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Ataeinia B, Heidari P. Artificial Intelligence and the Future of Diagnostic and Therapeutic Radiopharmaceutical Development:: In Silico Smart Molecular Design. PET Clin 2021; 16:513-523. [PMID: 34364818 PMCID: PMC8453048 DOI: 10.1016/j.cpet.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Novel diagnostic and therapeutic radiopharmaceuticals are increasingly becoming a central part of personalized medicine. Continued innovation in the development of new radiopharmaceuticals is key to sustained growth and advancement of precision medicine. Artificial intelligence has been used in multiple fields of medicine to develop and validate better tools for patient diagnosis and therapy, including in radiopharmaceutical design. In this review, we first discuss common in silico approaches and focus on their usefulness and challenges in radiopharmaceutical development. Next, we discuss the practical applications of in silico modeling in design of radiopharmaceuticals in various diseases.
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Affiliation(s)
- Bahar Ataeinia
- Department of Radiology, Massachusetts General Hospital, 55 Fruit St, Wht 427, Boston, MA 02114, USA
| | - Pedram Heidari
- Department of Radiology, Massachusetts General Hospital, 55 Fruit St, Wht 427, Boston, MA 02114, USA.
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Schaduangrat N, Prachayasittikul V, Choomwattana S, Wongchitrat P, Phopin K, Suwanjang W, Malik AA, Vincent B, Nantasenamat C. Multidisciplinary approaches for targeting the secretase protein family as a therapeutic route for Alzheimer's disease. Med Res Rev 2019; 39:1730-1778. [PMID: 30628099 DOI: 10.1002/med.21563] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/21/2018] [Accepted: 12/24/2018] [Indexed: 12/27/2022]
Abstract
The continual increase of the aging population worldwide renders Alzheimer's disease (AD) a global prime concern. Several attempts have been focused on understanding the intricate complexity of the disease's development along with the on- andgoing search for novel therapeutic strategies. Incapability of existing AD drugs to effectively modulate the pathogenesis or to delay the progression of the disease leads to a shift in the paradigm of AD drug discovery. Efforts aimed at identifying AD drugs have mostly focused on the development of disease-modifying agents in which effects are believed to be long lasting. Of particular note, the secretase enzymes, a group of proteases responsible for the metabolism of the β-amyloid precursor protein (βAPP) and β-amyloid (Aβ) peptides production, have been underlined for their promising therapeutic potential. This review article attempts to comprehensively cover aspects related to the identification and use of drugs targeting the secretase enzymes. Particularly, the roles of secretases in the pathogenesis of AD and their therapeutic modulation are provided herein. Moreover, an overview of the drug development process and the contribution of computational (in silico) approaches for facilitating successful drug discovery are also highlighted along with examples of relevant computational works. Promising chemical scaffolds, inhibitors, and modulators against each class of secretases are also summarized herein. Additionally, multitarget secretase modulators are also taken into consideration in light of the current growing interest in the polypharmacology of complex diseases. Finally, challenging issues and future outlook relevant to the discovery of drugs targeting secretases are also discussed.
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Affiliation(s)
- Nalini Schaduangrat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Saowapak Choomwattana
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Prapimpun Wongchitrat
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Kamonrat Phopin
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Wilasinee Suwanjang
- Faculty of Medical Technology, Center for Research and Innovation, Mahidol University, Bangkok, Thailand
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Bruno Vincent
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Centre National de la Recherche Scientifique, Paris, France
| | - Chanin Nantasenamat
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
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Verdurand M, Levigoureux E, Zeinyeh W, Berthier L, Mendjel-Herda M, Cadarossanesaib F, Bouillot C, Iecker T, Terreux R, Lancelot S, Chauveau F, Billard T, Zimmer L. In Silico, in Vitro, and in Vivo Evaluation of New Candidates for α-Synuclein PET Imaging. Mol Pharm 2018; 15:3153-3166. [DOI: 10.1021/acs.molpharmaceut.8b00229] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Mathieu Verdurand
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
| | - Elise Levigoureux
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
- Hospices Civils de Lyon, Lyon 69361, France
| | - Wael Zeinyeh
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
| | - Laurent Berthier
- Université de Lyon, Université Claude Bernard Lyon 1, Institute of Biology and Chemistry of Proteins, CNRS UMR5305, Lyon 69361, France
| | - Meriem Mendjel-Herda
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
| | | | | | | | - Raphaël Terreux
- Université de Lyon, Université Claude Bernard Lyon 1, Institute of Biology and Chemistry of Proteins, CNRS UMR5305, Lyon 69361, France
| | - Sophie Lancelot
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
- Hospices Civils de Lyon, Lyon 69361, France
| | - Fabien Chauveau
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
| | - Thierry Billard
- CERMEP-Imaging Platform, Bron 69677, France
- Université de Lyon, Université Claude Bernard Lyon 1, Institute of Chemistry and Biochemistry, CNRS UMR5246, Villeurbanne 69100, France
| | - Luc Zimmer
- Université de Lyon, Université Claude Bernard Lyon 1, Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon 69361, France
- Hospices Civils de Lyon, Lyon 69361, France
- CERMEP-Imaging Platform, Bron 69677, France
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Kawai R, Araki M, Yoshimura M, Kamiya N, Ono M, Saji H, Okuno Y. Core Binding Site of a Thioflavin-T-Derived Imaging Probe on Amyloid β Fibrils Predicted by Computational Methods. ACS Chem Neurosci 2018; 9:957-966. [PMID: 29381047 DOI: 10.1021/acschemneuro.7b00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Development of new diagnostic imaging probes for Alzheimer's disease, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT) probes, has been strongly desired. In this study, we investigated the most accessible amyloid β (Aβ) binding site of [123I]IMPY, a Thioflavin-T-derived SPECT probe, using experimental and computational methods. First, we performed a competitive inhibition assay with Orange-G, which recognizes the KLVFFA region in Aβ fibrils, suggesting that IMPY and Orange-G bind to different sites in Aβ fibrils. Next, we precisely predicted the IMPY binding site on a multiple-protofilament Aβ fibril model using computational approaches, consisting of molecular dynamics and docking simulations. We generated possible IMPY-binding structures using docking simulations to identify candidates for probe-binding sites. The binding free energy of IMPY with the Aβ fibril was calculated by a free energy simulation method, MP-CAFEE. These computational results suggest that IMPY preferentially binds to an interfacial pocket located between two protofilaments and is stabilized mainly through hydrophobic interactions. Finally, our computational approach was validated by comparing it with the experimental results. The present study demonstrates the possibility of computational approaches to screen new PET/SPECT probes for Aβ imaging.
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Affiliation(s)
- Ryoko Kawai
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN
| | - Masashi Yoshimura
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Masahiro Ono
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hideo Saji
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, JAPAN
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Balamurugan K, Murugan NA, Långström B, Nordberg A, Ågren H. Effect of Alzheimer Familial Chromosomal Mutations on the Amyloid Fibril Interaction with Different PET Tracers: Insight from Molecular Modeling Studies. ACS Chem Neurosci 2017; 8:2655-2666. [PMID: 28898051 DOI: 10.1021/acschemneuro.7b00215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder. Along with an increasing number of elderly worldwide, it poses a great challenge for the society and health care. Although sporadic AD is the common form of AD, 2-3% of the AD cases are expected to be due to mutations in the β region of the amyloid precursor protein, which is referred to as autosomal dominant AD (ADAD). These mutations may cause changes in the secondary structure of the amyloid β fibrils and may alter the fibrillization rate leading to changes in the disease development and could also affect the binding to tracers used in diagnosis. In particular, from some recent clinical studies using PET tracers for detection of fibrillar amyloids, it is evident that in ADAD patients with Arctic mutation no amyloid plaque binding can be detected with the 11C-Pittsburgh Compound B (11C-PIB). However, for in vitro conditions, significant binding of 3H-PIB has been reported for the amyloid fibrils carrying the Arctic mutation. The aim of the present study is to investigate if there is any mutation specific binding of commonly used amyloid tracers, namely, florbetaben, florbetapir, FPIB, AZD4694, and AZD2184, by means of molecular modeling techniques. Other than Arctic, ADAD mutations, such as the Dutch, Italian, Iowa, and Flemish mutations, are considered in this study. We report that all tracers except florbetapir show reduced binding affinity toward amyloid β fibrils with the Arctic mutation when compared to the native type. Moreover, florbetapir is the only tracer that binds to all mutants with increased affinity when compared to the native fibril. The results obtained from these studies could increase the understanding of the structural changes caused by mutation and concomitant changes in the interaction pattern of the PET tracers with the mutated variants, which in turn can be useful in selecting the appropriate tracers for the purpose of diagnosis as well as for designing new tracers with desirable properties.
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Affiliation(s)
- Kanagasabai Balamurugan
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, AlbaNova
University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
| | - Natarajan Arul Murugan
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, AlbaNova
University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
| | - Bengt Långström
- Department
of Chemistry, Uppsala University, 751 23 Uppsala, Sweden
| | - Agneta Nordberg
- Department
of Neurobiology, Care Sciences and Society, Center for Alzheimer Research,
Translational Alzheimer Neurobiology, Department of Geriatric Medicine,
Karolinska University Hospital, Karolinska Institute, Huddinge, 141
86 Stockholm, Sweden
| | - Hans Ågren
- Division
of Theoretical Chemistry and Biology, School of Biotechnology, AlbaNova
University Center, Royal Institute of Technology (KTH), S-106 91 Stockholm, Sweden
- Institute
of Nanotechnology, Spectroscopy and Quantum Chemistry, Siberian Federal University, Svobodny pr. 79, 660041 Krasnoyarsk, Russia
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