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Pinto MF, Sirina J, Holliday ND, McWhirter CL. High-throughput kinetics in drug discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100170. [PMID: 38964171 DOI: 10.1016/j.slasd.2024.100170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
The importance of a drug's kinetic profile and interplay of structure-kinetic activity with PK/PD has long been appreciated in drug discovery. However, technical challenges have often limited detailed kinetic characterization of compounds to the latter stages of projects. This review highlights the advances that have been made in recent years in techniques, instrumentation, and data analysis to increase the throughput of detailed kinetic and mechanistic characterization, enabling its application earlier in the drug discovery process.
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Affiliation(s)
- Maria Filipa Pinto
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom
| | - Julija Sirina
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom
| | - Nicholas D Holliday
- Excellerate Bioscience Ltd, 21 The Triangle, NG2 Business Park, Nottingham, NG2 1AE, United Kingdom; School of Life Sciences, The Medical School, University of Nottingham, Nottingham, NG7 2UH, United Kingdom
| | - Claire L McWhirter
- Artios Pharma Ltd, B940, Babraham Research Campus, Cambridge CB22 3FH, United Kingdom.
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2
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Pal S, Nare Z, Rao VA, Smith BO, Morrison I, Fitzgerald EA, Scott A, Bingham MJ, Pesnot T. Accelerating BRPF1b hit identification with BioPhysical and Active Learning Screening (BioPALS). ChemMedChem 2024; 19:e202300590. [PMID: 38372199 DOI: 10.1002/cmdc.202300590] [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: 10/29/2023] [Revised: 01/25/2024] [Accepted: 02/12/2024] [Indexed: 02/20/2024]
Abstract
We report the development of BioPhysical and Active Learning Screening (BioPALS); a rapid and versatile hit identification protocol combining AI-powered virtual screening with a GCI-driven biophysical confirmation workflow. Its application to the BRPF1b bromodomain afforded a range of novel micromolar binders with favorable ADMET properties. In addition to the excellent in silico/in vitro confirmation rate demonstrated with BRPF1b, binding kinetics were determined, and binding topologies predicted for all hits. BioPALS is a lean, data-rich, and standardized approach to hit identification applicable to a wide range of biological targets.
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Affiliation(s)
- Sandeep Pal
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Zandile Nare
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Vincenzo A Rao
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Brian O Smith
- University of Glasgow, School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, G12 8QQ, Glasgow, UK
| | - Ian Morrison
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | | | - Andrew Scott
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Matilda J Bingham
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
| | - Thomas Pesnot
- Concept Life Sciences, Frith Knoll Road, Chapel-en-le-Frith, SK23 0PG, High Peak, UK
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3
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Zhao X, Guo Z, Zhou Y, Guo J, Liu Z, Luo M, Li Y, Wang Q, Zhang M, Yang X, Wang Y, Sun YL, Wu X. Highly sensitive, modification-free, and dynamic real-time stereo-optical immuno-sensor. Biosens Bioelectron 2023; 237:115477. [PMID: 37352760 DOI: 10.1016/j.bios.2023.115477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/04/2023] [Accepted: 04/14/2023] [Indexed: 06/25/2023]
Abstract
Modification-free biosensing with high specificity and sensitivity is essential for miniaturized, online, integrated, and rapid, or even real-time molecular analyses. However, most optical biosensors are based on surface pre-modification or fluorescent labeling, and have either low sensitivity or low quality factor (Q). To address these difficulties, in this study, an optical sensor prototype was developed with a microbubble optofluidic channel integrated inside a Fabry-Pérot cavity to three-dimensionally tailor the intra-cavity light field via the intra-cavity lensing (microbubble) configuration. A high Q-factor (∼105), small mode volume, and high light energy density were experimentally achieved with this "stereo-sensor" while maintaining an ultrahigh refractive index (RI) sensitivity (679 nm/RIU) and ultra-small RI resolution (∼10-7 RIU at 950 nm). Moreover, specific detection of very low concentration of biomolecules (5 fg/mL for human IgG and 0.5 pg/mL for human serum albumin (HSA)) and wide range of protein concentrations (e.g., fg/mL-ng/mL for human IgG and pg/mL-ng/mL for HSA) without probe pre-modification were achieved owing to the RI change specifically associated with the probe-target binding and the corresponding bio-macromolecular conformation change. This modification-free stereosensing scenario is applicable to continuous, real-time, and multiplexed operations, thus showing potential for online, integrated, dynamic, biomolecular analyses in vitro or in vivo, such as the dynamic metabolic analysis of single cells or organoids and point-of-care tests.
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Affiliation(s)
- Xuyang Zhao
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Zhihe Guo
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Yi Zhou
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Junhong Guo
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Zhiran Liu
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Man Luo
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Yuxiang Li
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Qi Wang
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China
| | - Meng Zhang
- Southwest Institute of Technical Physics, Chengdu, Sichuan, 610041, China
| | - Xi Yang
- Southwest Institute of Technical Physics, Chengdu, Sichuan, 610041, China
| | - You Wang
- Southwest Institute of Technical Physics, Chengdu, Sichuan, 610041, China
| | - Yun-Lu Sun
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiang Wu
- The Key Laboratory of Micro and Nano Photonic Structures, Department of Optical Science and Engineering, Fudan University, Shanghai, 200438, China.
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Zhang DW, Xie L, Xu XS, Li Y, Xu X. A Broad-Spectrum Antiviral Molecule, Protoporphyrin IX, Acts as a Moderator of HIV-1 Capsid Assembly by Targeting the Capsid Hexamer. Microbiol Spectr 2023; 11:e0266322. [PMID: 36475726 PMCID: PMC9927277 DOI: 10.1128/spectrum.02663-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The capsid protein (CA), an essential component of human immunodeficiency virus type 1 (HIV-1), represents an appealing target for antivirals. Small molecules targeting the CAI-binding cavity in the C-terminal domain of HIV-1 CA (CA CTD) confer potent antiviral activities. In this study, we report that a small molecule, protoporphyrin IX (PPIX), targets the HIV-1 CA by binding to this pocket. PPIX was identified via in vitro drug screening, using a homogeneous and time-resolved fluorescence-based assay. CA multimerization and a biolayer interferometry (BLI) assay showed that PPIX promoted CA multimerization and bound directly to CA. The binding model of PPIX to CA CTD revealed that PPIX forms hydrogen bonds with the L211and E212 residues in the CA CTD. Moreover, the BLI assay demonstrated that this compound preferentially binds to the CA hexamer versus the monomer. The superposition of the CAI CTD-PPIX complex and the hexameric CA structure suggests that PPIX binds to the interface formed by the NTD and the CTD between adjacent protomers in the CA hexamer via the T72 and E212 residues, serving as a glue to enhance the multimerization of CA. Taken together, our studies demonstrate that PPIX, a hexamer-targeted CA assembly enhancer, should be a new chemical probe for the discovery of modulators of the HIV-1 capsid assembly. IMPORTANCE CA and its assembled viral core play essential roles in distinct steps during HIV-1 replication, including reverse transcription, integration, nuclear entry, virus assembly, and maturation through CA-CA or CA-host factor interactions. These functions of CA are fundamental for HIV-1 pathogenesis, making it an appealing target for antiviral therapy. In the present study, we identified protoporphyrin IX (PPIX) as a candidate CA modulator that can promote CA assembly and prefers binding the CA hexamer versus the monomer. PPIX, like a glue, bound at the interfaces between CA subunits to accelerate CA multimerization. Therefore, PPIX could be used as a new lead for a CA modulator, and it holds potential research applications.
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Affiliation(s)
- Da-Wei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Liangxu Xie
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Xiao-Shuang Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Yimin Li
- College of Pharmacy and Key Laboratory for Research and Development of “Qin Medicine” of Shaanxi Administration of Chinese Medicine, Shaanxi University of Chinese Medicine, Xixian New District, China
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
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5
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Malle MG, Löffler PMG, Bohr SSR, Sletfjerding MB, Risgaard NA, Jensen SB, Zhang M, Hedegård P, Vogel S, Hatzakis NS. Single-particle combinatorial multiplexed liposome fusion mediated by DNA. Nat Chem 2022; 14:558-565. [PMID: 35379901 DOI: 10.1038/s41557-022-00912-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/17/2022] [Indexed: 12/22/2022]
Abstract
Combinatorial high-throughput methodologies are central for both screening and discovery in synthetic biochemistry and biomedical sciences. They are, however, often reliant on large-scale analyses and thus limited by a long running time and excessive materials cost. We here present a single-particle combinatorial multiplexed liposome fusion mediated by DNA for parallelized multistep and non-deterministic fusion of individual subattolitre nanocontainers. We observed directly the efficient (>93%) and leakage free stochastic fusion sequences for arrays of surface-tethered target liposomes with six freely diffusing populations of cargo liposomes, each functionalized with individual lipidated single-stranded DNA and fluorescently barcoded by a distinct ratio of chromophores. The stochastic fusion resulted in a distinct permutation of fusion sequences for each autonomous nanocontainer. Real-time total internal reflection imaging allowed the direct observation of >16,000 fusions and 566 distinct fusion sequences accurately classified using machine learning. The high-density arrays of surface-tethered target nanocontainers (~42,000 containers per mm2) offers entire combinatorial multiplex screens using only picograms of material.
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Affiliation(s)
- Mette Galsgaard Malle
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Berg Sletfjerding
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Simon Bo Jensen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Hedegård
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Copenhagen, Denmark. .,Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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Sowa ST, Galera-Prat A, Wazir S, Alanen HI, Maksimainen MM, Lehtiö L. A molecular toolbox for ADP-ribosyl binding proteins. CELL REPORTS METHODS 2021; 1:100121. [PMID: 34786571 PMCID: PMC8580838 DOI: 10.1016/j.crmeth.2021.100121] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 11/04/2021] [Indexed: 12/24/2022]
Abstract
Proteins interacting with ADP-ribosyl groups are often involved in disease-related pathways or viral infections, making them attractive drug targets. We present a robust and accessible assay applicable to both hydrolyzing or non-hydrolyzing binders of mono- and poly-ADP-ribosyl groups. This technology relies on a C-terminal tag based on a Gi protein alpha subunit peptide (GAP), which allows for site-specific introduction of cysteine-linked mono- and poly-ADP-ribosyl groups or analogs. By fusing the GAP-tag and ADP-ribosyl binders to fluorescent proteins, we generate robust FRET partners and confirm the interaction with 22 known ADP-ribosyl binders. The applicability for high-throughput screening of inhibitors is demonstrated with the SARS-CoV-2 nsp3 macrodomain, for which we identify suramin as a moderate-affinity yet non-specific inhibitor. High-affinity ADP-ribosyl binders fused to nanoluciferase complement this technology, enabling simple blot-based detection of ADP-ribosylated proteins. All these tools can be produced in Escherichia coli and will help in ADP-ribosylation research and drug discovery.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Albert Galera-Prat
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Sarah Wazir
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Heli I. Alanen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Mirko M. Maksimainen
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 90220 Oulu, Finland
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7
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Abstract
The emerging risk of viral diseases has triggered the search for preventive and therapeutic agents. Since the beginning of the COVID-19 pandemic, greater efforts have been devoted to investigating virus entry mechanisms into host cells. The feasibility of plasmonic sensing technologies for screening interactions of small molecules in real time, while providing the pharmacokinetic drug profiling of potential antiviral compounds, offers an advantageous approach over other biophysical methods. This review summarizes recent advancements in the drug discovery process of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) inhibitors using Surface Plasmon Resonance (SPR) biosensors. A variety of SPR assay formats are discussed according to the binding kinetics and drug efficacies of both natural products and repurposed drugs. Special attention has been given to the targeting of antiviral agents that block the receptor binding domain of the spike protein (RBD-S) and the main protease (3CLpro) of SARS-CoV-2. The functionality of plasmonic biosensors for high-throughput screening of entry virus inhibitors was also reviewed taking into account experimental parameters (binding affinities, selectivity, stability), potential limitations and future applications.
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8
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Tao Y, Chen L, Pan M, Zhu F, Zhu D. Tailored Biosensors for Drug Screening, Efficacy Assessment, and Toxicity Evaluation. ACS Sens 2021; 6:3146-3162. [PMID: 34516080 DOI: 10.1021/acssensors.1c01600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biosensors have been flourishing in the field of drug discovery with pronounced developments in the past few years. They facilitate the screening and discovery of innovative drugs. However, there is still a lack of critical reviews that compare the merits and shortcomings of these biosensors from a pharmaceutical point of view. This contribution presents a critical and up-to-date overview on the recent progress of tailored biosensors, including surface plasmon resonance, fluorescent, photoelectrochemical, and electrochemical systems with emphasis on their mechanisms and applications in drug screening, efficacy assessment, and toxicity evaluation. Multiple functional nanomaterials have also been incorporated into the biosensors. Representative examples of each type of biosensors are discussed in terms of design strategy, response mechanism, and potential applications. In the end, we also compare the results and summarize the major insights gained from the works, demonstrating the challenges and prospects of biosensors-assisted drug discovery.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Lin Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Meiling Pan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fei Zhu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dong Zhu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
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Vaz R, Valpradinhos B, Frasco MF, Sales MGF. Emerging Optical Materials in Sensing and Discovery of Bioactive Compounds. SENSORS (BASEL, SWITZERLAND) 2021; 21:5784. [PMID: 34502675 PMCID: PMC8434157 DOI: 10.3390/s21175784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/20/2021] [Accepted: 08/22/2021] [Indexed: 11/16/2022]
Abstract
Optical biosensors are used in numerous applications and analytical fields. Advances in these sensor platforms offer high sensitivity, selectivity, miniaturization, and real-time analysis, among many other advantages. Research into bioactive natural products serves both to protect against potentially dangerous toxic compounds and to promote pharmacological innovation in drug discovery, as these compounds have unique chemical compositions that may be characterized by greater safety and efficacy. However, conventional methods for detecting these biomolecules have drawbacks, as they are time-consuming and expensive. As an alternative, optical biosensors offer a faster, simpler, and less expensive means of detecting various biomolecules of clinical interest. In this review, an overview of recent developments in optical biosensors for the detection and monitoring of aquatic biotoxins to prevent public health risks is first provided. In addition, the advantages and applicability of these biosensors in the field of drug discovery, including high-throughput screening, are discussed. The contribution of the investigated technological advances in the timely and sensitive detection of biotoxins while deciphering the pathways to discover bioactive compounds with great health-promoting prospects is envisaged to meet the increasing demands of healthcare systems.
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Affiliation(s)
- Raquel Vaz
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
| | - Beatriz Valpradinhos
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Manuela F. Frasco
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Maria Goreti F. Sales
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, 3030-790 Coimbra, Portugal; (R.V.); (M.G.F.S.)
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- BioMark@ISEP, School of Engineering, Polytechnic Institute of Porto, 4249-015 Porto, Portugal
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10
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Bian Y, Hou W, Chen X, Fang J, Xu N, Ruan BH. Glutamate Dehydrogenase as a Promising Target for Hyperinsulinism Hyperammonemia Syndrome Therapy. Curr Med Chem 2021; 29:2652-2672. [PMID: 34525914 DOI: 10.2174/0929867328666210825105342] [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: 04/05/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022]
Abstract
Hyperinsulinism-hyperammonemia syndrome (HHS) is a rare disease characterized by recurrent hypoglycemia and persistent elevation of plasma ammonia, and it can lead to severe epilepsy and permanent brain damage. It has been demonstrated that functional mutations of glutamate dehydrogenase (GDH), an enzyme in the mitochondrial matrix, are responsible for the HHS. Thus, GDH has become a promising target for the small molecule therapeutic intervention of HHS. Several medicinal chemistry studies are currently aimed at GDH, however, to date, none of the compounds reported has been entered clinical trials. This perspective summarizes the progress in the discovery and development of GDH inhibitors, including the pathogenesis of HHS, potential binding sites, screening methods, and research models. Future therapeutic perspectives are offered to provide a reference for discovering potent GDH modulators and encourage additional research that will provide more comprehensive guidance for drug development.
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Affiliation(s)
- Yunfei Bian
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
| | - Wei Hou
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
| | - Xinrou Chen
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
| | - Jinzhang Fang
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
| | - Ning Xu
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
| | - Benfang Helen Ruan
- College of Pharmaceutical Science, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hantgzhou 310014. China
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11
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Aldewachi H, Al-Zidan RN, Conner MT, Salman MM. High-Throughput Screening Platforms in the Discovery of Novel Drugs for Neurodegenerative Diseases. Bioengineering (Basel) 2021; 8:30. [PMID: 33672148 PMCID: PMC7926814 DOI: 10.3390/bioengineering8020030] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases (NDDs) are incurable and debilitating conditions that result in progressive degeneration and/or death of nerve cells in the central nervous system (CNS). Identification of viable therapeutic targets and new treatments for CNS disorders and in particular, for NDDs is a major challenge in the field of drug discovery. These difficulties can be attributed to the diversity of cells involved, extreme complexity of the neural circuits, the limited capacity for tissue regeneration, and our incomplete understanding of the underlying pathological processes. Drug discovery is a complex and multidisciplinary process. The screening attrition rate in current drug discovery protocols mean that only one viable drug may arise from millions of screened compounds resulting in the need to improve discovery technologies and protocols to address the multiple causes of attrition. This has identified the need to screen larger libraries where the use of efficient high-throughput screening (HTS) becomes key in the discovery process. HTS can investigate hundreds of thousands of compounds per day. However, if fewer compounds could be screened without compromising the probability of success, the cost and time would be largely reduced. To that end, recent advances in computer-aided design, in silico libraries, and molecular docking software combined with the upscaling of cell-based platforms have evolved to improve screening efficiency with higher predictability and clinical applicability. We review, here, the increasing role of HTS in contemporary drug discovery processes, in particular for NDDs, and evaluate the criteria underlying its successful application. We also discuss the requirement of HTS for novel NDD therapies and examine the major current challenges in validating new drug targets and developing new treatments for NDDs.
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Affiliation(s)
- Hasan Aldewachi
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield S1 1WB, UK;
- College of Pharmacy, Nineveh University, Mosul 41002, Iraq
| | - Radhwan N. Al-Zidan
- College of Pharmacy, University of Mosul, Mosul 41002, Iraq;
- School of Applied Sciences, Edinburgh Napier University, Edinburgh EH11 4BN, UK
| | - Matthew T. Conner
- School of Sciences, Research Institute in Healthcare Science, University of Wolverhampton, Wolverhampton WV1 1LY, UK;
| | - Mootaz M. Salman
- College of Pharmacy, University of Mosul, Mosul 41002, Iraq;
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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12
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Abstract
Optical biosensors have exhibited worthwhile performance in detecting biological systems and promoting significant advances in clinical diagnostics, drug discovery, food process control, and environmental monitoring. Without complexity in their pretreatment and probable influence on the nature of target molecules, these biosensors have additional advantages such as high sensitivity, robustness, reliability, and potential to be integrated on a single chip. In this review, the state of the art optical biosensor technologies, including those based on surface plasmon resonance (SPR), optical waveguides, optical resonators, photonic crystals, and optical fibers, are presented. The principles for each type of biosensor are concisely introduced and particular emphasis has been placed on recent achievements. The strengths and weaknesses of each type of biosensor have been outlined as well. Concluding remarks regarding the perspectives of future developments are discussed.
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Affiliation(s)
- Chen Chen
- College of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
| | - Junsheng Wang
- College of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China.
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13
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Akkilic N, Geschwindner S, Höök F. Single-molecule biosensors: Recent advances and applications. Biosens Bioelectron 2019; 151:111944. [PMID: 31999573 DOI: 10.1016/j.bios.2019.111944] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023]
Abstract
Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.
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Affiliation(s)
- Namik Akkilic
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead Generation, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Höök
- Department of Applied Physics, Division of Biological Physics, Chalmers University of Technology, Gothenburg, Sweden.
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14
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Kim DM, Yao X, Vanam RP, Marlow MS. Measuring the effects of macromolecular crowding on antibody function with biolayer interferometry. MAbs 2019; 11:1319-1330. [PMID: 31401928 PMCID: PMC6748605 DOI: 10.1080/19420862.2019.1647744] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biotherapeutic proteins are commonly dosed at high concentrations into the blood, which is an inherently complex, crowded solution with substantial protein content. The effects of macromolecular crowding may lead to an appreciable level of non-specific hetero-association in this physiological environment. Therefore, developing a method to characterize the diverse consequences of non-specific interactions between proteins under such non-ideal, crowded conditions, which deviate substantially from those commonly employed for in vitro characterization, is vital to achieving a more complete picture of antibody function in a biological context. In this study, we investigated non-specific interactions between human serum albumin (HSA) and two monoclonal antibodies (mAbs) by static light scattering and determined these interactions are both ionic strength-dependent and mAb-dependent. Using biolayer interferometry (BLI), we assessed the effect of HSA on antigen binding by mAbs, demonstrating that these non-specific interactions have a functional impact on mAb:antigen interactions, particularly at low ionic strength. While this effect is mitigated at physiological ionic strength, our in vitro data support the notion that HSA in the blood may lead to non-specific interactions with mAbs in vivo, with a potential impact on their interactions with antigen. Furthermore, the BLI method offers a high-throughput advantage compared to orthogonal techniques such as analytical ultracentrifugation and is amenable to a greater variety of solution conditions compared to nuclear magnetic resonance spectroscopy. Our study demonstrates that BLI is a viable technology for examining the impact of non-specific interactions on specific biologically relevant interactions, providing a direct method to assess binding events in crowded conditions.
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Affiliation(s)
- Dorothy M Kim
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Xiao Yao
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Ram P Vanam
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA
| | - Michael S Marlow
- Pre-Clinical Development and Protein Chemistry, Regeneron Pharmaceuticals, Inc ., Tarrytown , NY , USA.,Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc ., Ridgefield , CT , USA
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15
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Yavas O, Aćimović SS, Garcia-Guirado J, Berthelot J, Dobosz P, Sanz V, Quidant R. Self-Calibrating On-Chip Localized Surface Plasmon Resonance Sensing for Quantitative and Multiplexed Detection of Cancer Markers in Human Serum. ACS Sens 2018; 3:1376-1384. [PMID: 29947221 DOI: 10.1021/acssensors.8b00305] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The need for point-of-care devices able to detect diseases early and monitor their status, out of a lab environment, has stimulated the development of compact biosensing configurations. Whereas localized surface plasmon resonance (LSPR) sensing integrated into a state-of-the-art microfluidic chip stands as a promising approach to meet this demand, its implementation into an operating sensing platform capable of quantitatively detecting a set of molecular biomarkers in an unknown biological sample is only in its infancy. Here, we present an on-chip LSPR sensor capable of performing automatic, quantitative, and multiplexed screening of biomarkers. We demonstrate its versatility by programming it to detect and quantify in human serum four relevant human serum protein markers associated with breast cancer.
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Affiliation(s)
- Ozlem Yavas
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Srdjan S. Aćimović
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Jose Garcia-Guirado
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Johann Berthelot
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Paulina Dobosz
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Vanesa Sanz
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
| | - Romain Quidant
- ICFO-Institut de Ciéncies Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels, Barcelona, Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
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16
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Kaminski T, Geschwindner S. Perspectives on optical biosensor utility in small-molecule screening. Expert Opin Drug Discov 2017; 12:1083-1086. [PMID: 28777014 DOI: 10.1080/17460441.2017.1364727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tim Kaminski
- a Discovery Sciences, Innovative Medicines and Early Development Biotech Unit , AstraZeneca R&D Gothenburg , Mölndal , Sweden
| | - Stefan Geschwindner
- a Discovery Sciences, Innovative Medicines and Early Development Biotech Unit , AstraZeneca R&D Gothenburg , Mölndal , Sweden
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17
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Chilton M, Clennell B, Edfeldt F, Geschwindner S. Hot-Spotting with Thermal Scanning: A Ligand- and Structure-Independent Assessment of Target Ligandability. J Med Chem 2017; 60:4923-4931. [PMID: 28537726 DOI: 10.1021/acs.jmedchem.7b00208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Evaluating the ligandability of a protein target is a key component when defining hit-finding strategies or when prioritize among drug targets. Computational as well as biophysical approaches based on nuclear magnetic resonance (NMR) fragment screening are powerful approaches but suffer from specific constraints that limit their usage. Here, we demonstrate the applicability of high-throughput thermal scanning (HTTS) as a simple and generic biophysical fragment screening method to reproduce assessments from NMR-based screening. By applying this method to a large set of proteins we can furthermore show that the assessment is predictive of the success of high-throughput screening (HTS). The few divergences for targets of low ligandability originate from the sensitivity differences of the orthogonal biophysical methods. We thus applied a new strategy making use of modulations in the solvent structure to improve assay sensitivity. This novel approach enables improved ligandability assessments in accordance with NMR-based assessments and more importantly positions the methodology as a valuable option for biophysical fragment screening.
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Affiliation(s)
- Molly Chilton
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Ben Clennell
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Fredrik Edfeldt
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
| | - Stefan Geschwindner
- Innovative Medicines and Early Development Biotech Unit, Discovery Sciences, AstraZeneca R&D Gothenburg , 43183 Mölndal, Sweden
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