys 2017; 19:12665-12673. [DOI: 10.1039/c7cp01723e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The solvation of prilocaine has been investigated in pure water and in amphiphilic solutions using a combination of neutron diffraction and simulations.
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Affiliation(s)
- Alvaro Silva-Santisteban
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU
- UK
- Departament de Física i Enginyeria Nuclear & Barcelona Research Center in Multiscale Science and Engineering
| | - Nicola Steinke
- Department of Biochemistry
- University of Oxford
- Oxford OX1 3QU
- UK
| | | | - Guadalupe N. Ruiz
- Departament de Física i Enginyeria Nuclear & Barcelona Research Center in Multiscale Science and Engineering
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
| | - Luis Carlos Pardo
- Departament de Física i Enginyeria Nuclear & Barcelona Research Center in Multiscale Science and Engineering
- Universitat Politècnica de Catalunya
- 08019 Barcelona
- Spain
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