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Li S, Li X, Ma L, Luo Z, Yin F, Zhang Y, Chen Y, Wan S, Zhou H, Wang X, Kong L. Polypharmacological Drug Design Guided by Integrating Phenotypic and Restricted Fragment Docking Strategies. J Med Chem 2024. [PMID: 39300597 DOI: 10.1021/acs.jmedchem.4c01731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Polypharmacological drugs are of great value for treating complex human diseases by the combinative modulation of several biological targets. However, multitarget drug design with more than two targets is challenging and generally discovered by serendipity. Herein, a restricted fragment docking (RFD) computational method combined with a phenotypic discovery approach was developed for rational polypharmacological drug design. Via genetic and drug combination studies in a microglial phenotype, we first identified novel synergistic effects by triple target modulation toward RIPK1, MAP4K4, and ALK. Drawing on the RFD method to explore virtual chemical spaces in three target pockets, we identified a lead compound, LP-10d, that precisely modulated RIPK1/MAP4K4/ALK for synergistic microglial protection with low nanomolar potency. LP-10d showed polypharmacology against multiple neuropathologies in the 3xTg Alzheimer's disease mouse model. Our study revealed a potential application of the RFD method, which is valuable to further polypharmacological drug discovery involved in clinical studies for treating complex human diseases.
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Affiliation(s)
- Shang Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xinxin Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Liangliang Ma
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Zhongwen Luo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Fucheng Yin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yonglei Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yifan Chen
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Siyuan Wan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Han Zhou
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaobing Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, People's Republic of China
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Hoxie N, Qiu Y, Kales SC, Schneider R, Hu X, Dalal A, Ford-Scheimer SL, Wiseman R, Tsukamoto T, Wei H, Slusher BS, Janiszewski JS, Hall MD. Development of a high-throughput dual-stream liquid chromatography-tandem mass spectrometry method to screen for inhibitors of glutamate carboxypeptidase II. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024:e9772. [PMID: 38867136 DOI: 10.1002/rcm.9772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/25/2024] [Accepted: 05/01/2024] [Indexed: 06/14/2024]
Abstract
RATIONALE Glutamate carboxypeptidase II (GCPII) catalyzes the hydrolysis of N-acetylaspartylglutamate (NAAG) to yield glutamate (Glu) and N-acetylaspartate (NAA). Inhibition of GCPII has been shown to remediate the neurotoxicity of excess Glu in a variety of cell and animal disease models. A robust high-throughput liquid chromatography-tandem mass spectrometry (LC/MS/MS) method was needed to quantify GCPII enzymatic activity in a biochemical high-throughput screening assay. METHODS A dual-stream LC/MS/MS method was developed. Two parallel eluent streams ran identical HILIC gradient methods on BEH-Amide (2 × 30 mm) columns. Each LC channel was run independently, and the cycle time was 2 min per channel. Overall throughput was 1 min per sample for the dual-channel integrated system. Multiply injected acquisition files were split during data review, and batch metadata were automatically paired with raw data during the review process. RESULTS Two LC sorbents, BEH-Amide and Penta-HILIC, were tested to separate the NAAG cleavage product Glu from isobaric interference and ion suppressants in the bioassay matrix. Early elution of NAAG and NAA on BEH-Amide allowed interfering species to be diverted to waste. The limit of quantification was 0.1 pmol for Glu. The Z-factor of this assay averaged 0.85. Over 36 000 compounds were screened using this method. CONCLUSIONS A fast gradient dual-stream LC/MS/MS method for Glu quantification in GCPII biochemical screening assay samples was developed and validated. HILIC separation chemistry offers robust performance and unique selectivity for targeted positive mode quantification of Glu, NAA, and NAAG.
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Affiliation(s)
- Nate Hoxie
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Yixuan Qiu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Rick Schneider
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Anu Dalal
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Stephanie L Ford-Scheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Robyn Wiseman
- Johns Hopkins Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins Drug Discovery and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Huijun Wei
- Johns Hopkins Drug Discovery and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John S Janiszewski
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
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Chen C, Qi J, Li Y, Li D, Wu L, Li R, Chen Q, Sun N. Applications of Raman spectroscopy in the diagnosis and monitoring of neurodegenerative diseases. Front Neurosci 2024; 18:1301107. [PMID: 38370434 PMCID: PMC10869569 DOI: 10.3389/fnins.2024.1301107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Raman scattering is an inelastic light scattering that occurs in a manner reflective of the molecular vibrations of molecular structures and chemical conditions in a given sample of interest. Energy changes in the scattered light can be assessed to determine the vibration mode and associated molecular and chemical conditions within the sample, providing a molecular fingerprint suitable for sample identification and characterization. Raman spectroscopy represents a particularly promising approach to the molecular analysis of many diseases owing to clinical advantages including its instantaneous nature and associated high degree of stability, as well as its ability to yield signal outputs corresponding to a single molecule type without any interference from other molecules as a result of its narrow peak width. This technology is thus ideally suited to the simultaneous assessment of multiple analytes. Neurodegenerative diseases represent an increasingly significant threat to global public health owing to progressive population aging, imposing a severe physical and social burden on affected patients who tend to develop cognitive and/or motor deficits beginning between the ages of 50 and 70. Owing to a relatively limited understanding of the etiological basis for these diseases, treatments are lacking for the most common neurodegenerative diseases, which include Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. The present review was formulated with the goal of briefly explaining the principle of Raman spectroscopy and discussing its potential applications in the diagnosis and evaluation of neurodegenerative diseases, with a particular emphasis on the research prospects of this novel technological platform.
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Affiliation(s)
- Chao Chen
- Central Laboratory, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
| | - Jinfeng Qi
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ying Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ding Li
- Department of Clinical Laboratory, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
| | - Lihong Wu
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Ruihua Li
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
| | - Qingfa Chen
- Institute of Tissue Engineering and Regenerative Medicine, Liaocheng People’s Hospital and Liaocheng School of Clinical Medicine, Shandong First Medical University, Liaocheng, China
- Research Center of Basic Medicine, Jinan Central Hospital, Jinan, China
| | - Ning Sun
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Geriatrics Institute, Tianjin, China
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Balestri W, Sharma R, da Silva VA, Bobotis BC, Curle AJ, Kothakota V, Kalantarnia F, Hangad MV, Hoorfar M, Jones JL, Tremblay MÈ, El-Jawhari JJ, Willerth SM, Reinwald Y. Modeling the neuroimmune system in Alzheimer's and Parkinson's diseases. J Neuroinflammation 2024; 21:32. [PMID: 38263227 PMCID: PMC10807115 DOI: 10.1186/s12974-024-03024-8] [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: 10/26/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
Parkinson's disease (PD) and Alzheimer's disease (AD) are neurodegenerative disorders caused by the interaction of genetic, environmental, and familial factors. These diseases have distinct pathologies and symptoms that are linked to specific cell populations in the brain. Notably, the immune system has been implicated in both diseases, with a particular focus on the dysfunction of microglia, the brain's resident immune cells, contributing to neuronal loss and exacerbating symptoms. Researchers use models of the neuroimmune system to gain a deeper understanding of the physiological and biological aspects of these neurodegenerative diseases and how they progress. Several in vitro and in vivo models, including 2D cultures and animal models, have been utilized. Recently, advancements have been made in optimizing these existing models and developing 3D models and organ-on-a-chip systems, holding tremendous promise in accurately mimicking the intricate intracellular environment. As a result, these models represent a crucial breakthrough in the transformation of current treatments for PD and AD by offering potential for conducting long-term disease-based modeling for therapeutic testing, reducing reliance on animal models, and significantly improving cell viability compared to conventional 2D models. The application of 3D and organ-on-a-chip models in neurodegenerative disease research marks a prosperous step forward, providing a more realistic representation of the complex interactions within the neuroimmune system. Ultimately, these refined models of the neuroimmune system aim to aid in the quest to combat and mitigate the impact of debilitating neuroimmune diseases on patients and their families.
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Affiliation(s)
- Wendy Balestri
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Medical Technologies Innovation Facility, Nottingham Trent University, Nottingham, UK
| | - Ruchi Sharma
- Department of Mechanical Engineering, University of Victoria, Victoria, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
| | - Victor A da Silva
- Department of Mechanical Engineering, University of Victoria, Victoria, Canada
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
| | - Bianca C Bobotis
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
| | - Annabel J Curle
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Vandana Kothakota
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | | | - Maria V Hangad
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
- Department of Chemistry, University of Victoria, Victoria, BC, Canada
| | - Mina Hoorfar
- Department of Mechanical Engineering, University of Victoria, Victoria, Canada
| | - Joanne L Jones
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada
- Neurosciences Axis, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada
- Department of Molecular Medicine, Université Laval, Québec City, QC, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Institute On Aging and Lifelong Health, University of Victoria, Victoria, BC, Canada
| | - Jehan J El-Jawhari
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Stephanie M Willerth
- Department of Mechanical Engineering, University of Victoria, Victoria, Canada.
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.
- Centre for Advanced Materials and Related Technology (CAMTEC), University of Victoria, Victoria, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
| | - Yvonne Reinwald
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, UK.
- Medical Technologies Innovation Facility, Nottingham Trent University, Nottingham, UK.
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Escobar-Peso A, Martínez-Alonso E, Masjuan J, Alcázar A. Development of Pharmacological Strategies with Therapeutic Potential in Ischemic Stroke. Antioxidants (Basel) 2023; 12:2102. [PMID: 38136221 PMCID: PMC10740896 DOI: 10.3390/antiox12122102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Acute ischemic stroke constitutes a health challenge with great social impact due to its high incidence, with the social dependency that it generates being an important source of inequality. The lack of treatments serving as effective neuroprotective therapies beyond thrombolysis and thrombectomy is presented as a need. With this goal in mind, our research group's collaborative studies into cerebral ischemia and subsequent reperfusion concluded that there is a need to develop compounds with antioxidant and radical scavenger features. In this review, we summarize the path taken toward the identification of lead compounds as potential candidates for the treatment of acute ischemic stroke. Evaluations of the antioxidant capacity, neuroprotection of primary neuronal cultures and in vivo experimental models of cerebral ischemia, including neurological deficit score assessments, are conducted to characterize the biological efficacy of the various neuroprotective compounds developed. Moreover, the initial results in preclinical development, including dose-response studies, the therapeutic window, the long-term neuroprotective effect and in vivo antioxidant evaluation, are reported. The results prompt these compounds for clinical trials and are encouraging regarding new drug developments aimed at a successful therapy for ischemic stroke.
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Affiliation(s)
- Alejandro Escobar-Peso
- Department of Research, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
| | - Emma Martínez-Alonso
- Department of Research, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
| | - Jaime Masjuan
- Department of Neurology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- Department of Neurology, Facultad de Medicina, Universidad de Alcalá, 28871 Alcalá de Henares, Spain
| | - Alberto Alcázar
- Department of Research, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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Abstract
The Human Genome Project ultimately aimed to translate DNA sequence into drugs. With the draft in hand, the Molecular Libraries Program set out to prosecute all genome-encoded proteins for drug discovery with automated high-throughput screening (HTS). This ambitious vision remains unfulfilled, even while innovations in sequencing technology have fully democratized access to genome-scale sequencing. Why? While the central dogma of biology allows us to chart the entirety of cellular metabolism through sequencing, there is no direct coding for chemistry. The rules of base pairing that relate DNA gene to RNA transcript and amino acid sequence do not exist for relating small-molecule structure with macromolecular binding partners and subsequently cellular function. Obtaining such relationships genome-wide is unapproachable via state-of-the-art HTS, akin to attempting genome-wide association studies using turn-of-the-millennium Sanger DNA sequencing.Our laboratory has been engaged in a multipronged technology development campaign to revolutionize molecular screening through miniaturization in pursuit of genome-scale drug discovery capabilities. The compound library was ripe for miniaturization: it clearly needed to become a consumable. We employed DNA-encoded library (DEL) synthesis principles in the development of solid-phase DELs prepared on microscopic beads, each harboring 100 fmol of a single library member and a DNA tag whose sequence describes the structure of the library member. Loading these DEL beads into 100 pL microfluidic droplets followed by online photocleavage, incubation, fluorescence-activated droplet sorting, and DNA sequencing of the sorted DEL beads reveals the chemical structures of bioactive compounds. This scalable library synthesis and screening platform has proven useful in several proof-of-concept projects involving current clinical targets.Moving forward, we face the problem of druggability and proteome-scale assay development. Developing biochemical or cellular assays for all genome-encoded targets is not scalable and likely impossible as most proteins have ill-defined or unknown activity and may not function outside of their native contexts. These are the dark undruggable expanses, and charting them will require advanced synthesis and analytical technologies that can generalize probe discovery, irrespective of mature protein function, to fulfill the Genome Project's vision of proteome-wide control of cellular pharmacology.
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Current Pharmacotherapy and Multi-Target Approaches for Alzheimer's Disease. Pharmaceuticals (Basel) 2022; 15:ph15121560. [PMID: 36559010 PMCID: PMC9781592 DOI: 10.3390/ph15121560] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/26/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by decreased synaptic transmission and cerebral atrophy with appearance of amyloid plaques and neurofibrillary tangles. Cognitive, functional, and behavioral alterations are commonly associated with the disease. Different pathophysiological pathways of AD have been proposed, some of which interact and influence one another. Current treatment for AD mainly involves the use of therapeutic agents to alleviate the symptoms in AD patients. The conventional single-target treatment approaches do not often cause the desired effect in the disease due to its multifactorial origin. Thus, multi-target strategies have since been undertaken, which aim to simultaneously target multiple targets involved in the development of AD. In this review, we provide an overview of the pathogenesis of AD and the current drug therapies for the disease. Additionally, rationales of the multi-target approaches and examples of multi-target drugs with pharmacological actions against AD are also discussed.
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Abstract
Molecular chaperones and co-chaperones facilitate the assembly of newly synthesized polypeptides and refolding of unfolded or misfolded proteins, thereby maintaining protein homeostasis in cells. As co-chaperones of the master chaperone heat shock protein (HSP) 70, the HSP40 (DNAJ) proteins are largest chaperone family in eukaryotic cells. They contain a characteristic J-domain which mediates interaction with HSP70, thereby helping protein folding. It is well perceived that protein homeostasis is vital for neuronal health. DNAJ family proteins have been linked to the occurrence and progression of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, spinocerebellar ataxia, Charcot-Marie-Tooth disease, spinal muscular atrophy, distal hereditary motor neuropathy, limb-girdle type muscular dystrophy, neuronal ceroid lipofuscinosis and essential tremor in recent studies. DNAJA1 effectively degrades huntington aggregates; DNAJB1 can degrade protein aggregates ataxin-3; DNAJB2 can inhibit the formation of huntington aggregates; DNAJB6 can inhibit the aggregation of Aβ 42 and α-synuclein; DNAJC5 can promote the release of TDP-43, τ protein, and α-synuclein into the extracellular space. Mutations in the essential tremor-associated DNAJC13 gene can prevent endosome protein trafficking. This article reviews the mechanism of DNAJ protein family in neurodegenerative diseases.
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Imai Y, Iida M, Kanie K, Katsuno M, Kato R. Label-free morphological sub-population cytometry for sensitive phenotypic screening of heterogenous neural disease model cells. Sci Rep 2022; 12:9296. [PMID: 35710681 PMCID: PMC9203459 DOI: 10.1038/s41598-022-12250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Label-free image analysis has several advantages with respect to the development of drug screening platforms. However, the evaluation of drug-responsive cells based exclusively on morphological information is challenging, especially in cases of morphologically heterogeneous cells or a small subset of drug-responsive cells. We developed a novel label-free cell sub-population analysis method called “in silico FOCUS (in silico analysis of featured-objects concentrated by anomaly discrimination from unit space)” to enable robust phenotypic screening of morphologically heterogeneous spinal and bulbar muscular atrophy (SBMA) model cells. This method with the anomaly discrimination concept can sensitively evaluate drug-responsive cells as morphologically anomalous cells through in silico cytometric analysis. As this algorithm requires only morphological information of control cells for training, no labeling or drug administration experiments are needed. The responses of SBMA model cells to dihydrotestosterone revealed that in silico FOCUS can identify the characteristics of a small sub-population with drug-responsive phenotypes to facilitate robust drug response profiling. The phenotype classification model confirmed with high accuracy the SBMA-rescuing effect of pioglitazone using morphological information alone. In silico FOCUS enables the evaluation of delicate quality transitions in cells that are difficult to profile experimentally, including primary cells or cells with no known markers.
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Affiliation(s)
- Yuta Imai
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Madoka Iida
- Department of Neurology, Nagoya University Graduate School of Medicine, Tokai National Higher Education and Research System, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan
| | - Kei Kanie
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, Tokai National Higher Education and Research System, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.,Department of Clinical Research Education, Nagoya University Graduate School of Medicine, Tokai National Higher Education and Research System, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi, 466-8550, Japan.,Institute for Glyco-Core Research (iGCORE), Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Ryuji Kato
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan. .,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan. .,Institute for Glyco-Core Research (iGCORE), Nagoya University, Tokai National Higher Education and Research System, Furocho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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Cell models for Alzheimer’s and Parkinson’s disease: At the interface of biology and drug discovery. Biomed Pharmacother 2022; 149:112924. [DOI: 10.1016/j.biopha.2022.112924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 11/23/2022] Open
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12
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Prieto Kullmer CN, Kautzky JA, Krska SW, Nowak T, Dreher SD, MacMillan DWC. Accelerating reaction generality and mechanistic insight through additive mapping. Science 2022; 376:532-539. [PMID: 35482871 DOI: 10.1126/science.abn1885] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reaction generality is crucial in determining the overall impact and usefulness of synthetic methods. Typical generalization protocols require a priori mechanistic understanding and suffer when applied to complex, less understood systems. We developed an additive mapping approach that rapidly expands the utility of synthetic methods while generating concurrent mechanistic insight. Validation of this approach on the metallaphotoredox decarboxylative arylation resulted in the discovery of a phthalimide ligand additive that overcomes many lingering limitations of this reaction and has important mechanistic implications for nickel-catalyzed cross-couplings.
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Affiliation(s)
| | - Jacob A Kautzky
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Shane W Krska
- Department of Process and Analytical Chemistry, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Timothy Nowak
- Department of Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Spencer D Dreher
- Department of Process and Analytical Chemistry, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
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13
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Kuang Y, Ye N, Kyani A, Ljungman M, Paulsen M, Chen H, Zhou M, Wild C, Chen H, Zhou J, Neamati N. Induction of Genes Implicated in Stress Response and Autophagy by a Novel Quinolin-8-yl-nicotinamide QN523 in Pancreatic Cancer. J Med Chem 2022; 65:6133-6156. [PMID: 35439009 PMCID: PMC9195374 DOI: 10.1021/acs.jmedchem.1c02207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using a cytotoxicity-based phenotypic screen of a highly diverse library of 20,000 small-molecule compounds, we identified a quinolin-8-yl-nicotinamide, QN519, as a promising lead. QN519 represents a novel scaffold with drug-like properties, showing potent in vitro cytotoxicity in a panel of 12 cancer cell lines. Subsequently, lead optimization campaign generated compounds with IC50 values < 1 μM. An optimized compound, QN523, shows significant in vivo efficacy in a pancreatic cancer xenograft model. QN523 treatment significantly increased the expression of HSPA5, DDIT3, TRIB3, and ATF3 genes, suggesting activation of the stress response pathway. We also observed a significant increase in the expression of WIPI1, HERPUD1, GABARAPL1, and MAP1LC3B, implicating autophagy as a major mechanism of action. Due to the lack of effective treatments for pancreatic cancer, discovery of novel agents such as the QN series of compounds with unique mechanism of action has the potential to fulfill a clear unmet medical need.
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Affiliation(s)
- Yuting Kuang
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Na Ye
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Armita Kyani
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Michelle Paulsen
- Department of Radiation Oncology, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Haijun Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Mingxiang Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Christopher Wild
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77550, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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14
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Mahmud F, Lai NS, How SE, Gansau JA, Mustaffa KMF, Leow CH, Osman H, Sidek HM, Embi N, Lee PC. Bioactivities and Mode of Actions of Dibutyl Phthalates and Nocardamine from Streptomyces sp. H11809. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27072292. [PMID: 35408690 PMCID: PMC9000801 DOI: 10.3390/molecules27072292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Dibutyl phthalate (DBP) produced by Streptomyces sp. H11809 exerted inhibitory activity against human GSK-3β (Hs GSK-3β) and Plasmodiumfalciparum 3D7 (Pf 3D7) malaria parasites. The current study aimed to determine DBP’s plausible mode of action against Hs GSK-3β and Pf 3D7. Molecular docking analysis indicated that DBP has a higher binding affinity to the substrate-binding site (pocket 2; −6.9 kcal/mol) than the ATP-binding site (pocket 1; −6.1 kcal/mol) of Hs GSK-3β. It was suggested that the esters of DBP play a pivotal role in the inhibition of Hs GSK-3β through the formation of hydrogen bonds with Arg96/Glu97 amino acid residues in pocket 2. Subsequently, an in vitro Hs GSK-3β enzymatic assay revealed that DBP inhibits the activity of Hs GSK-3β via mixed inhibition inhibitory mechanisms, with a moderate IC50 of 2.0 µM. Furthermore, the decrease in Km value with an increasing DBP concentration suggested that DBP favors binding on free Hs GSK-3β over its substrate-bound state. However, the antimalarial mode of action of DBP remains unknown since the generation of a Pf 3D7 DBP-resistant clone was not successful. Thus, the molecular target of DBP might be indispensable for Pf survival. We also identified nocardamine as another active compound from Streptomyces sp. H11809 chloroform extract. It showed potent antimalarial activity with an IC50 of 1.5 μM, which is ~10-fold more potent than DBP, but with no effect on Hs GSK-3β. The addition of ≥12.5 µM ferric ions into the Pf culture reduced nocardamine antimalarial activity by 90% under in vitro settings. Hence, the iron-chelating ability of nocardamine was shown to starve the parasites from their iron source, eventually inhibiting their growth.
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Affiliation(s)
- Fauze Mahmud
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Malaysia; (F.M.); (K.M.F.M.); (C.H.L.)
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (S.E.H.); (J.A.G.)
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Malaysia; (F.M.); (K.M.F.M.); (C.H.L.)
- Correspondence: (N.S.L.); (P.-C.L.); Tel.: +60-4653-4862 (N.S.L.); +60-8832-0000 (P.-C.L.); Fax: +60-4653-4803 (N.S.L.); +60-8843-2324 (P.-C.L.)
| | - Siew Eng How
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (S.E.H.); (J.A.G.)
| | - Jualang Azlan Gansau
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (S.E.H.); (J.A.G.)
| | - Khairul Mohd Fadzli Mustaffa
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Malaysia; (F.M.); (K.M.F.M.); (C.H.L.)
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Malaysia; (F.M.); (K.M.F.M.); (C.H.L.)
| | - Hasnah Osman
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Malaysia;
| | - Hasidah Mohd Sidek
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (H.M.S.); (N.E.)
| | - Noor Embi
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (H.M.S.); (N.E.)
| | - Ping-Chin Lee
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia; (S.E.H.); (J.A.G.)
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
- Correspondence: (N.S.L.); (P.-C.L.); Tel.: +60-4653-4862 (N.S.L.); +60-8832-0000 (P.-C.L.); Fax: +60-4653-4803 (N.S.L.); +60-8843-2324 (P.-C.L.)
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15
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Hatstat AK, Quan B, Bailey MA, Fitzgerald MC, Reinhart MC, McCafferty DG. Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity. RSC Chem Biol 2022; 3:96-111. [PMID: 35128413 PMCID: PMC8729260 DOI: 10.1039/d1cb00103e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/08/2021] [Indexed: 11/21/2022] Open
Abstract
The development of phenotypic models of Parkinson's disease (PD) has enabled screening and identification of phenotypically active small molecules that restore complex biological pathways affected by PD toxicity.
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Affiliation(s)
| | - Baiyi Quan
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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16
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Hatstat AK, Pupi MD, Reinhart MC, McCafferty DG. Small Molecule Improvement of Trafficking Defects in Models of Neurodegeneration. ACS Chem Neurosci 2021; 12:3972-3984. [PMID: 34652126 DOI: 10.1021/acschemneuro.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Disrupted cellular trafficking and transport processes are hallmarks of many neurodegenerative disorders (NDs). Recently, efforts have been made toward developing and implementing experimental platforms to identify small molecules that may help restore normative trafficking functions. There have been a number of successes in targeting endomembrane trafficking with the identification of compounds that restore cell viability through rescue of protein transport and trafficking. Here, we describe some of the experimental platforms implemented for small molecule screening efforts for rescue of trafficking defects in neurodegeneration. A survey of phenotypically active small molecules identified to date is provided, including a summary of medicinal chemistry efforts and insights into putative targets and mechanisms of action. In particular, emphasis is put on ligands that demonstrate activity in more than one model of neurodegeneration as retention of phenotypic activity across ND models suggests conservation of biological targets across NDs.
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Affiliation(s)
- A. Katherine Hatstat
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Pupi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michaela C. Reinhart
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dewey G. McCafferty
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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17
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MacMullen C, Davis RL. High-Throughput Phenotypic Assay for Compounds That Influence Mitochondrial Health Using iPSC-Derived Human Neurons. SLAS DISCOVERY 2021; 26:811-822. [PMID: 33724077 DOI: 10.1177/24725552211000671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There is a critical need to develop high-throughput assays to identify compounds that offer therapy for individuals suffering from neurodegenerative diseases. Most brain disorders, including neurodegenerative diseases, share the common neuropathology of mitochondria dysfunction, which can lead to apoptosis of neurons, overproduction of reactive oxygen species (ROS), and other cellular neuropathologies characteristic of these diseases. Human induced pluripotent stem cells (iPSCs) with a stable genomic insertion of the neurogenin-2 transcription factor under the control of the TetOn promoter can be differentiated into excitatory human neurons (i3Neurons) within 3 days of exposure to doxycycline. These neurons have been used to develop and validate a live-cell assay for parameters of mitochondrial dynamics and function using two compounds known to promote mitochondrial elongation in mouse neurons, 4-hydroxychalcone and 2,4-dihyrdroxychalcone. The assay involves plating the neurons in 384-well microtiter plates, treating them with known or unknown substances, and then capturing morphological information for the neuronal mitochondria using a lentivirus vector to express a mitochondrial-targeted fluorescence reporter. The i3Neuron cultures exposed to these two compounds for 24 h exhibit significantly decreased circularity and significantly increased length compared to controls, two morphological parameters correlated with increased mitochondrial health. The assay is rapid, with results obtained after a one-week-long i3Neuron culture or one month if neurons are co-cultured with astrocytes. This live-cell, mitochondrial phenotypic assay can be used for high-throughput screening or as an orthogonal assay for compounds obtained via other high-throughput screening campaigns.
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Affiliation(s)
- Courtney MacMullen
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
| | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute, Jupiter, FL, USA
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18
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Tan MA, Zakharova E, An SSA. Diaportheone A Analogues Instigate a Neuroprotective Effect by Protecting Neuroblastoma SH-SY5Y Cells from Oxidative Stress. BIOLOGY 2021; 10:biology10030199. [PMID: 33807686 PMCID: PMC8002093 DOI: 10.3390/biology10030199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/17/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) remains an incurable neurodegenerative illness. Oxidative stress resulting in the formation of reactive oxygen species (ROS) and the abnormal deposition of amyloid-beta (Aβ) are the major pathological hallmarks associated with AD. In search for small molecules targeting multiple pathways of AD and of no known molecular targets, the neuroprotective effects of the synthetic chromones diaportheone A1 and diaportheone A2, analogues of the natural product diaportheone A, were investigated. Chromones are heterocyclic compounds bearing the benzoannelated γ-pyrone moiety and were regarded as an important class of organic molecules due to their diverse pharmacological activities. The influence of the compounds on the inhibition of Aβ aggregation was determined by Thioflavin T (ThT) assay, and the cell viability, ROS, and mitochondrial membrane potential were evaluated with human neuroblastoma SH-SY5Y cells. Results showed that both compounds inhibited the Aβ aggregation at 80.41% and 73.68% for diaportheone A1 and diaportheone A2, respectively. Increased cell viabilities were observed from the protection by both compounds using Aβ- or H2O2-induced SH-SY5Y cells. Both compounds also reduced the intracellular ROS level in Aβ- or H2O2-induced SH-SY5Y cells at 10 and 20 μM concentrations, and increased the mitochondrial membrane potentials in Aβ-induced SH-SY5Y cells at 20 μM concentration. Molecular docking experiments using the Aβ protein models 2MXU and 2BEG also indicated a good agreement with the experimental data. The results demonstrated for the first time the oxidative stress effects associated with the chromones diaportheone A1 and diaportheone A2 as potential neuroprotective therapeutic agents against AD.
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Affiliation(s)
- Mario A. Tan
- Department of Bionano Technology, Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Korea
- College of Science and Research Center for the Natural and Applied Sciences, University of Santo Tomas, Espana, Manila 1015, Philippines
- Correspondence: (M.A.T.); (S.S.A.A.); Tel.: +63-2-7314031 (M.A.T.); +82-31-7508755 (S.S.A.A.)
| | - Elena Zakharova
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland;
| | - Seong Soo A. An
- Department of Bionano Technology, Bionano Research Institute, Gachon University, 1342 Seongnam-daero, Sujung-gu, Seongnam-si 461-701, Korea
- Correspondence: (M.A.T.); (S.S.A.A.); Tel.: +63-2-7314031 (M.A.T.); +82-31-7508755 (S.S.A.A.)
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19
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Oboh G, Oladun FL, Ademosun AO, Ogunsuyi OB. Anticholinesterase activity and antioxidant properties of Heinsia crinita and Pterocarpus soyauxii in Drosophila melanogaster model. J Ayurveda Integr Med 2021; 12:254-260. [PMID: 33514461 PMCID: PMC8185959 DOI: 10.1016/j.jaim.2020.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
Background Plant alkaloids have become important sources of nutraceuticals owing to their pharmacological importance especially in the management of neurodegenerative diseases such as Alzheimer’s disease. In assessing the therapeutic potentials of plant phytochemicals, the fruit fly (Drosophila melanogaster) has emerged as a very veritable tool and has been largely accepted as an alternative model in biomedical research. Objectives In this study, alkaloid extracts from bush apple (Heinsia crinita (Afzel.) G. Taylor and padauk (Pterocarpus soyauxii Taub.) leaves were assessed on D. melanogaster exposed to aluminum toxicity. Materials and methods Alkaloid extracts were prepared by solvent extraction method. Thereafter, the extracts were evaluated for their in vitro antioxidant properties, Fe2+-chelating abilities and inhibitory effects on drosophila acetylcholinesterase (AChE) activity. The samples were also characterized for their constituent alkaloids via HPLC. Thereafter, effective safe dose of the extracts were determined in D. melanogaster (Harwich strain). Subsequently, flies assaulted with AlCl3 were co-treated with the extracts (8.3 and 16.6 μg/g) for seven days, during which their survival rate was monitored. This was followed by assaying for the activities of AChE, antioxidant enzymes [superoxide dismutase (SOD), catalase and glutathione-S-transferase (GST)]. Also, the flies were assayed for levels of thiobarbituric acid reaction substance (TBARS) and reactive oxygen species (ROS). Results The results revealed that both extracts showed in vitro antioxidant properties with Padauk showing significantly higher antioxidant properties in vitro. However, there was no significant difference in their in vitro AChE inhibition. In vivo, Al-induced toxicity reduced survival rate, elevated AChE, SOD and GST activities, as well as TBARS and ROS levels which were ameliorated by the extracts. It was also revealed that piperine was predominant in PA, while 1-cyclohexen-1-yl-pyrrolidine was predominant in BA. Conclusion Our data suggest that the protective abilities of these extracts against Al-induced toxicity can be primarily associated with their anticholinesterase and metal chelating abilities. Thus, these vegetables can be potential sources of nutraceuticals against aluminum toxicity and associated diseases.
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Affiliation(s)
- Ganiyu Oboh
- Federal University of Technology, Department of Biochemistry, P.M.B. 704, Akure, Nigeria.
| | - Folasade L Oladun
- Federal University of Technology, Department of Biochemistry, P.M.B. 704, Akure, Nigeria
| | - Ayokunle O Ademosun
- Federal University of Technology, Department of Biochemistry, P.M.B. 704, Akure, Nigeria
| | - Opeyemi B Ogunsuyi
- Federal University of Technology, Department of Biochemistry, P.M.B. 704, Akure, Nigeria; Federal University of Technology, Department of Biomedical Technology, P.M.B. 704, Akure, Nigeria
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20
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Characterization of Small-Molecule-Induced Changes in Parkinson's-Related Trafficking via the Nedd4 Ubiquitin Signaling Cascade. Cell Chem Biol 2021; 28:14-25.e9. [PMID: 33176158 PMCID: PMC9812001 DOI: 10.1016/j.chembiol.2020.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/18/2020] [Accepted: 10/19/2020] [Indexed: 01/07/2023]
Abstract
The benzdiimidazole NAB2 rescues α-synuclein-associated trafficking defects associated with early onset Parkinson's disease in a Nedd4-dependent manner. Despite identification of E3 ubiquitin ligase Nedd4 as a putative target of NAB2, its molecular mechanism of action has not been elucidated. As such, the effect of NAB2 on Nedd4 activity and specificity was interrogated through biochemical, biophysical, and proteomic analyses. NAB2 was found to bind Nedd4 (KDapp = 42 nM), but this binding is side chain mediated and does not alter its conformation or ubiquitination kinetics in vitro. Nedd4 co-localizes with trafficking organelles, and NAB2 exposure did not alter its co-localization. Ubiquitin enrichment coupled proteomics revealed that NAB2 stimulates ubiquitination of trafficking-associated proteins, most likely through modulating the substrate specificity of Nedd4, providing a putative protein network involved in the NAB2 mechanism and revealing trafficking scaffold protein TFG as a Nedd4 substrate.
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21
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Gao L, Wang W, Wang X, Yang F, Xie L, Shen J, Brimble MA, Xiao Q, Yao SQ. Fluorescent probes for bioimaging of potential biomarkers in Parkinson's disease. Chem Soc Rev 2021; 50:1219-1250. [DOI: 10.1039/d0cs00115e] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review comprehensively summarizes various types of fluorescent probes for PD and their applications for detection of various PD biomarkers.
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Affiliation(s)
- Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Fen Yang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Liuxing Xie
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Jun Shen
- Department of Radiology
- Sun Yat-Sen Memorial Hospital
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland 1010
- New Zealand
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore
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22
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Zhou J, Jangili P, Son S, Ji MS, Won M, Kim JS. Fluorescent Diagnostic Probes in Neurodegenerative Diseases. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001945. [PMID: 32902000 DOI: 10.1002/adma.202001945] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/19/2020] [Indexed: 05/22/2023]
Abstract
Neurodegenerative diseases are debilitating disorders that feature progressive and selective loss of function or structure of anatomically or physiologically associated neuronal systems. Both chronic and acute neurodegenerative diseases are associated with high morbidity and mortality along with the death of neurons in different areas of the brain; moreover, there are few or no effective curative therapy options for treating these disorders. There is an urgent need to diagnose neurodegenerative disease as early as possible, and to distinguish between different disorders with overlapping symptoms that will help to decide the best clinical treatment. Recently, in neurodegenerative disease research, fluorescent-probe-mediated biomarker visualization techniques have been gaining increasing attention for the early diagnosis of neurodegenerative diseases. A survey of fluorescent probes for sensing and imaging biomarkers of neurodegenerative diseases is provided. These imaging probes are categorized based on the different potential biomarkers of various neurodegenerative diseases, and their advantages and disadvantages are discussed. Guides to develop new sensing strategies, recognition mechanisms, as well as the ideal features to further improve neurodegenerative disease fluorescence imaging are also explored.
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Affiliation(s)
- Jin Zhou
- College of Pharmacy, Weifang Medical University, Weifang, 261053, China
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Paramesh Jangili
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Subin Son
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Myung Sun Ji
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Miae Won
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
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23
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Childers WE, Elokely KM, Abou-Gharbia M. The Resurrection of Phenotypic Drug Discovery. ACS Med Chem Lett 2020; 11:1820-1828. [PMID: 33062159 DOI: 10.1021/acsmedchemlett.0c00006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Prior to genetic mapping, the majority of drug discovery efforts involved phenotypic screening, wherein compounds were screened in either in vitro or in vivo models thought to mimic the disease state of interest. While never completely abandoning phenotypic approaches, the labor intensive nature of such tests encouraged the pharmaceutical industry to move away from them in favor of target-based drug discovery, which facilitated throughput and allowed for the efficient screening of large numbers of compounds. However, a consequence of reliance on target-based screening was an increased number of failures in clinical trials due to poor correlation between novel mechanistic targets and the actual disease state. As a result, the field has seen a recent resurrection in phenotypic drug discovery approaches. In this work, we highlight some recent phenotypic projects from our industrial past and in our current academic drug discovery environment that have provided encouraging results.
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Affiliation(s)
- Wayne E. Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N. Broad Street, Philadelphia, Pennsylvania 19140, United States
| | - Khaled M. Elokely
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N. Broad Street, Philadelphia, Pennsylvania 19140, United States
- Department of Chemistry, College of Science and Technology, Temple University, 1925 N. 12th Street, Philadelphia, Pennsylvania 19122, United States
- Department of Pharmaceutical Chemistry, Tanta University, Tanta 31527, Egypt
| | - Magid Abou-Gharbia
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, 3307 N. Broad Street, Philadelphia, Pennsylvania 19140, United States
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24
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Davis RL. Mechanism of Action and Target Identification: A Matter of Timing in Drug Discovery. iScience 2020; 23:101487. [PMID: 32891054 PMCID: PMC7479624 DOI: 10.1016/j.isci.2020.101487] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/11/2020] [Accepted: 08/18/2020] [Indexed: 01/14/2023] Open
Abstract
Two opposing viewpoints are held regarding the need for understanding a drug's molecular target and mechanism of action. One extreme viewpoint is that it is unnecessary, because, after all, there are many beneficial drugs in use for which the target and mechanism of action remain unknown. A second extreme viewpoint is that target identification and mechanism of action should be elucidated very early in the drug discovery process due to the tangible benefits provided by this knowledge. I offer an intermediate perspective that considers the complexity of the disease of interest, the existence of a standard-of-care treatment, and the resources available to the investigator.
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Affiliation(s)
- Ronald L Davis
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, FL 33458, USA.
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25
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Moos WH, Faller DV, Glavas IP, Harpp DN, Kanara I, Mavrakis AN, Pernokas J, Pernokas M, Pinkert CA, Powers WR, Sampani K, Steliou K, Vavvas DG, Zamboni RJ, Kodukula K, Chen X. Klotho Pathways, Myelination Disorders, Neurodegenerative Diseases, and Epigenetic Drugs. Biores Open Access 2020; 9:94-105. [PMID: 32257625 PMCID: PMC7133426 DOI: 10.1089/biores.2020.0004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this review we outline a rationale for identifying neuroprotectants aimed at inducing endogenous Klotho activity and expression, which is epigenetic action, by definition. Such an approach should promote remyelination and/or stimulate myelin repair by acting on mitochondrial function, thereby heralding a life-saving path forward for patients suffering from neuroinflammatory diseases. Disorders of myelin in the nervous system damage the transmission of signals, resulting in loss of vision, motion, sensation, and other functions depending on the affected nerves, currently with no effective treatment. Klotho genes and their single-pass transmembrane Klotho proteins are powerful governors of the threads of life and death, true to the origin of their name, Fates, in Greek mythology. Among its many important functions, Klotho is an obligatory co-receptor that binds, activates, and/or potentiates critical fibroblast growth factor activity. Since the discovery of Klotho a little over two decades ago, it has become ever more apparent that when Klotho pathways go awry, oxidative stress and mitochondrial dysfunction take over, and age-related chronic disorders are likely to follow. The physiological consequences can be wide ranging, potentially wreaking havoc on the brain, eye, kidney, muscle, and more. Central nervous system disorders, neurodegenerative in nature, and especially those affecting the myelin sheath, represent worthy targets for advancing therapies that act upon Klotho pathways. Current drugs for these diseases, even therapeutics that are disease modifying rather than treating only the symptoms, leave much room for improvement. It is thus no wonder that this topic has caught the attention of biomedical researchers around the world.
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Affiliation(s)
- Walter H. Moos
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, San Francisco, California
- ShangPharma Innovation, Inc., South San Francisco, California
| | - Douglas V. Faller
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Cancer Research Center, Boston University School of Medicine, Boston, Massachusetts
| | - Ioannis P. Glavas
- Department of Ophthalmology, New York University School of Medicine, New York, New York
| | - David N. Harpp
- Department of Chemistry, McGill University, Montreal, Canada
| | | | - Anastasios N. Mavrakis
- Department of Medicine, Tufts University School of Medicine, St. Elizabeth's Medical Center, Boston, Massachusetts
| | - Julie Pernokas
- Advanced Dental Associates of New England, Woburn, Massachusetts
| | - Mark Pernokas
- Advanced Dental Associates of New England, Woburn, Massachusetts
| | - Carl A. Pinkert
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama
| | - Whitney R. Powers
- Department of Health Sciences, Boston University, Boston, Massachusetts
- Department of Anatomy, Boston University School of Medicine, Boston, Massachusetts
| | - Konstantina Sampani
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts
| | - Kosta Steliou
- Cancer Research Center, Boston University School of Medicine, Boston, Massachusetts
- PhenoMatriX, Inc., Natick, Massachusetts
| | - Demetrios G. Vavvas
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
- Retina Service, Angiogenesis Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | | | | | - Xiaohong Chen
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
- Retina Service, Angiogenesis Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
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26
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Singh N, Chaput L, Villoutreix BO. Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. Brief Bioinform 2020; 22:1790-1818. [PMID: 32187356 PMCID: PMC7986591 DOI: 10.1093/bib/bbaa034] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interplay between life sciences and advancing technology drives a continuous cycle of chemical data growth; these data are most often stored in open or partially open databases. In parallel, many different types of algorithms are being developed to manipulate these chemical objects and associated bioactivity data. Virtual screening methods are among the most popular computational approaches in pharmaceutical research. Today, user-friendly web-based tools are available to help scientists perform virtual screening experiments. This article provides an overview of internet resources enabling and supporting chemical biology and early drug discovery with a main emphasis on web servers dedicated to virtual ligand screening and small-molecule docking. This survey first introduces some key concepts and then presents recent and easily accessible virtual screening and related target-fishing tools as well as briefly discusses case studies enabled by some of these web services. Notwithstanding further improvements, already available web-based tools not only contribute to the design of bioactive molecules and assist drug repositioning but also help to generate new ideas and explore different hypotheses in a timely fashion while contributing to teaching in the field of drug development.
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Affiliation(s)
- Natesh Singh
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 Drugs and Molecules for Living Systems, F-59000 Lille, France
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