1
|
Kellermann L, Gupta R. Photoactive hydrogels for pre-concentration, labelling, and controlled release of proteins. Analyst 2023; 148:4127-4137. [PMID: 37493470 PMCID: PMC10440800 DOI: 10.1039/d3an00811h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
We report a novel hydrogel for pre-concentration, fluorescent labelling, and light-triggered release of proteins for detection of low abundance biomarkers. The hydrogel was a co-polymer of acrylamide/bisacrylamide and methacrylamide attached to fluorescein isothiocyanate via a light cleavable bond and a poly(ethylene glycol) spacer arm of molecular weight of 3400 g mol-1. Unlike previous work, proteins were captured by an irreversible chemical reaction rather than by non-covalent affinity binding or physical entrapment. Because the protein-reactive group was attached to fluorescein, which in turn was coupled to the hydrogel by a photocleavable bond, on release the protein was labelled with fluorescein. Our hydrogel offered a pre-concentration factor of up to 236 for a model protein, streptavidin. Each protein molecule was labelled with 85 fluorescein molecules, and 50% of the proteins in the hydrogel were released after UV exposure for ∼100 s. The proteins released from the hydrogel were captured in biotinylated microtitre plates and detected by fluorescence, allowing measurement of at least 0.01 ppm (or ∼166 pM) of protein in sample solutions. The reported hydrogel is promising for detection of low abundance proteins while being less laborious than enzyme-linked immunosorbent assay and less affected by changes in environmental conditions than label-free biosensors.
Collapse
Affiliation(s)
- Leanne Kellermann
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
| | - Ruchi Gupta
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
| |
Collapse
|
2
|
Singhal A, Singh A, Shrivastava A, Khan R. Epitope imprinted polymeric materials: application in electrochemical detection of disease biomarkers. J Mater Chem B 2023; 11:936-954. [PMID: 36606445 DOI: 10.1039/d2tb02135h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epitope imprinting is a promising method for creating specialized recognition sites that resemble natural biorecognition elements. Epitope-imprinted materials have gained a lot of attention recently in a variety of fields, including bioanalysis, drug delivery, and clinical therapy. The vast applications of epitope imprinted polymers are due to the flexibility in choosing monomers, the simplicity in obtaining templates, specificity toward targets, and resistance to harsh environments along with being cost effective in nature. The "epitope imprinting technique," which uses only a tiny subunit of the target as the template during imprinting, offers a way around various drawbacks inherent to biomacromolecule systems i.e., traditional molecular imprinting techniques with regards to the large size of proteins, such as the size, complexity, accessibility, and conformational flexibility of the template. Electrochemical based sensors are proven to be promising tool for the quick, real-time monitoring of biomarkers. This review unravels epitope imprinting techniques, approaches, and strategies and highlights the applicability of these techniques for the electrochemical quantification of biomarkers for timely disease monitoring. In addition, some challenges are discussed along with future prospective developments.
Collapse
Affiliation(s)
- Ayushi Singhal
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Amrita Singh
- Department of Biotechnology, Barkatullah University, Habibganj, Bhopal, Madhya Pradesh 462026, India
| | - Apoorva Shrivastava
- Dr D. Y. Patil Biotechnology and Bioinformatics Institute, Dr D. Y. Patil Vidyapeeth, Sr. No. 87-88, Mumbai-Bangalore Highway, Tathawade, Pune, Maharashtra, 411033, India
| | - Raju Khan
- CSIR-Advanced Materials and Processes Research Institute (AMPRI), Hoshangabad Road, Bhopal - 462026, MP, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| |
Collapse
|
3
|
Perrella F, Li X, Petrone A, Rega N. Nature of the Ultrafast Interligands Electron Transfers in Dye-Sensitized Solar Cells. JACS AU 2023; 3:70-79. [PMID: 36711100 PMCID: PMC9875239 DOI: 10.1021/jacsau.2c00556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 05/14/2023]
Abstract
Charge-transfer dynamics and interligand electron transfer (ILET) phenomena play a pivotal role in dye-sensitizers, mostly represented by the Ru-based polypyridyl complexes, for TiO2 and ZnO-based solar cells. Starting from metal-to-ligand charge-transfer (MLCT) excited states, charge dynamics and ILET can influence the overall device efficiency. In this letter, we focus on N34- dye ( [Ru(dcbpy)2(NCS)2]4-, dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) to provide a first direct observation with high time resolution (<20 fs) of the ultrafast electron exchange between bpy-like ligands. ILET is observed in water solution after photoexcitation in the ∼400 nm MLCT band, and assessment of its ultrafast time-scale is here given through a real-time electronic dynamics simulation on the basis of state-of-the-art electronic structure methods. Indirect effects of water at finite temperature are also disentangled by investigating the system in a symmetric gas-phase structure. As main result, remarkably, the ILET mechanism appears to be based upon a purely electronic evolution among the dense, experimentally accessible, MLCT excited states manifold at ∼400 nm, which rules out nuclear-electronic couplings and proves further the importance of the dense electronic manifold in improving the efficiency of dye sensitizers in solar cell devices.
Collapse
Affiliation(s)
- Fulvio Perrella
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alessio Petrone
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed.
6, via Cintia, 80126 Napoli, Italy
| | - Nadia Rega
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, I-80138 Napoli, Italy
- Istituto
Nazionale Di Fisica Nucleare, sezione di Napoli, Complesso Universitario di Monte S. Angelo ed.
6, via Cintia, 80126 Napoli, Italy
- CRIB,
Centro Interdipartimentale di Ricerca sui Biomateriali, Piazzale Tecchio 80, I-80125 Napoli, Italy
| |
Collapse
|
4
|
Ferreira VRA, Azenha MA, Pereira CM, Silva AF. Molecularly Imprinted Methyl-Modified Hollow TiO 2 Microspheres. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238510. [PMID: 36500600 PMCID: PMC9735797 DOI: 10.3390/molecules27238510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022]
Abstract
The possibility of generating organically modified hollow TiO2 microspheres via a simple sol-gel synthesis was demonstrated for the first time in this work. A mixture of titania precursors, including an organically modified precursor, was used to obtain methyl-modified hollow TiO2 microspheres selective for bilirubin by the molecular imprinting technique (Methyl-HTM-MIM). Methyl-HTM-MIM were prepared by a sol-gel method using titanium (IV) isopropoxide (TTIP), and methyltitanium triisopropoxide (MTTIP) as precursors. Two ratios of titania precursors were tested (1/6 and 1/30 molMTTIP/molTTIP). With the characterization results obtained by the SEM and ATR-FTIR techniques, it was possible to establish that only the 1/30 molMTTIP/molTTIP ratio allowed for the preparation of hollow spheres with a reasonably homogeneous methylated-TiO2 shell. It was possible to obtain a certain degree of organization of the hybrid network, which increased with calcination temperatures. By adjusting isothermal adsorption models, imprinting parameters were determined, indicating that the new methylated microspheres presented greater selectivity for bilirubin than the totally inorganic hollow TiO2 microspheres. The effectiveness of the molecular imprinting technique was proven for the first time in an organically modified titania material, with imprinting factor values greater than 1.4, corresponding to a significant increase in the maximum adsorption capacity of the template represented by the molecularly imprinted microspheres. In summary, the results obtained with the new methyl-HTM-MIM open the possibility of exploring the application of these microspheres for selective sorption (separation or sensing, for example) or perhaps even for selective photocatalysis, particularly for the degradation of organic compounds.
Collapse
|
5
|
Chen H, Guo J, Wang Y, Dong W, Zhao Y, Sun L. Bio-Inspired Imprinting Materials for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202038. [PMID: 35908804 PMCID: PMC9534966 DOI: 10.1002/advs.202202038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/08/2022] [Indexed: 05/27/2023]
Abstract
Inspired by the recognition mechanism of biological molecules, molecular imprinting techniques (MITs) are imparted with numerous merits like excellent stability, recognition specificity, adsorption properties, and easy synthesis processes, and thus broaden the avenues for convenient fabrication protocol of bio-inspired molecularly imprinted polymers (MIPs) with desirable functions to satisfy the extensive demands of biomedical applications. Herein, the recent research progress made with respect to bio-inspired imprinting materials is discussed in this review. First, the underlying mechanism and basic components of a typical molecular imprinting procedure are briefly explored. Then, emphasis is put on the introduction of diverse MITs and novel bio-inspired imprinting materials. Following these two sections, practical applications of MIPs in the field of biomedical science are focused on. Last but not least, perspectives on the remaining challenges and future development of bio-inspired imprinting materials are presented.
Collapse
Affiliation(s)
- Hanxu Chen
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096P. R. China
| | - Jiahui Guo
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096P. R. China
| | - Yu Wang
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials‐Oriented Chemical EngineeringCollege of Biotechnology and Pharmaceutical EngineeringNanjing Tech UniversityNanjing211800P. R. China
| | - Yuanjin Zhao
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health)Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325001P. R. China
| | - Lingyun Sun
- Department of Rheumatology and ImmunologyNanjing Drum Tower HospitalSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjing210096P. R. China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health)Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang325001P. R. China
| |
Collapse
|
6
|
Coppola F, Cimino P, Perrella F, Crisci L, Petrone A, Rega N. Electronic and Vibrational Manifold of Tetracyanoethylene-Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics. J Phys Chem A 2022; 126:7179-7192. [PMID: 36174118 PMCID: PMC9574931 DOI: 10.1021/acs.jpca.2c05001] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/17/2022] [Indexed: 11/29/2022]
Abstract
The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results [Mathies, R. A.; et al. J. Phys. Chem. A 2018, 122 (14), 3594] was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the C═C axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central C═C and C≡N bonds, compared to the isolated case. An important red shift of the C═C stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear C═C axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.
Collapse
Affiliation(s)
- Federico Coppola
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Paola Cimino
- Department
of Pharmaceutical Sciences, University of
Salerno, 84084 Fisciano, Italy
| | - Fulvio Perrella
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
| | - Luigi Crisci
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
| | - Alessio Petrone
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
- Istituto
Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italy
| | - Nadia Rega
- Department
of Chemical Sciences, University of Napoli
Federico II, Complesso Universitario di M.S. Angelo, 80126 Napoli, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
- Istituto
Nazionale di Fisica Nucleare, Sezione di Napoli, Complesso Universitario di Monte S. Angelo ed. 6, 80126 Napoli, Italy
- Centro
Interdipartimentale di Ricerca sui Biomateriali (CRIB), Piazzale Tecchio, 80125 Napoli, Italy
| |
Collapse
|
7
|
Jin S, Li D, Feng X, Fu G. Synthesis of carbon dots-based surface protein-imprinted nanoparticles via sandwich-structured template pre-assemble and post-imprinting modification for enhanced fluorescence detection. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
8
|
Huang R, Ma Y, Peng A. The Colorimetric Identification of NO
2
−
in Latent Fingerprints by Hydroxypropyl‐β‐cyclodextrin. ChemistrySelect 2022. [DOI: 10.1002/slct.202104392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rui Huang
- Criminal Investigation School Southwest University of Political Science and Law Chongqing 401120 China
- Chongqing University Physical Evidence Technology Engineering Research Center Chongqing 401120 China
- Chongqing Criminal Technology Key Laboratory Chongqing 401120 China
- National Drug Governance Research Center Southwest University of Political Science and Law Chongqing 401120 China
| | - Yuyao Ma
- Criminal Investigation School Southwest University of Political Science and Law Chongqing 401120 China
| | - An Peng
- Criminal Investigation School Southwest University of Political Science and Law Chongqing 401120 China
| |
Collapse
|
9
|
Ungarala R, Munikumar M, Sinha SN, Kumar D, Sunder RS, Challa S. Assessment of Antioxidant, Immunomodulatory Activity of Oxidised Epigallocatechin-3-Gallate (Green Tea Polyphenol) and Its Action on the Main Protease of SARS-CoV-2—An In Vitro and In Silico Approach. Antioxidants (Basel) 2022; 11:antiox11020294. [PMID: 35204178 PMCID: PMC8868081 DOI: 10.3390/antiox11020294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Owing to the instability of Epigallocatechin Gallate (EGCG), it may undergo auto-oxidation and form oxidised products or dimers. In the present study, we aimed to evaluate the therapeutic effects, including antioxidation and immunomodulatory action, of the Oxidised Epigallocatechin Gallate (O-EGCG) as compared to native EGCG and the action of these compounds on main protease (Mpro) docking against SARS-CoV-2. HCT-116 (Human Colon Cancer) cell lines were used to estimate the total antioxidant capacity and lipid peroxidation levels and pro-inflammatory markers (human IL-6, IL-1β, TNF-α). Further, molecular docking analysis was performed by AutoDock and visualised in Discovery studio. Improved antioxidant capacity of O-EGCG was observed, and there was a significant decrease in the inflammatory markers (IL-1β, IL-6, and TNF-α) when O-EGCG was applied as compared to EGCG. The O-EGCG was shown to be strongly associated with the highest docking score and active site residues of IL-1, IL-6, and TNF- α, as well as the Mpro of SARS-CoV-2, according to in silico approach. The in vitro and in silico analyses indicate an improved therapeutic action of the oxidised form of EGCG. The effective inhibitory action of O-EGCG against SARS-CoV-2 suggests further exploration of the compound against COVID-19 and its efficacy. However, in vivo studies and understanding of the mechanism of action of O-EGCG may yield a better opinion on the use of O-EGCG and future human clinical trials.
Collapse
Affiliation(s)
- Ramakrishna Ungarala
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
| | - Manne Munikumar
- Clinical Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India;
| | - Sukesh Narayan Sinha
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
- Correspondence: ; Tel.: +91-7032426802
| | - Dileshwar Kumar
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
| | - R. Shyam Sunder
- University College of Technology, Osmania University, Tarnaka, Hyderabad, Telangana 500007, India;
| | - Suresh Challa
- Cell Biology Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India;
| |
Collapse
|
10
|
De Masi A, Scognamiglio PL, Battista E, Netti PA, Causa F. PEG-based Cleavable Hydrogel Microparticles with controlled porosity for permiselective trafficking of biomolecular complexes in biosensing applications. J Mater Chem B 2022; 10:1980-1990. [PMID: 35229850 DOI: 10.1039/d1tb02751d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the last decade, PEG-based hydrogels have been extensively used for the production of microparticles for biosensing applications. The biomolecule accessibility and mass transport rate represent key parameters for the...
Collapse
Affiliation(s)
- Alessandra De Masi
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
| | - Pasqualina L Scognamiglio
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
| | - Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy.
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli "Federico II", Piazzale Tecchio 80, 80125 Naples, Italy.
| |
Collapse
|
11
|
Perrella F, Petrone A, Rega N. Direct observation of the solvent organization and nuclear vibrations of [Ru(dcbpy) 2(NCS) 2] 4-, [dcbpy = (4,4'-dicarboxy-2,2'-bipyridine)], via ab initio molecular dynamics. Phys Chem Chem Phys 2021; 23:22885-22896. [PMID: 34668499 DOI: 10.1039/d1cp03151a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Environmental effects can drastically influence the optical properties and photoreactivity of molecules, particularly in the presence of polar and/or protic solvents. In this work we investigate a negatively charged Ru(II) complex, [Ru(dcbpy)2(NCS)2]4- [dcbpy = (4,4'-dicarboxy-2,2'-bipyridine)], in water solution, since this system belongs to a broader class of transition-metal compounds undergoing upon photo-excitation rapid and complex charge transfer (CT) dynamics, which can be dictated by structural rearrangement and solvent environment. Ab initio molecular dynamics (AIMD) relying on a hybrid quantum/molecular mechanics scheme is used to probe the equilibrium microsolvation around the metal complex in terms of radial distribution functions of the main solvation sites and solvent effects on the overall equilibrium structure. Then, using our AIMD-based generalized normal mode approach, we investigate how the ligand vibrational spectroscopic features are affected by water solvation, also contributing to the interpretation of experimental Infra-Red spectra. Two solvation sites are found for the ligands: the sulfur and the oxygen sites can interact on average with ∼4 and ∼3 water molecules, respectively, where a stronger interaction of the oxygen sites is highlighted. On average an overall dynamic distortion of the C2 symmetric gas-phase structure was found to be induced by water solvation. Vibrational analysis reproduced experimental values for ligand symmetric and asymmetric stretchings, linking the observed shifts with respect to the gas-phase to a complex solvent distribution around the system. This is the groundwork for future excited-state nuclear and electronic dynamics to monitor non-equilibrium processes of CT excitation in complex environments, such as exciton migration in photovoltaic technologies.
Collapse
Affiliation(s)
- Fulvio Perrella
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy.
| | - Alessio Petrone
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy. .,Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138, Napoli, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M.S. Angelo, via Cintia 21, I-80126, Napoli, Italy. .,Scuola Superiore Meridionale, Largo San Marcellino 10, I-80138, Napoli, Italy.,CRIB, Centro Interdipartimentale di Ricerca sui Biomateriali, Piazzale Tecchio 80, I-80125, Napoli, Italy
| |
Collapse
|
12
|
Epitope-imprinted polymers for biomacromolecules: Recent strategies, future challenges and selected applications. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116414] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
13
|
Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
Collapse
Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
| | | |
Collapse
|
14
|
Coppola F, Perrella F, Petrone A, Donati G, Rega N. A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics. Front Mol Biosci 2020; 7:569990. [PMID: 33195416 PMCID: PMC7653547 DOI: 10.3389/fmolb.2020.569990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues).
Collapse
Affiliation(s)
- Federico Coppola
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Fulvio Perrella
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessio Petrone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Greta Donati
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Nadia Rega
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
| |
Collapse
|
15
|
Donati G, Petrone A, Rega N. Multiresolution continuous wavelet transform for studying coupled solute-solvent vibrations via ab initio molecular dynamics. Phys Chem Chem Phys 2020; 22:22645-22661. [PMID: 33015693 DOI: 10.1039/d0cp02495c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Vibrational analysis in solution and the theoretical determination of infrared and Raman spectra are of key importance in many fields of chemical interest. Vibrational band dynamics of molecules and their sensitivity to the environment can also be captured by these spectroscopies in their time dependent version. However, it is often difficult to provide an interpretation of the experimental data at the molecular scale, such as molecular mechanisms or the processes hidden behind them. In this work, we present a theoretical-computational protocol based on ab initio molecular dynamics simulations and a combination of normal-like (generalized) mode analysis of solute-solvent clusters with a wavelet transform, for the first time. The case study is the vibrational dynamics of N-methyl-acetamide (NMA) in water solution, a well-known model of hydration of peptides and proteins. Amide modes are typical bands of peptide and protein backbone, and their couplings with the environment are very challenging in terms of the accurate prediction of solvent induced intensity and frequency shifts. The contribution of water molecules surrounding NMA to the composition of generalized and time resolved modes is introduced in our vibrational analysis, showing unequivocally its influence on the amide mode spectra. It is also shown that such mode compositions need the inclusion of the first shell solvent molecules to be accurately described. The wavelet analysis is proven to be strongly recommended to follow the time evolution of the spectra, and to capture vibrational band couplings and frequency shifts over time, preserving at the same time a well-balanced time-frequency resolution. This peculiar feature also allows one to perform a combined structural-vibrational analysis, where the different strengths of hydrogen bond interactions can quantitatively affect the amide bands over time at finite temperature. The proposed method allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, in this case the peptide backbone, and its hydration layouts.
Collapse
Affiliation(s)
- Greta Donati
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario di M. S. Angelo, Via Cintia, I-80126 Napoli, Italy.
| | | | | |
Collapse
|
16
|
Li Y, Tan J, Huang L, Chen Y, Lin Q. A Portable Visual Sensor by Molecularly Imprinted Hydrogels for HRP Recognition. CURR ANAL CHEM 2020. [DOI: 10.2174/1573411015666190723151351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Molecular imprinting is a technology used to produce artificial receptors
that simulate the molecular recognition in the nature and prepare the polymer network structure in the
presence of template molecule. Molecularly imprinted visual sensor combines the advantages of specific
recognition via molecular imprinting and fast response speed via visualization. The aims of this
paper are to prepare a portable visual sensor for Horseradish Peroxidase (HRP) recognition based on
molecularly imprinted hydrogel.
Methods:
At first, HRP-imprinted polyacrylamide hydrogels with 1 mm thickness were obtained by
one-step synthesis via radical induced in-situ polymerization of acrylamide using acrylamide (AAm)
as the functional monomer, N,N'-Methylenebisacrylamide (MBA) as the crosslink agent and HRP as
the template molecule.
Results:
Compared with nonimprinted hydrogels, the HRP-imprinted hydrogel sensor showed significant
color changes in response to the target HRP. This visual sensor was constructed based on 3, 3',
5, 5'- tetramethyl benzidine (TMB) - H2O2 color reaction system by HRP catalyzing to produce color
change through digital photography and image analysis (RGB system). The HRP-imprinted hydrogel
showed good response in the range of 0.001-0.5 mg/mL and had a significant specific recognition
compared to other proteins via selective test.
Conclusion:
The proposed portable visual sensor could be used for qualitative and semi-quantitative
analysis of HRP with high selectivity and reasonable regeneration. The sensor has the advantages of
simple operation, low cost, no special equipment, and can be applied to serum sample with less sample
consumption and no need of sample preparation. It has wide application prospects in microfluidic
devices, biomimetic sensors, flexible biosensor and membrane separation technology.
Collapse
Affiliation(s)
- Yanxia Li
- Department of Chemical Engineering, Ocean College, Minjiang University, Fuzhou, 350108, China
| | - Juanjuan Tan
- Department of Chemical Engineering, Ocean College, Minjiang University, Fuzhou, 350108, China
| | - Lu Huang
- Department of Chemical Engineering, Ocean College, Minjiang University, Fuzhou, 350108, China
| | - Yiting Chen
- Department of Chemical Engineering, Ocean College, Minjiang University, Fuzhou, 350108, China
| | - Qi Lin
- Department of Chemical Engineering, Ocean College, Minjiang University, Fuzhou, 350108, China
| |
Collapse
|
17
|
Raucci U, Perrella F, Donati G, Zoppi M, Petrone A, Rega N. Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study. J Comput Chem 2020; 41:2228-2239. [PMID: 32770577 DOI: 10.1002/jcc.26384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 12/15/2022]
Abstract
Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.
Collapse
Affiliation(s)
- Umberto Raucci
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Fulvio Perrella
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Greta Donati
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, Fisciano, Italy
| | - Maria Zoppi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Alessio Petrone
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy
| | - Nadia Rega
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S. Angelo, Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Naples, Italy
| |
Collapse
|
18
|
Regasa MB, Refera Soreta T, Femi OE, C. Ramamurthy P. Development of Molecularly Imprinted Conducting Polymer Composite Film-Based Electrochemical Sensor for Melamine Detection in Infant Formula. ACS OMEGA 2020; 5:4090-4099. [PMID: 32149237 PMCID: PMC7057703 DOI: 10.1021/acsomega.9b03747] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/03/2020] [Indexed: 05/02/2023]
Abstract
Simple, fast, and sensitive molecularly imprinted composite thin-film-based electrochemical sensor developed by using in situ co-electropolymerization of aniline and acrylic acid in the presence of melamine as a template is described here. The prepolymerization complex formation was studied by using Fourier transform infrared (FTIR) spectrophotometry, while the film formation was performed and characterized by cyclic voltammetry, Fourier transform infrared (FTIR), and scanning electron microscopy (SEM). The optimization of important parameters and removal of melamine generated the binding sites in the polymer matrix, which can recognize melamine specifically. Electrochemical measurements were performed to achieve the linear range, the limit of quantification, and limit of detection of 0.1-180, 0.0573, and 0.0172 nM, respectively. The sensitivity of the sensor was attributed to the synergistic effects of amine from aniline and the carboxylic group from acrylic acid to form multiple noncovalent interactions with the template. Melamine-spiked infant formula and raw milk were analyzed by the developed sensor, and the recovery range of 95.87-105.63% with a relative standard deviation of 1.11-2.23% was obtained. The results showed that the developed sensor using the new composite polymer receptor is promising for the online monitoring of melamine in the food industries in the future.
Collapse
Affiliation(s)
- Melkamu Biyana Regasa
- School
of Materials Science and Engineering, Jimma
Institute of Technology, Jimma University, Jimma 378, Ethiopia
| | - Tesfaye Refera Soreta
- Materials
Engineering Department, Addis Ababa Institute
of Technology, Addis Ababa University, Addis Ababa 1000, Ethiopia
| | - Olu Emmanuel Femi
- School
of Materials Science and Engineering, Jimma
Institute of Technology, Jimma University, Jimma 378, Ethiopia
| | - Praveen C. Ramamurthy
- Materials
Engineering Department, Indian Institute
of Science, Bangalore 560012, India
| |
Collapse
|
19
|
Saylan Y, Akgönüllü S, Yavuz H, Ünal S, Denizli A. Molecularly Imprinted Polymer Based Sensors for Medical Applications. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1279. [PMID: 30871280 PMCID: PMC6472044 DOI: 10.3390/s19061279] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/04/2019] [Accepted: 03/10/2019] [Indexed: 02/08/2023]
Abstract
Sensors have been extensively used owing to multiple advantages, including exceptional sensing performance, user-friendly operation, fast response, high sensitivity and specificity, portability, and real-time analysis. In recent years, efforts in sensor realm have expanded promptly, and it has already presented a broad range of applications in the fields of medical, pharmaceutical and environmental applications, food safety, and homeland security. In particular, molecularly imprinted polymer based sensors have created a fascinating horizon for surface modification techniques by forming specific recognition cavities for template molecules in the polymeric matrix. This method ensures a broad range of versatility to imprint a variety of biomolecules with different size, three dimensional structure, physical and chemical features. In contrast to complex and time-consuming laboratory surface modification methods, molecular imprinting offers a rapid, sensitive, inexpensive, easy-to-use, and highly selective approaches for sensing, and especially for the applications of diagnosis, screening, and theranostics. Due to its physical and chemical robustness, high stability, low-cost, and reusability features, molecularly imprinted polymer based sensors have become very attractive modalities for such applications with a sensitivity of minute structural changes in the structure of biomolecules. This review aims at discussing the principle of molecular imprinting method, the integration of molecularly imprinted polymers with sensing tools, the recent advances and strategies in molecular imprinting methodologies, their applications in medical, and future outlook on this concept.
Collapse
Affiliation(s)
- Yeşeren Saylan
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
| | - Semra Akgönüllü
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
| | - Handan Yavuz
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
| | - Serhat Ünal
- Department of Infectious Disease and Clinical Microbiology, Hacettepe University, Ankara 06230, Turkey.
| | - Adil Denizli
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey.
| |
Collapse
|
20
|
Di Natale C, Celetti G, Scognamiglio PL, Cosenza C, Battista E, Causa F, Netti PA. Molecularly endowed hydrogel with an in silico-assisted screened peptide for highly sensitive small molecule harvesting. Chem Commun (Camb) 2018; 54:10088-10091. [DOI: 10.1039/c8cc04943b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Schematic representation of in silico-assisted screening of an AFM1 binding peptide and the working principle of toxin harvesting by molecularly endowed hydrogel.
Collapse
Affiliation(s)
- Concetta Di Natale
- Center for Advanced Biomaterials for Healthcare
- Istituto Italiano di Tecnologia (IIT)
- Naples 80125
- Italy
| | - Giorgia Celetti
- Center for Advanced Biomaterials for Healthcare
- Istituto Italiano di Tecnologia (IIT)
- Naples 80125
- Italy
| | | | - Chiara Cosenza
- Interdisciplinary Research Centre on Biomaterials (CRIB)
- University “Federico II”
- Naples 80125
- Italy
| | - Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB)
- University “Federico II”
- Naples 80125
- Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare
- Istituto Italiano di Tecnologia (IIT)
- Naples 80125
- Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB)
| | - Paolo A. Netti
- Center for Advanced Biomaterials for Healthcare
- Istituto Italiano di Tecnologia (IIT)
- Naples 80125
- Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB)
| |
Collapse
|