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Porcu S, Corpino R, Carbonaro CM, Ricci PC, Vargiu AV, Sanna AL, Sforazzini G, Chiriu D. Promising Molecular Architectures for Two-Photon Probes in the Diagnosis of α-Synuclein Aggregates. Molecules 2024; 29:2817. [PMID: 38930882 PMCID: PMC11207056 DOI: 10.3390/molecules29122817] [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: 04/18/2024] [Revised: 05/24/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The abnormal deposition of protein in the brain is the central factor in neurodegenerative disorders (NDs). These detrimental aggregates, stemming from the misfolding and subsequent irregular aggregation of α-synuclein protein, are primarily accountable for conditions such as Parkinson's disease, Alzheimer's disease, and dementia. Two-photon-excited (TPE) probes are a promising tool for the early-stage diagnosis of these pathologies as they provide accurate spatial resolution, minimal intrusion, and the ability for prolonged observation. To identify compounds with the potential to function as diagnostic probes using two-photon techniques, we explore three distinct categories of compounds: Hydroxyl azobenzene (AZO-OH); Dicyano-vinyl bithiophene (DCVBT); and Tetra-amino phthalocyanine (PcZnNH2). The molecules were structurally and optically characterized using a multi-technique approach via UV-vis absorption, Raman spectroscopy, three-dimensional fluorescence mapping (PLE), time-resolved photoluminescence (TRPL), and pump and probe measurements. Furthermore, quantum chemical and molecular docking calculations were performed to provide insights into the photophysical properties of the compounds as well as to assess their affinity with the α-synuclein protein. This innovative approach seeks to enhance the accuracy of in vivo probing, contributing to early Parkinson's disease (PD) detection and ultimately allowing for targeted intervention strategies.
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Affiliation(s)
- Stefania Porcu
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
| | - Riccardo Corpino
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
| | - Carlo Maria Carbonaro
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
| | - Pier Carlo Ricci
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
| | - Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
| | - Anna Laura Sanna
- Department of Chemistry and Hearth Science, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy;
| | - Giuseppe Sforazzini
- Department of Chemistry and Hearth Science, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy;
| | - Daniele Chiriu
- Department of Physics, University of Cagliari, Cittadella Universitaria, SP n°8, 09042 Monserrato, CA, Italy; (S.P.); (R.C.); (C.M.C.); (P.C.R.); (A.V.V.)
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Murugan NA, Zaleśny R. Computational Investigations into Two-Photon Fibril Imaging Using the DANIR-2c Probe. J Phys Chem B 2023; 127:3119-3125. [PMID: 37015058 PMCID: PMC10108348 DOI: 10.1021/acs.jpcb.2c07783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The design of novel fibril imaging molecules for medical diagnosis requires the simultaneous optimization of fibril-specific optical properties and binding specificity toward amyloid fibrils. Because of the possibility to monitor internal organs and deep tissues, the two-photon probes that can absorb in the infrared (IR) and near-IR (NIR) region with a significant two-photon absorption cross section are of immense interest. To contribute to this exploration of chemical compounds suitable for two-photon fibril imaging, we have computationally studied the one- and two-photon properties of a donor-acceptor-substituted DANIR-2c probe, which was used for in vivo detection of β-amyloid deposits using fluorescence spectroscopy. In particular, a multiscale computational approach was employed involving molecular docking, molecular dynamics, hybrid QM/MM molecular dynamics, and coupled-cluster/MM to study the binding of the studied probe to amyloid fibril and its one- and two-photon absorption properties in the fibrillar environment. Multiple binding sites are available for this probe in amyloid fibril, and the one corresponding to the largest binding affinity exhibits also the largest and experimentally meaningful two-photon absorption cross section, thus demonstrating the potential of the studied probe in two-photon microscopy.
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Affiliation(s)
- N Arul Murugan
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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Zhang M, Fu H, Hu W, Leng J, Zhang Y. Versatile Dicyanomethylene-Based Fluorescent Probes for the Detection of β-Amyloid in Alzheimer's Disease: A Theoretical Perspective. Int J Mol Sci 2022; 23:8619. [PMID: 35955758 PMCID: PMC9369443 DOI: 10.3390/ijms23158619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/05/2023] Open
Abstract
Motivated by the growing demand for target chemosensors designed with diagnostic or therapeutic capability for fibrils related to amyloidosis diseases, we investigated in the present work the response mechanism of dicyanomethylene-based fluorescent probes for amyloid fibril using a combined approach, including molecular docking, quantum mechanics/molecular mechanics (QM/MM), and the quantum chemical method. Various binding modes for the probes in β-amyloid (Aβ) are discussed, and the fibril environment-induced molecular optical changes at the most stable site are compared to the fibril-free situation in aqueous environments. The results reveal that the fluorescence enhancement for the probes in Aβ observed experimentally is an average consequence over multiple binding sites. In particular, the conformational difference, including conjugation length and donor effect, significantly contributes to the optical property of the studied probes both in water and fibril. To further estimate the transition nature of the molecular photoabsorption and photoemission processes, the hole-electron distribution and the structural variation on the first excited state of the probes are investigated in detail. On the basis of the calculations, structure-property relationships for the studied chemosensors are established. Our computational approach with the ability to elucidate the available experimental results can be used for designing novel molecular probes with applications to Aβ imaging and the early diagnosis of Alzheimer's disease.
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Affiliation(s)
| | | | | | - Jiancai Leng
- International School for Optoelectronic Engineering, School of Electrical Engineering and Automation, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; (M.Z.); (H.F.); (W.H.)
| | - Yujin Zhang
- International School for Optoelectronic Engineering, School of Electrical Engineering and Automation, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; (M.Z.); (H.F.); (W.H.)
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Saini A, Singh J, Kumar S. Optically superior fluorescent probes for selective imaging of cells, tumors, and reactive chemical species. Org Biomol Chem 2021; 19:5208-5236. [PMID: 34037048 DOI: 10.1039/d1ob00509j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fluorescent chemical probes have become powerful tools to study biological events in living cells. They provide a great opportunity to quantitatively and qualitatively analyze the physiological and biochemical properties of living cells in real time. The ability of researchers to manipulate these probes for a desired specific purpose has turned many heads in the scientific community. Despite a slow start, fluorescent probe research has seen exponential growth over the last decade in the world. This change required some adventurous and creative scientists from different fields-like biology, medicine, and chemistry-to come together to facilitate the constant expansion of this field. This review article introduces some fundamental concepts related to fluorescent probe designing and development. It also summarizes various fluorescent probes with superior optical properties used in fields like cell biology, cellular imaging, medical research, and cancer diagnosis. It is hoped that this article will encourage more young and creative scientists to contribute their talents to this field.
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Affiliation(s)
- Abhishek Saini
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
| | - Jyoti Singh
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
| | - Sonu Kumar
- Department of Chemistry, Hansraj College, University of Delhi, Delhi-110007, India.
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Ahmadzadeh K, Scott M, Brand M, Vahtras O, Li X, Rinkevicius Z, Norman P. Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation. J Chem Phys 2021; 154:024111. [PMID: 33445884 DOI: 10.1063/5.0031851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only ∼3.3% (one-photon off-resonance regions) and ∼10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than ∼5% when using the reduced expression as compared to the full form of the isotropic cubic response function.
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Affiliation(s)
- Karan Ahmadzadeh
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mikael Scott
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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