1
|
Sobek J, Li J, Combes BF, Gerez JA, Henrich MT, Geibl FF, Nilsson PR, Shi K, Rominger A, Oertel WH, Nitsch RM, Nordberg A, Ågren H, Ni R. Efficient characterization of multiple binding sites of small molecule imaging ligands on amyloid-beta, tau and alpha-synuclein. Eur J Nucl Med Mol Imaging 2024:10.1007/s00259-024-06806-7. [PMID: 38953933 DOI: 10.1007/s00259-024-06806-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]
Abstract
PURPOSE There is an unmet need for compounds to detect fibrillar forms of alpha-synuclein (αSyn) and 4-repeat tau, which are critical in many neurodegenerative diseases. Here, we aim to develop an efficient surface plasmon resonance (SPR)-based assay to facilitate the characterization of small molecules that can bind these fibrils. METHODS SPR measurements were conducted to characterize the binding properties of fluorescent ligands/compounds toward recombinant amyloid-beta (Aβ)42, K18-tau, full-length 2N4R-tau and αSyn fibrils. In silico modeling was performed to examine the binding pockets of ligands on αSyn fibrils. Immunofluorescence staining of postmortem brain tissue slices from Parkinson's disease patients and mouse models was performed with fluorescence ligands and specific antibodies. RESULTS We optimized the protocol for the immobilization of Aβ42, K18-tau, full-length 2N4R-tau and αSyn fibrils in a controlled aggregation state on SPR-sensor chips and for assessing their binding to ligands. The SPR results from the analysis of binding kinetics suggested the presence of at least two binding sites for all fibrils, including luminescent conjugated oligothiophenes, benzothiazole derivatives, nonfluorescent methylene blue and lansoprazole. In silico modeling studies for αSyn (6H6B) revealed four binding sites with a preference for one site on the surface. Immunofluorescence staining validated the detection of pS129-αSyn positivity in the brains of Parkinson's disease patients and αSyn preformed-fibril injected mice, 6E10-positive Aβ in arcAβ mice, and AT-8/AT-100-positivity in pR5 mice. CONCLUSION SPR measurements of small molecules binding to Aβ42, K18/full-length 2N4R-tau and αSyn fibrils suggested the existence of multiple binding sites. This approach may provide efficient characterization of compounds for neurodegenerative disease-relevant proteinopathies.
Collapse
Affiliation(s)
- Jens Sobek
- Functional Genomics Center, University of Zurich & ETH Zurich, Zürich, Switzerland
| | - Junhao Li
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Benjamin F Combes
- Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952, Zürich, Switzerland
| | - Juan A Gerez
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zürich, Switzerland
| | - Martin T Henrich
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
- Department of Neurology, Philipps-University Marburg, Marburg, Germany
| | - Fanni F Geibl
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
- Department of Neurology, Philipps-University Marburg, Marburg, Germany
| | - Peter R Nilsson
- Divison of Chemistry, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Kuangyu Shi
- Department of Nuclear Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Axel Rominger
- Department of Nuclear Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Wolfgang H Oertel
- Department of Psychiatry and Psychotherapy, Philipps-University Marburg, Marburg, Germany
- Department of Neurology, Philipps-University Marburg, Marburg, Germany
| | - Roger M Nitsch
- Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952, Zürich, Switzerland
| | - Agneta Nordberg
- Divison of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Hans Ågren
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Ruiqing Ni
- Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952, Zürich, Switzerland.
- Department of Nuclear Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zürich, Switzerland.
| |
Collapse
|
2
|
Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [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: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
Collapse
Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
| |
Collapse
|
3
|
Uzuegbunam BC, Li J, Paslawski W, Weber W, Svenningsson P, Ågren H, Hooshyar Yousefi B. In Silico and In Vitro Study towards the Rational Design of 4,4'-Disarylbisthiazoles as a Selective α-Synucleinopathy Biomarker. Int J Mol Sci 2023; 24:16445. [PMID: 38003637 PMCID: PMC10671360 DOI: 10.3390/ijms242216445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The α-synucleinopathies are a group of neurodegenerative diseases characterized by the deposition of α-synuclein aggregates (α-syn) in the brain. Currently, there is no suitable tracer to enable a definitive early diagnosis of these diseases. We reported candidates based on 4,4'-disarylbisthiazole (DABTA) scaffold with a high affinity towards α-syn and excellent selectivity over Aβ and tau fibrils. Based on prior in silico studies, a focused library of 23 halogen-containing and O-methylated DABTAs was prepared. The DABTAs were synthesized via a modified two-step Hantzsch thiazole synthesis, characterized, and used in competitive binding assays against [3H]PiB and [3H]DCVJ. The DABTAs were obtained with an overall chemical yield of 15-71%, and showed a calculated lipophilicity of 2.5-5.7. The ligands demonstrated an excellent affinity to α-syn with both [3H]PiB and [3H]DCVJ: Ki 0.1-4.9 nM and up to 20-3900-fold selectivity over Aβ and tau fibrils. It could be concluded that in silico simulation is useful for the rational design of a new generation of DABTAs. Further investigation of the leads in the next step is encouraged: radiolabeling of the ligands with radioisotopes such as fluorine-18 or carbon-11 for in vivo, ex vivo, and translational research and for further in vitro experiments on human-derived protein aggregates.
Collapse
Affiliation(s)
- Bright C. Uzuegbunam
- Department of Nuclear Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Junhao Li
- Department of Physics and Astronomy, Uppsala University, 751 20 Uppsala, Sweden
| | - Wojciech Paslawski
- Department of Clinical Neuroscience, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Wolfgang Weber
- Department of Nuclear Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Hans Ågren
- Department of Physics and Astronomy, Uppsala University, 751 20 Uppsala, Sweden
| | | |
Collapse
|
4
|
Kaur G, Mankoo OK, Goyal D, Goyal B. Unveiling How Hydroxytyrosol Destabilizes α-Syn Oligomers Using Molecular Simulations. J Phys Chem B 2023. [PMID: 37319389 DOI: 10.1021/acs.jpcb.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The etiology of Parkinson's disease (PD) is mainly linked to the α-synuclein (α-Syn) fibrillogenesis. Hydroxytyrosol (HT), also known as 3,4-dihydroxyphenylethanol, is a naturally occurring polyphenol, found in extra virgin olive oil, and has been shown to have cardioprotective, anticancer, antiobesity, and antidiabetic properties. HT has neuroprotective benefits in neurodegenerative diseases and lessens the severity of PD by reducing the aggregation of α-Syn and destabilizing the preformed toxic α-Syn oligomers. However, the molecular mechanism by which HT destabilizes α-Syn oligomers and alleviates the accompanying cytotoxicity remains unexplored. The impact of HT on the α-Syn oligomer structure and its potential binding mechanism was examined in this work by employing molecular dynamics (MD) simulations. The secondary structure analysis depicted that HT significantly reduces the β-sheet and concomitantly increases the coil content of α-Syn trimer. Visualization of representative conformations from the clustering analysis depicted the hydrogen bond interactions of the hydroxyl groups in HT with the N-terminal and nonamyloid-β component (NAC) region residues of α-Syn trimer, which, in turn, leads to the weakening of interchain interactions in α-Syn trimer and resulted in the disruption of the α-Syn oligomer. The binding free energy calculations depict that HT binds favorably to α-Syn trimer (ΔGbinding = -23.25 ± 7.86 kcal/mol) and a notable reduction in the interchain binding affinity of α-Syn trimer on the incorporation of HT, which, in turn, highlights its potential to disrupt α-Syn oligomers. The current research provided mechanistic insights into the destabilization of α-Syn trimer by HT, which, in turn, will provide new clues for developing therapeutics against PD.
Collapse
Affiliation(s)
- Gagandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh-160011, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147004, Punjab, India
| |
Collapse
|
5
|
Mankoo OK, Kaur A, Goyal D, Goyal B. Unravelling the destabilization potential of ellagic acid on α-synuclein fibrils using molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:8128-8143. [PMID: 36877087 DOI: 10.1039/d2cp06006j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The aberrant deposition of α-synuclein (α-Syn) protein into the intracellular neuronal aggregates termed Lewy bodies and Lewy neurites characterizes the devastating neurodegenerative condition known as Parkinson's disease (PD). The disruption of pre-existing disease-relevant α-Syn fibrils is recognized as a viable therapeutic approach for PD. Ellagic acid (EA), a natural polyphenolic compound, is experimentally proven as a potential candidate that prevents or reverses the α-Syn fibrillization process. However, the detailed inhibitory mechanism of EA against the destabilization of α-Syn fibril remains largely unclear. In this work, the influence of EA on α-Syn fibril and its putative binding mechanism were explored using molecular dynamics (MD) simulations. EA interacted primarily with the non-amyloid-β component (NAC) of α-Syn fibril, disrupting its β-sheet content and thereby increasing the coil content. The E46-K80 salt bridge, critical for the stability of Greek-key-like α-Syn fibril, was disrupted in the presence of EA. The binding free energy analysis using the MM-PBSA method demonstrates the favourable binding of EA to α-Syn fibril (ΔGbinding = -34.62 ± 11.33 kcal mol-1). Interestingly, the binding affinity between chains H and J of the α-Syn fibril was significantly reduced on the incorporation of EA, which highlights the disruptive ability of EA towards α-Syn fibril. The MD simulations provide mechanistic insights into the α-Syn fibril disruption by EA, which gives a valuable direction for the development of potential inhibitors of α-Syn fibrillization and its associated cytotoxicity.
Collapse
Affiliation(s)
- Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anupamjeet Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh 160011, India.
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry, Thapar Institute of Engineering & Technology, Patiala 147004, Punjab, India.
| |
Collapse
|
6
|
Prange S, Theis H, Banwinkler M, van Eimeren T. Molecular Imaging in Parkinsonian Disorders—What’s New and Hot? Brain Sci 2022; 12:brainsci12091146. [PMID: 36138882 PMCID: PMC9496752 DOI: 10.3390/brainsci12091146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022] Open
Abstract
Highlights Abstract Neurodegenerative parkinsonian disorders are characterized by a great diversity of clinical symptoms and underlying neuropathology, yet differential diagnosis during lifetime remains probabilistic. Molecular imaging is a powerful method to detect pathological changes in vivo on a cellular and molecular level with high specificity. Thereby, molecular imaging enables to investigate functional changes and pathological hallmarks in neurodegenerative disorders, thus allowing to better differentiate between different forms of degenerative parkinsonism, improve the accuracy of the clinical diagnosis and disentangle the pathophysiology of disease-related symptoms. The past decade led to significant progress in the field of molecular imaging, including the development of multiple new and promising radioactive tracers for single photon emission computed tomography (SPECT) and positron emission tomography (PET) as well as novel analytical methods. Here, we review the most recent advances in molecular imaging for the diagnosis, prognosis, and mechanistic understanding of parkinsonian disorders. First, advances in imaging of neurotransmission abnormalities, metabolism, synaptic density, inflammation, and pathological protein aggregation are reviewed, highlighting our renewed understanding regarding the multiplicity of neurodegenerative processes involved in parkinsonian disorders. Consequently, we review the role of molecular imaging in the context of disease-modifying interventions to follow neurodegeneration, ensure stratification, and target engagement in clinical trials.
Collapse
Affiliation(s)
- Stéphane Prange
- Multimodal Neuroimaging Group, Department of Nuclear Medicine, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Institut des Sciences Cognitives Marc Jeannerod, CNRS, UMR 5229, Université de Lyon, 69675 Bron, France
- Correspondence: (S.P.); (T.v.E.); Tel.: +49-221-47882843 (T.v.E.)
| | - Hendrik Theis
- Multimodal Neuroimaging Group, Department of Nuclear Medicine, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Department of Neurology, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
| | - Magdalena Banwinkler
- Multimodal Neuroimaging Group, Department of Nuclear Medicine, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
| | - Thilo van Eimeren
- Multimodal Neuroimaging Group, Department of Nuclear Medicine, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Department of Neurology, Faculty of Medicine, University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
- Correspondence: (S.P.); (T.v.E.); Tel.: +49-221-47882843 (T.v.E.)
| |
Collapse
|
7
|
Uzuegbunam BC, Li J, Paslawski W, Weber W, Svenningsson P, Ågren H, Yousefi BH. Toward Novel [18F]Fluorine-Labeled Radiotracers for the Imaging of α-Synuclein Fibrils. Front Aging Neurosci 2022; 14:830704. [PMID: 35572127 PMCID: PMC9099256 DOI: 10.3389/fnagi.2022.830704] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/27/2022] [Indexed: 12/05/2022] Open
Abstract
The accumulation of α-synuclein aggregates (α-syn) in the human brain is an occurrence common to all α-synucleinopathies. Non-invasive detection of these aggregates in a living brain with a target-specific radiotracer is not yet possible. We have recently discovered that the inclusion of a methylenedioxy group in the structure of diarylbisthiazole (DABTA)-based tracers improves binding affinity and selectivity to α-syn. Subsequently, complementary in silico modeling and machine learning (ML) of tracer–protein interactions were employed to predict surface sites and structure–property relations for the binding of the ligands. Based on this observation, we developed a small focused library of DABTAs from which 4-(benzo[d][1,3]dioxol-5-yl)-4′-(3-[18F]fluoro-4-methoxyphenyl)-2,2′-bithiazole [18F]d2, 6-(4′-(3-[18F]fluoro-4-methoxyphenyl)-[2,2′-bithiazol]-4-yl)-[1,3]dioxolo[4,5-b]pyridine [18F]d4, 4-(benzo [d][1,3]dioxol-5-yl)-4′-(6-[18F]fluoropyridin-3-yl)-2,2′-bithiazole [18F]d6, and 6-(4′-(6-[18F]fluoropyridin-3-yl)-[2,2′-bithiazol]-4-yl)-[1,3]dioxolo[4,5-b]pyridine [18F]d8 were selected based on their high binding affinity to α-syn and were further evaluated. Binding assay experiments carried out with the non-radioactive versions of the above tracers d2, d4, d6, and d8 showed high binding affinity of the ligands to α-syn: 1.22, 0.66, 1.21, and 0.10 nM, respectively, as well as excellent selectivity over β-amyloid plaques (Aβ) and microtubular tau aggregates (>200-fold selectivity). To obtain the tracers, their precursors were radiolabeled either via an innovative ruthenium-mediated (SNAr) reaction ([18F]d2 and [18F]d4) or typical SNAr reaction ([18F]d6 and [18F]d8) with moderate-to-high radiochemical yields (13% – 40%), and high molar activity > 60 GBq/μmol. Biodistribution experiments carried out with the tracers in healthy mice revealed that [18F]d2 and [18F]d4 showed suboptimal brain pharmacokinetics: 1.58 and 4.63 %ID/g at 5 min post-injection (p.i.), and 1.93 and 3.86 %ID/g at 60 min p.i., respectively. However, [18F]d6 and [18F]d8 showed improved brain pharmacokinetics: 5.79 and 5.13 %ID/g at 5 min p.i.; 1.75 and 1.07 %ID/g at 60 min p.i.; and 1.04 and 0.58 %ID/g at 120 min p.i., respectively. The brain uptake kinetics of [18F]d6 and [18F]d8 were confirmed in a dynamic PET study. Both tracers also showed no brain radiometabolites at 20 min p.i. in initial in vivo stability experiments carried out in healthy mice. [18F]d8 seems very promising based on its binding properties and in vivo stability, thus encouraging further validation of its usefulness as a radiotracer for the in vivo visualization of α-syn in preclinical and clinical settings. Additionally, in silico and ML-predicted values correlated with the experimental binding affinity of the ligands.
Collapse
Affiliation(s)
| | - Junhao Li
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Wojciech Paslawski
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Wolfgang Weber
- Department of Nuclear Medicine, Technical University of Munich, Munich, Germany
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Hans Ågren
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Behrooz Hooshyar Yousefi
- Department of Nuclear Medicine, Philipps University of Marburg, Marburg, Germany
- *Correspondence: Behrooz Hooshyar Yousefi,
| |
Collapse
|
8
|
Biswas B, Dogra S, Dey G, Murugan NA, Mondal P, Ghosh S. Near-infrared emissive cyanine probes for selective visualization of the physiological and pathophysiological modulation of albumin levels. J Mater Chem B 2022; 10:3657-3666. [PMID: 35421884 DOI: 10.1039/d1tb02613e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With the promising advantages of the near-infrared region (NIR) emissive markers for serum albumin becoming very prominent recently, we devised CyG-NHS as the cyanine derived longest NIR-I emissive optical marker possessing albumin selective recognition ability in diverse biological milieu. Multiscale modeling involving molecular docking, molecular dynamics, and implicit solvent binding free energy calculations have been employed to gain insights into the unique binding ability of the developed probe at domain-I of albumin, in contrast to the good number of domain IIA or IIIA binding probes available in the literature reports. The binding free energy was found to be -31.8 kcal mol-1 majorly predominated by hydrophobic interactions. Besides, the conformational dynamics of CyG-NHS in an aqueous medium and the albumin microenvironment have been comprehensively studied and discussed. The potentiality of this optical platform to monitor the intracellular albumin levels in human hepatoma (HepG2) cells in different pathophysiological states has been demonstrated here. Also, the competency of the phenformin drug in restoring the albumin levels in chronic hyperinsulinemic and hypercholesterolemic in vitro models has been established through the visualization approach. Altogether, the findings of this study throw light on the significance of the development of a suitable optical marker for the visualization of critical bioevents related to albumin.
Collapse
Affiliation(s)
- Bidisha Biswas
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, 175001, Himachal Pradesh, India.
| | - Surbhi Dogra
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, 175001, Himachal Pradesh, India.
| | - Gourab Dey
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, 175001, Himachal Pradesh, India.
| | - N Arul Murugan
- Department of Computer Science, School of Electrical Engineering and Computer Science, KTH Royal Institute of Technology, S-100 44 Stockholm, Sweden. .,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, 110020, India
| | - Prosenjit Mondal
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, 175001, Himachal Pradesh, India.
| | - Subrata Ghosh
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, 175001, Himachal Pradesh, India.
| |
Collapse
|
9
|
Mondal IC, Galkin M, Sharma S, Murugan NA, Yushchenko DA, Girdhar K, Karmakar A, Mondal P, Gaur P, Ghosh S. Organosulfur/selenium-based Highly Fluorogenic Molecular Probes for Live-Cell Nucleolus Imaging. Chem Asian J 2022; 17:e202101281. [PMID: 35129298 DOI: 10.1002/asia.202101281] [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: 11/12/2021] [Revised: 01/16/2022] [Indexed: 11/10/2022]
Abstract
We present rationally designed cationic organochalcogens highly selective to RNA. We have demonstrated that the conformational dynamics and subsequently the optical properties of these dyes can be controlled to facilitate efficient bioimaging. We report organoselenium and organosulfur-based cell-permeable red-emissive probes bearing favorable cyclic sidearm with potential for selective and high contrast imaging of cell nucleoli. The probes exhibit high quantum yield upon interaction with RNA in an aqueous solution. An in-depth multiscale simulation study reveals that the prominent rotational freezing of the electron-donating sidearm of the probes in the microenvironment of RNA helps in attaining more planar conformation when compared to DNA. It exerts a greater extent of intramolecular charge transfer and hence leads to enhanced fluorescence emission. A systematic structure-interaction relationship study highlighted the impact of heavy-chalcogens toward the improved emissive properties of the probes.
Collapse
Affiliation(s)
| | - Maksym Galkin
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
| | - Shubham Sharma
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - N Arul Murugan
- KTH Royal Institute of Technology, Department of Computer Science, SWEDEN
| | - Dmytro A Yushchenko
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
| | - Khyati Girdhar
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - Anirban Karmakar
- Instituto Superior Tecnico Avenida Rovisco Pais, Centro de Quimica Estrutural, PORTUGAL
| | - Prosenjit Mondal
- IIT Mandi: Indian Institute of Technology Mandi, School of Basic Sciences, INDIA
| | - Pankaj Gaur
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Laboratory of Chemical Biology, CZECH REPUBLIC
| | | |
Collapse
|
10
|
Ni R, Nitsch RM. Recent Developments in Positron Emission Tomography Tracers for Proteinopathies Imaging in Dementia. Front Aging Neurosci 2022; 13:751897. [PMID: 35046791 PMCID: PMC8761855 DOI: 10.3389/fnagi.2021.751897] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
An early detection and intervention for dementia represent tremendous unmet clinical needs and priorities in society. A shared feature of neurodegenerative diseases causing dementia is the abnormal accumulation and spreading of pathological protein aggregates, which affect the selective vulnerable circuit in a disease-specific pattern. The advancement in positron emission tomography (PET) biomarkers has accelerated the understanding of the disease mechanism and development of therapeutics for Alzheimer's disease and Parkinson's disease. The clinical utility of amyloid-β PET and the clinical validity of tau PET as diagnostic biomarker for Alzheimer's disease continuum have been demonstrated. The inclusion of biomarkers in the diagnostic criteria has introduced a paradigm shift that facilitated the early and differential disease diagnosis and impacted on the clinical management. Application of disease-modifying therapy likely requires screening of patients with molecular evidence of pathological accumulation and monitoring of treatment effect assisted with biomarkers. There is currently still a gap in specific 4-repeat tau imaging probes for 4-repeat tauopathies and α-synuclein imaging probes for Parkinson's disease and dementia with Lewy body. In this review, we focused on recent development in molecular imaging biomarkers for assisting the early diagnosis of proteinopathies (i.e., amyloid-β, tau, and α-synuclein) in dementia and discussed future perspectives.
Collapse
Affiliation(s)
- Ruiqing Ni
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, ETH & University of Zurich, Zurich, Switzerland
| | - Roger M. Nitsch
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
Zhang X, Zhou J, Gu Z, Zhang H, Gong Q, Luo K. Advances in nanomedicines for diagnosis of central nervous system disorders. Biomaterials 2020; 269:120492. [PMID: 33153757 DOI: 10.1016/j.biomaterials.2020.120492] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/18/2020] [Accepted: 10/23/2020] [Indexed: 02/08/2023]
Abstract
In spite of a great improvement in medical health services and an increase in lifespan, we have witnessed a skyrocket increase in the incidence of central nervous system (CNS) disorders including brain tumors, neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease), ischemic stroke, and epilepsy, which have seriously undermined the quality of life and substantially increased economic and societal burdens. Development of diagnostic methods for CNS disorders is still in the early stage, and the clinical outcomes suggest these methods are not ready for the challenges associated with diagnosis of CNS disorders, such as early detection, specific binding, sharp contrast, and continuous monitoring of therapeutic interventions. Another challenge is to overcome various barrier structures during delivery of diagnostic agents, especially the blood-brain barrier (BBB). Fortunately, utilization of nanomaterials has been pursued as a potential and promising strategy to address these challenges. This review will discuss anatomical and functional structures of BBB and transport mechanisms of nanomaterials across the BBB, and special emphases will be placed on the state-of-the-art advances in the development of nanomedicines from a variety of nanomaterials for diagnosis of CNS disorders. Meanwhile, current challenges and future perspectives in this field are also highlighted.
Collapse
Affiliation(s)
- Xun Zhang
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Zhou
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhongwei Gu
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hu Zhang
- Amgen Bioprocessing Centre, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Kui Luo
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
12
|
Murugan NA, Zaleśny R. Multiscale Modeling of Two-Photon Probes for Parkinson's Diagnostics Based on Monoamine Oxidase B Biomarker. J Chem Inf Model 2020; 60:3854-3863. [PMID: 32786232 PMCID: PMC7458361 DOI: 10.1021/acs.jcim.0c00423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Monoamine oxidase B (MAO-B) is a potential biomarker for Parkinson's disease (PD), a neurodegenerative disease associated with the loss of motor activities in human subjects. The disease state is associated with dopamine deprival, and so the inhibitors of MAO-B can serve as therapeutic drugs for PD. Since the expression level of MAO-B directly correlates to the disease progress, the distribution and population of this enzyme can be employed to monitor disease development. One of the approaches available for estimating the population is two-photon imaging. The ligands used for two-photon imaging should have high binding affinity and binding specificity toward MAO-B along with significant two-photon absorption cross sections when they are bound to the target. In this article, we study using a multiscale modeling approach, the binding affinity and spectroscopic properties (one- and two-photon absorption) of three (Flu1, Flu2, Flu3) of the currently available probes for monitoring the MAO-B level. We report that the binding affinity of the probes can be explained using the molecular size and binding cavity volume. The experimentally determined one-photon absorption spectrum is well reproduced by the employed QM/MM approaches, and the most accurate spectral shifts, on passing from one probe to another, are obtained at the coupled-cluster (CC2) level of theory. An important conclusion from this study is also the demonstration that intrinsic molecular two-photon absorption strengths (δ2PA) increase in the order δ2PA (Flu1) > δ2PA (Flu2) > δ2PA (Flu3). This is in contrast with experimental data, which predict similar values of two-photon absorption cross sections for Flu1 and Flu3. We demontrate, based on the results of electronic-structure calculations for Flu1 that this discrepancy cannot be explained by an explicit account for neighboring residues (which could lead to charge transfer between a probe and neighboring aromatic amino acids thus boosting δ2PA). In summary, we show that the employed multiscale approach not only can optimize two-photon absorption properties and verify binding affinity, but it can also help in detailed analyses of experimental data.
Collapse
Affiliation(s)
- N Arul Murugan
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Robert Zaleśny
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
| |
Collapse
|
13
|
Auclair J, Peyrot C, Wilkinson KJ, Gagné F. Biophysical effects of polystyrene nanoparticles on Elliptio complanata mussels. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:25093-25102. [PMID: 32342426 DOI: 10.1007/s11356-020-08920-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
The presence of nanoplastics (NPs) in various products and from the weathering of released plastic materials are of concern for the environment's safety. The purpose of this study was to examine the biophysical effects of polystyrene NPs on freshwater mussels. Mussels were exposed to a range of concentrations of NPs (0.1, 0.5, 1, and 5 mg/L) for 24 h and allowed to depurate for 12 h in clean aquarium water. The digestive gland was isolated and analyzed for NPs, lipids, viscosity, protein aggregation, anisotropic changes (liquid crystals: LCs), and the oscillatory modulation in viscosity during the formation of self-organizing enzyme complex of fumarase, malate dehydrogenase, and citrate synthase. The results revealed that mussels accumulated NPs in the digestive gland and their levels were significantly correlated with lipids levels, LCs, the increase in the malate dehydrogenase/citrate synthase activity ratio, and oscillations in viscosity. Protein aggregation was also found to be correlated with lipid levels. The data suggests that the presence of NPs in the digestive gland involves changes in lipid content and LC formation and perturbs the normal oscillations in viscosity during sequential enzyme reactions of the above enzymes. It is concluded that the uptake of NPs in cells could disrupt the internal organization of cells which can interfere with the normal association of enzymes involved in energy metabolism.
Collapse
Affiliation(s)
- Joëlle Auclair
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, 105 McGill, Montreal, Quebec, Canada
| | - Caroline Peyrot
- Chemistry Department, Montréal University, Montreal, QC, H3C3J7, Canada
| | | | - François Gagné
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, 105 McGill, Montreal, Quebec, Canada.
| |
Collapse
|
14
|
Sensing Performance Investigations on Two-Photon Fluorescent Probes for Detecting β-Amyloid in Alzheimer's Disease. SENSORS 2020; 20:s20061760. [PMID: 32235776 PMCID: PMC7146205 DOI: 10.3390/s20061760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/28/2022]
Abstract
Alzheimer’s disease (AD) is one of the most common forms of senile disease. In recent years, the incidence of AD has been increasing significantly with the acceleration of the aging process of the global population. However, current clinical drugs can only alleviate the symptoms of AD patients without healing the disease fundamentally. Therefore, it is of great significance to develop an effective small molecule diagnostic reagent for the early diagnosis of AD. In this paper, we employ an integrated approach, including molecular docking simulation and quantum mechanics/molecular mechanics calculation, to investigate the sensing performance of a series of donor–acceptor structural probes for the marker protein of AD (β-amyloid). Results show that the probes display evident fluorescence enhancement when bound to the β-amyloid, suggesting the effect of the environment on the molecular properties. Especially, the two-photon absorption cross-section of the probes increase drastically in the β-amyloid compared to that in vacuum, which results from the larger electron delocalization and dipole moment in the fibrillary-like environment. Thus, one can propose that the studied probes are capable of application in two-photon fluorescent imaging, particularly those containing naphthalene rings as the donor or with a longer spacer group. Our calculations elucidate the experimental measurements reasonably, and further establish possible structure–property relationships that can be used to design novel biocompatible two-photon fluorescent probes for the diagnosis of Alzheimer’s.
Collapse
|
15
|
Kuang G, Murugan NA, Zhou Y, Nordberg A, Ågren H. Computational Insight into the Binding Profile of the Second-Generation PET Tracer PI2620 with Tau Fibrils. ACS Chem Neurosci 2020; 11:900-908. [PMID: 32069017 DOI: 10.1021/acschemneuro.9b00578] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Abnormal deposition of hyperphosphorylated tau as neurofibrillary tangles (NFTs) is an important pathological hallmark of Alzheimer's disease (AD) and of other neurodegenerative disorders. A noninvasive positron emission tomography (PET) tracer that quantifies neurofibrillary tangles in vivo can enhance the clinical diagnosis of AD and can also be used to evaluate the efficacy of therapeutics aimed at reducing the abnormal aggregation of the tau fibril in the brain. In this paper, we study the binding profile of fibrillar tau aggregates with a PET tracer PI2620, which is a new second generation tau PET tracer that is presently experimentally and clinically studied. The target structure for the tau fibril is based on cryo-electron microscopy (cryo-EM) structure. A multiscale simulation workflow including molecular docking, molecular dynamics simulation, metadynamics simulation, and free energy calculations was implemented. We find that PI2620 can bind to eight surface binding sites, three core binding sites, and one entry site. The binding at the core sites and entry site is found to be much more favorable than that on the surface sites due to stronger hydrophobic interactions and less solvent exposure. Furthermore, the entry site which is formed by the terminal β-sheets of the fibril is found to have the highest binding affinity to PI2620. Importantly, the binding capacity at the entry site can be much higher than that at other core sites, due to its easy accessibility. Therefore, the entry site is believed to be the major binding site for PI2620. A previous computational study on tracers with tau fibrils reports a maximum of four binding sites. Through use of methods that allow us to locate "cryptic binding sites", we report here additional core sites available for binding and we address the limitation of using the cryo-EM structure alone for structure-based tracer design. Our results could be helpful for elucidating the binding mechanism of imaging tracers with the fibrillar form of tau, a knowledge that in turn can be used to guide the development of compounds with higher affinity and selectivity for tau using structure-based design strategies.
Collapse
Affiliation(s)
- Guanglin Kuang
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm 10691, Sweden
| | - N. Arul Murugan
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm 10691, Sweden
| | - Yang Zhou
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm 10691, Sweden
| | - Agneta Nordberg
- Division of Clinical Geriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Center for Alzheimer Research, Stockholm 17177, Sweden
- Aging Theme, Karolinska University Hospital, Stockholm 14186, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, Stockholm 10691, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
| |
Collapse
|
16
|
Zou R, Kuang G, Ågren H, Nordberg A, Långström B, Tu Y. Free Energy Profile for Penetration of Pittsburgh Compound-B into the Amyloid β Fibril. ACS Chem Neurosci 2019; 10:1783-1790. [PMID: 30698013 DOI: 10.1021/acschemneuro.8b00662] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The amyloid β (Aβ) fibril is a hallmark of Alzheimer's disease (AD) and has therefore served as an important target for early diagnosis of AD. The Pittsburgh Compound-B (PiB) is one of the most famous positron emission tomography (PET) tracers commonly used for in vivo detection of Aβ fibrils. Many theoretical studies have predicted the existence of various core binding sites with different microenvironments for probes binding to the Aβ fibril. However, little attention has been devoted to how the probes actually penetrate into the different core binding sites. In this study, an integrated molecular modeling scheme is used to study the penetration of PiB into the core binding sites of the Aβ1-42 fibril structure recently obtained by cryogenic electron microscopy. We find that there are two core binding sites for PiB with dramatic differences in cavity size and microenvironment properties, and furthermore that the penetration of PiB into site-1 is energetically prohibitive, whereas the penetration into site-2 is much more favorable. Therefore, the binding capacity at site-2 may be larger than that at site-1 despite its lower binding affinity. Our results thus suggest that site-2 may be a major binding site for PiB binding to Aβ fibril and emphasize the importance to adopt a full dynamical picture when studying tracer-fibril binding problems in general, something that in turn can be used to guide the development of tracers with higher affinity and selectivity for the Aβ fibril.
Collapse
Affiliation(s)
- Rongfeng Zou
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - Hans Ågren
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, P. R. China
| | - Agneta Nordberg
- Department of Neurobiology, Care Sciences and Society, Center of Alzheimer Research, Clinical Geriatrics, Neo and Theme Aging, Karolinska University Hospital, Karolinska Institute, 141 83 Huddinge, Sweden
| | - Bengt Långström
- Department of Chemistry—BMC, Physical Organic Chemistry, Uppsala University, 751 23 Uppsala, Sweden
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91 Stockholm, Sweden
| |
Collapse
|