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Singh A, Dhau J, Kumar R, Badru R, Kaushik A. Exploring the fluorescence properties of tellurium-containing molecules and their advanced applications. Phys Chem Chem Phys 2024; 26:9816-9847. [PMID: 38497121 DOI: 10.1039/d3cp05740b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
This review article explores the fascinating realm of fluorescence using organochalcogen molecules, with a particular emphasis on tellurium (Te). The discussion encompasses the underlying mechanisms, structural motifs influencing fluorescence, and the applications of these intriguing phenomena. This review not only elucidates the current state of knowledge but also identifies avenues for future research, thereby serving as a valuable resource for researchers and enthusiasts in the field of fluorescence chemistry with a focus on Te-based molecules. By highlighting challenges and prospects, this review sparks a conversation on the transformative potential of Te-containing compounds across different fields, ranging from environmental solutions to healthcare and materials science applications. This review aims to provide a comprehensive understanding of the distinct fluorescence behaviors exhibited by Te-containing compounds, contributing valuable insights to the evolving landscape of chalcogen-based fluorescence research.
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Affiliation(s)
- Avtar Singh
- Research and Development, Molekule Group Inc., 3802 Spectrum Blvd., Tampa, Florida 33612, USA.
- Department of Chemistry, Sri Guru Teg Bahadur Khalsa College, Anandpur Sahib, Punjab 140118, India
| | - Jaspreet Dhau
- Research and Development, Molekule Group Inc., 3802 Spectrum Blvd., Tampa, Florida 33612, USA.
| | - Rajeev Kumar
- Department of Environment Studies, Panjab University, Chandigarh 160014, India
| | - Rahul Badru
- Department of Chemistry, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab 140406, India
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, FL 33805, USA
- School of Engineering, University of Petroleum and Energy Studies (UPES), Dehradun, Uttarakhand, India
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2
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Fuchs N, Zhang L, Calvo-Barreiro L, Kuncewicz K, Gabr M. Inhibitors of Immune Checkpoints: Small Molecule- and Peptide-Based Approaches. J Pers Med 2024; 14:68. [PMID: 38248769 PMCID: PMC10817355 DOI: 10.3390/jpm14010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
The revolutionary progress in cancer immunotherapy, particularly the advent of immune checkpoint inhibitors, marks a significant milestone in the fight against malignancies. However, the majority of clinically employed immune checkpoint inhibitors are monoclonal antibodies (mAbs) with several limitations, such as poor oral bioavailability and immune-related adverse effects (irAEs). Another major limitation is the restriction of the efficacy of mAbs to a subset of cancer patients, which triggered extensive research efforts to identify alternative approaches in targeting immune checkpoints aiming to overcome the restricted efficacy of mAbs. This comprehensive review aims to explore the cutting-edge developments in targeting immune checkpoints, focusing on both small molecule- and peptide-based approaches. By delving into drug discovery platforms, we provide insights into the diverse strategies employed to identify and optimize small molecules and peptides as inhibitors of immune checkpoints. In addition, we discuss recent advances in nanomaterials as drug carriers, providing a basis for the development of small molecule- and peptide-based platforms for cancer immunotherapy. Ongoing research focused on the discovery of small molecules and peptide-inspired agents targeting immune checkpoints paves the way for developing orally bioavailable agents as the next-generation cancer immunotherapies.
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Affiliation(s)
- Natalie Fuchs
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Longfei Zhang
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Laura Calvo-Barreiro
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
| | - Katarzyna Kuncewicz
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
- Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland
| | - Moustafa Gabr
- Molecular Imaging Innovations Institute (MI3), Department of Radiology, Weill Cornell Medicine, New York, NY 10065, USA; (N.F.); (L.Z.); (L.C.-B.); (K.K.)
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3
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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4
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Wlodkowic D, Jansen M. High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges. CHEMOSPHERE 2022; 307:135929. [PMID: 35944679 DOI: 10.1016/j.chemosphere.2022.135929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/09/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.
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Affiliation(s)
- Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Melbourne, VIC, 3083, Australia.
| | - Marcus Jansen
- LemnaTec GmbH, Nerscheider Weg 170, 52076, Aachen, Germany
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Putt KS, Du Y, Fu H, Zhang ZY. High-throughput screening strategies for space-based radiation countermeasure discovery. LIFE SCIENCES IN SPACE RESEARCH 2022; 35:88-104. [PMID: 36336374 DOI: 10.1016/j.lssr.2022.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
As humanity begins to venture further into space, approaches to better protect astronauts from the hazards found in space need to be developed. One particular hazard of concern is the complex radiation that is ever present in deep space. Currently, it is unlikely enough spacecraft shielding could be launched that would provide adequate protection to astronauts during long-duration missions such as a journey to Mars and back. In an effort to identify other means of protection, prophylactic radioprotective drugs have been proposed as a potential means to reduce the biological damage caused by this radiation. Unfortunately, few radioprotectors have been approved by the FDA for usage and for those that have been developed, they protect normal cells/tissues from acute, high levels of radiation exposure such as that from oncology radiation treatments. To date, essentially no radioprotectors have been developed that specifically counteract the effects of chronic low-dose rate space radiation. This review highlights how high-throughput screening (HTS) methodologies could be implemented to identify such a radioprotective agent. Several potential target, pathway, and phenotypic assays are discussed along with potential challenges towards screening for radioprotectors. Utilizing HTS strategies such as the ones proposed here have the potential to identify new chemical scaffolds that can be developed into efficacious radioprotectors that are specifically designed to protect astronauts during deep space journeys. The overarching goal of this review is to elicit broader interest in applying drug discovery techniques, specifically HTS towards the identification of radiation countermeasures designed to be efficacious towards the biological insults likely to be encountered by astronauts on long duration voyages.
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Affiliation(s)
- Karson S Putt
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Zhong-Yin Zhang
- Institute for Drug Discovery, Purdue University, West Lafayette IN 47907 USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette IN 47907 USA.
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6
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Zhang SY, Zhao J, Ni JJ, Li H, Quan ZZ, Qing H. Application and prospects of high-throughput screening for in vitro neurogenesis. World J Stem Cells 2022; 14:393-419. [PMID: 35949394 PMCID: PMC9244953 DOI: 10.4252/wjsc.v14.i6.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/07/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Over the past few decades, high-throughput screening (HTS) has made great contributions to new drug discovery. HTS technology is equipped with higher throughput, minimized platforms, more automated and computerized operating systems, more efficient and sensitive detection devices, and rapid data processing systems. At the same time, in vitro neurogenesis is gradually becoming important in establishing models to investigate the mechanisms of neural disease or developmental processes. However, challenges remain in generating more mature and functional neurons with specific subtypes and in establishing robust and standardized three-dimensional (3D) in vitro models with neural cells cultured in 3D matrices or organoids representing specific brain regions. Here, we review the applications of HTS technologies on in vitro neurogenesis, especially aiming at identifying the essential genes, chemical small molecules and adaptive microenvironments that hold great prospects for generating functional neurons or more reproductive and homogeneous 3D organoids. We also discuss the developmental tendency of HTS technology, e.g., so-called next-generation screening, which utilizes 3D organoid-based screening combined with microfluidic devices to narrow the gap between in vitro models and in vivo situations both physiologically and pathologically.
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Affiliation(s)
- Shu-Yuan Zhang
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Juan Zhao
- Aerospace Medical Center, Aerospace Center Hospital, Beijing 100049, China
| | - Jun-Jun Ni
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hui Li
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Zhen-Zhen Quan
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy in the Ministry of Industry and Information Technology, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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7
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Salame N, Fooks K, El-Hachem N, Bikorimana JP, Mercier FE, Rafei M. Recent Advances in Cancer Drug Discovery Through the Use of Phenotypic Reporter Systems, Connectivity Mapping, and Pooled CRISPR Screening. Front Pharmacol 2022; 13:852143. [PMID: 35795568 PMCID: PMC9250974 DOI: 10.3389/fphar.2022.852143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Multi-omic approaches offer an unprecedented overview of the development, plasticity, and resistance of cancer. However, the translation from anti-cancer compounds identified in vitro to clinically active drugs have a notoriously low success rate. Here, we review how technical advances in cell culture, robotics, computational biology, and development of reporter systems have transformed drug discovery, enabling screening approaches tailored to clinically relevant functional readouts (e.g., bypassing drug resistance). Illustrating with selected examples of “success stories,” we describe the process of phenotype-based high-throughput drug screening to target malignant cells or the immune system. Second, we describe computational approaches that link transcriptomic profiling of cancers with existing pharmaceutical compounds to accelerate drug repurposing. Finally, we review how CRISPR-based screening can be applied for the discovery of mechanisms of drug resistance and sensitization. Overall, we explore how the complementary strengths of each of these approaches allow them to transform the paradigm of pre-clinical drug development.
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Affiliation(s)
- Natasha Salame
- Department of Biomedical Sciences, Université de Montréal, Montreal, QC, Canada
| | - Katharine Fooks
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Nehme El-Hachem
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Bikorimana
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
| | - François E. Mercier
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
| | - Moutih Rafei
- Department of Pharmacology and Physiology, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Université de Montréal, Montreal, QC, Canada
- Molecular Biology Program, Université de Montréal, Montreal, QC, Canada
- *Correspondence: François E. Mercier, ; Moutih Rafei,
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8
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DNA-encoded chemistry technology yields expedient access to SARS-CoV-2 M pro inhibitors. Proc Natl Acad Sci U S A 2021; 118:2111172118. [PMID: 34426525 PMCID: PMC8433497 DOI: 10.1073/pnas.2111172118] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed more than 4 million humans globally, but there is no bona fide Food and Drug Administration-approved drug-like molecule to impede the COVID-19 pandemic. The sluggish pace of traditional therapeutic discovery is poorly suited to producing targeted treatments against rapidly evolving viruses. Here, we used an affinity-based screen of 4 billion DNA-encoded molecules en masse to identify a potent class of virus-specific inhibitors of the SARS-CoV-2 main protease (Mpro) without extensive and time-consuming medicinal chemistry. CDD-1714, the initial three-building-block screening hit (molecular weight [MW] = 542.5 g/mol), was a potent inhibitor (inhibition constant [K i] = 20 nM). CDD-1713, a smaller two-building-block analog (MW = 353.3 g/mol) of CDD-1714, is a reversible covalent inhibitor of Mpro (K i = 45 nM) that binds in the protease pocket, has specificity over human proteases, and shows in vitro efficacy in a SARS-CoV-2 infectivity model. Subsequently, key regions of CDD-1713 that were necessary for inhibitory activity were identified and a potent (K i = 37 nM), smaller (MW = 323.4 g/mol), and metabolically more stable analog (CDD-1976) was generated. Thus, screening of DNA-encoded chemical libraries can accelerate the discovery of efficacious drug-like inhibitors of emerging viral disease targets.
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9
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Yang L, Pijuan-Galito S, Rho HS, Vasilevich AS, Eren AD, Ge L, Habibović P, Alexander MR, de Boer J, Carlier A, van Rijn P, Zhou Q. High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology. Chem Rev 2021; 121:4561-4677. [PMID: 33705116 PMCID: PMC8154331 DOI: 10.1021/acs.chemrev.0c00752] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/07/2023]
Abstract
The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount of potential material parameter combinations to identify the optimal cell responses and involve a combination of serendipity and many series of trial-and-error experiments. For advanced tissue engineering and regenerative medicine, highly efficient and complex bioanalysis platforms are expected to explore the complex interaction of cells with biomaterials using combinatorial approaches that offer desired complex microenvironments during healing, development, and homeostasis. In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.
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Affiliation(s)
- Liangliang Yang
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Sara Pijuan-Galito
- School
of Pharmacy, Biodiscovery Institute, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Hoon Suk Rho
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aliaksei S. Vasilevich
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lu Ge
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pamela Habibović
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Morgan R. Alexander
- School
of Pharmacy, Boots Science Building, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Jan de Boer
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aurélie Carlier
- Department
of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Patrick van Rijn
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qihui Zhou
- Institute
for Translational Medicine, Department of Stomatology, The Affiliated
Hospital of Qingdao University, Qingdao
University, Qingdao 266003, China
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Functional metabolomics innovates therapeutic discovery of traditional Chinese medicine derived functional compounds. Pharmacol Ther 2021; 224:107824. [PMID: 33667524 DOI: 10.1016/j.pharmthera.2021.107824] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Traditional Chinese medicines (TCMs) produce chemically diverse functional compounds that are importantly chemical resource for facilitating new drug discovery and development against a diversity of diseases. However, modern exploration of TCM derived functional compounds is significantly hindered by the inefficient elucidation of pharmacological functions over past decades, because conventional research methods are incapable of efficiently elucidating therapeutic potential of TCM conferred by multiple functional compounds. Functional metabolomics has the priority-capacity to characterize systems therapeutic actions of TCM by precisely capturing molecular interactions between disease response metabolite biomarkers (DRMB) and functional compounds (secondary metabolites), which underline pharmacological efficiency and associated therapeutic mechanisms. In this critical review, we innovatively summarize systems therapeutic feature of TCM derived functional compounds from a functional-metabolism perspective, then systems metabolic targets (SMT) identified by functional metabolomics method are strategically proposed to better understanding of therapeutic discovery of TCM derived functional compounds. In addition, we propose the perspective strategy as Spatial Temporal Operative Real Metabolomics (STORM) to considerably improve analytical capacity of functional metabolomics method by selectively incorporating the cutting edge technologies of mass spectrometry imaging, isotope-metabolic fluxomics, synthetic and biosynthetic chemistry, which could considerably enhance the precision and resolution of elucidating pharmacological efficiency and associated therapeutic mechanisms of TCM derived functional compounds. Collectively, such critical review is expected to provide novel perspective-strategy that could significantly improve modern exploration and exploitation of TCM derived functional compounds that further promote new drug discovery and development against the complex diseases.
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Shiuan D, Tai DF, Huang KJ, Yu Z, Ni F, Li J. Target-based discovery of therapeutic agents from food ingredients. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Ishigami-Yuasa M, Kagechika H. Chemical Screening of Nuclear Receptor Modulators. Int J Mol Sci 2020; 21:E5512. [PMID: 32752136 PMCID: PMC7432305 DOI: 10.3390/ijms21155512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 12/15/2022] Open
Abstract
Nuclear receptors are ligand-inducible transcriptional factors that control multiple biological phenomena, including proliferation, differentiation, reproduction, metabolism, and the maintenance of homeostasis. Members of the nuclear receptor superfamily have marked structural and functional similarities, and their domain functionalities and regulatory mechanisms have been well studied. Various modulators of nuclear receptors, including agonists and antagonists, have been developed as tools for elucidating nuclear receptor functions and also as drug candidates or lead compounds. Many assay systems are currently available to evaluate the modulation of nuclear receptor functions, and are useful as screening tools in the discovery and development of new modulators. In this review, we cover the chemical screening methods for nuclear receptor modulators, focusing on assay methods and chemical libraries for screening. We include some recent examples of the discovery of nuclear receptor modulators.
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Affiliation(s)
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan;
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13
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Biological and Computational Studies for Dual Cholinesterases Inhibitory Effect of Zerumbone. Nutrients 2020; 12:nu12051215. [PMID: 32344943 PMCID: PMC7281973 DOI: 10.3390/nu12051215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022] Open
Abstract
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) mediate the degradation of acetylcholine (ACh), a primary neurotransmitter in the brain. Cholinergic deficiency occurs during the progression of Alzheimer’s disease (AD), resulting in widespread cognitive dysfunction and decline. We evaluated the potential effect of a natural cholinesterase inhibitor, zerumbone, using in vitro target enzyme assays, as well as in silico docking and ADMET (absorption, distribution, metabolism, excretion, and toxicity) simulation. Zerumbone showed a predominant cholinesterase inhibitory property with IC50 values of 2.74 ± 0.48 µM and 4.12 ± 0.42 µM for AChE and BChE, respectively; however, the modes of inhibition were different. Computational docking simulation indicated that Van der Waals interactions between zerumbone and both the cholinesterases were the main forces responsible for its inhibitory effects. Furthermore, zerumbone showed the best physicochemical properties for both bioavailability and blood–brain barrier (BBB) permeability. Together, in the present study, zerumbone was clearly identified as a unique dual AChE and BChE inhibitor with high permeability across the BBB, suggesting a strong potential for its physiological benefits and/or pharmacological efficacy in the prevention of AD.
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14
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Affiliation(s)
- Soumava Santra
- Department of ChemistryLovelyProfessional University, NH-41, Phagwara Punjab 144411 India
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15
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Lee EY, Kim S, Kim MH. Aminoacyl-tRNA synthetases, therapeutic targets for infectious diseases. Biochem Pharmacol 2018; 154:424-434. [PMID: 29890143 PMCID: PMC7092877 DOI: 10.1016/j.bcp.2018.06.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
Despite remarkable advances in medical science, infection-associated diseases remain among the leading causes of death worldwide. There is a great deal of interest and concern at the rate at which new pathogens are emerging and causing significant human health problems. Expanding our understanding of how cells regulate signaling networks to defend against invaders and retain cell homeostasis will reveal promising strategies against infection. It has taken scientists decades to appreciate that eukaryotic aminoacyl-tRNA synthetases (ARSs) play a role as global cell signaling mediators to regulate cell homeostasis, beyond their intrinsic function as protein synthesis enzymes. Recent discoveries revealed that ubiquitously expressed standby cytoplasmic ARSs sense and respond to danger signals and regulate immunity against infections, indicating their potential as therapeutic targets for infectious diseases. In this review, we discuss ARS-mediated anti-infectious signaling and the emerging role of ARSs in antimicrobial immunity. In contrast to their ability to defend against infection, host ARSs are inevitably co-opted by viruses for survival and propagation. We therefore provide a brief overview of the communication between viruses and the ARS system. Finally, we discuss encouraging new approaches to develop ARSs as therapeutics for infectious diseases.
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Affiliation(s)
- Eun-Young Lee
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea; College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34141, Republic of Korea.
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16
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Kozak K, Rinn B, Leven O, Emmenlauer M. Strategies and Solutions to Maintain and Retain Data from High Content Imaging, Analysis, and Screening Assays. Methods Mol Biol 2018; 1683:131-148. [PMID: 29082491 DOI: 10.1007/978-1-4939-7357-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Data analysis and management in high content screening (HCS) has progressed significantly in the past 10 years. The analysis of the large volume of data generated in HCS experiments represents a significant challenge and is currently a bottleneck in many screening projects. In most screening laboratories, HCS has become a standard technology applied routinely to various applications from target identification to hit identification to lead optimization. An HCS data management and analysis infrastructure shared by several research groups can allow efficient use of existing IT resources and ensures company-wide standards for data quality and result generation. This chapter outlines typical HCS workflows and presents IT infrastructure requirements for multi-well plate-based HCS.
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Affiliation(s)
- K Kozak
- Carl Gustav Carus University Hospital, Clinic for Neurology, Medical Faculty, Technical University Dresden, Fetscherstraße 74, 01307, Dresden, Germany. .,Fraunhofer IWS, Winterbergstraße 28, Dresden, 01277, Germany. .,Wroclaw University of Economics, Wrocław, Poland.
| | - B Rinn
- Scientific IT Services, ETH Zürich, Zurich, Switzerland
| | - O Leven
- Screener Business Unit, Genedata AG, Basel, Switzerland
| | - M Emmenlauer
- University of Basel and SyBIT, Basel, Switzerland
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17
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Kist R, Timmers LFSM, Caceres RA. Searching for potential mTOR inhibitors: Ligand-based drug design, docking and molecular dynamics studies of rapamycin binding site. J Mol Graph Model 2017; 80:251-263. [PMID: 29414044 DOI: 10.1016/j.jmgm.2017.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/19/2017] [Accepted: 12/21/2017] [Indexed: 12/17/2022]
Abstract
The PI3K/Akt/mTOR pathway is an important intracellular signaling pathway in cell cycle regulation and its dysregulation is associated with various types of diseases. mTOR (mechanistic or mammalian target of rapamycin) is the main enzyme that performs intermediate control of the signaling pathway through a phosphotransfer process. The classical inhibition of the mTOR pathway is effected by rapamycin and its analogous blocking allosterically the catalytic phosphorylation site, avoiding the deleterious side effects induced by ATP-competitive inhibitors. We employed ligand-based drug design strategies such as pharmacophore searching and analysis, molecular docking, absorption, distribution, metabolism, excretion and toxicity (ADMETox) properties filtering, and molecular dynamics to select potential molecules to become non-ATP competitive inhibitors of the mTOR complex. According to our findings, we propose eight novel potential mTOR inhibitors with similar or better properties than the classic inhibitor complex, rapamycin.
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Affiliation(s)
- Roger Kist
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil
| | - Luis Fernando Saraiva Macedo Timmers
- Laboratory for Bioinformatics, Modelling and Simulation of Biosystems-LABIO, Pontifical Catholic University of Rio Grande do Sul-PUCRS, Porto Alegre City, Brazil; Graduate Program in Cellular and Molecular Biology (PPGBCM), PUCRS, Porto Alegre, RS, Brazil
| | - Rafael Andrade Caceres
- Graduate Program in Health Sciences of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil; Pharmacosciences Department of Federal University of Health Sciences of Porto Alegre-UFCSPA, Porto Alegre City, Brazil.
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18
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Fetz V, Prochnow H, Brönstrup M, Sasse F. Target identification by image analysis. Nat Prod Rep 2017; 33:655-67. [PMID: 26777141 DOI: 10.1039/c5np00113g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covering: 1997 to the end of 2015Each biologically active compound induces phenotypic changes in target cells that are characteristic for its mode of action. These phenotypic alterations can be directly observed under the microscope or made visible by labelling structural elements or selected proteins of the cells with dyes. A comparison of the cellular phenotype induced by a compound of interest with the phenotypes of reference compounds with known cellular targets allows predicting its mode of action. While this approach has been successfully applied to the characterization of natural products based on a visual inspection of images, recent studies used automated microscopy and analysis software to increase speed and to reduce subjective interpretation. In this review, we give a general outline of the workflow for manual and automated image analysis, and we highlight natural products whose bacterial and eucaryotic targets could be identified through such approaches.
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Affiliation(s)
- V Fetz
- Helmholtz Centre for Infection Research, Department of Chemical Biology, Inhoffenstrasse 7, D-38124 Braunschweig, Germany. and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany and School of Engineering and Science, Jacobs University Bremen, Germany
| | - H Prochnow
- Helmholtz Centre for Infection Research, Department of Chemical Biology, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
| | - M Brönstrup
- Helmholtz Centre for Infection Research, Department of Chemical Biology, Inhoffenstrasse 7, D-38124 Braunschweig, Germany. and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - F Sasse
- Helmholtz Centre for Infection Research, Department of Chemical Biology, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.
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19
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Abstract
Molecular docking was earlier considered to predict the binding affinity of the receptor and ligand molecules. With the progress in computational power and developing approaches, new horizons are now opening for accurate prediction of molecular binding affinity. In the current book chapter, recent strategies for Computer-Aided Drug Designing (CADD) including virtual screening and molecular docking, encompassing molecular dynamics simulations, and binding free energy calculation methods are discussed. Brief overview of different binding free energy methods MMPBSA, MMGBSA, LIE and TI have also been given along with the recent Relaxed Complex Scheme protocol.
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Affiliation(s)
| | - Akhil Kumar
- CSIR-Central Institute of Medicinal and Aromatic Plants, India
| | | | - Ashok Sharma
- CSIR-Central Institute of Medicinal and Aromatic Plants, India
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20
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Andrade EL, Bento AF, Cavalli J, Oliveira SK, Freitas CS, Marcon R, Schwanke RC, Siqueira JM, Calixto JB. Non-clinical studies required for new drug development - Part I: early in silico and in vitro studies, new target discovery and validation, proof of principles and robustness of animal studies. Braz J Med Biol Res 2016; 49:e5644. [PMID: 27783811 PMCID: PMC5089235 DOI: 10.1590/1414-431x20165644] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 01/23/2023] Open
Abstract
This review presents a historical overview of drug discovery and the non-clinical stages of the drug development process, from initial target identification and validation, through in silico assays and high throughput screening (HTS), identification of leader molecules and their optimization, the selection of a candidate substance for clinical development, and the use of animal models during the early studies of proof-of-concept (or principle). This report also discusses the relevance of validated and predictive animal models selection, as well as the correct use of animal tests concerning the experimental design, execution and interpretation, which affect the reproducibility, quality and reliability of non-clinical studies necessary to translate to and support clinical studies. Collectively, improving these aspects will certainly contribute to the robustness of both scientific publications and the translation of new substances to clinical development.
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Affiliation(s)
- E L Andrade
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - A F Bento
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J Cavalli
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - S K Oliveira
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - C S Freitas
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - R Marcon
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - R C Schwanke
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J M Siqueira
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J B Calixto
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
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21
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Rožman K, Sosič I, Fernandez R, Young RJ, Mendoza A, Gobec S, Encinas L. A new 'golden age' for the antitubercular target InhA. Drug Discov Today 2016; 22:492-502. [PMID: 27663094 DOI: 10.1016/j.drudis.2016.09.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 11/16/2022]
Abstract
The increasing prevalence of multidrug-resistant strains of Mycobacterium tuberculosis is the main contributing factor in unfavorable outcomes in the treatment of tuberculosis. Studies suggest that direct inhibitors of InhA, an enoyl-ACP-reductase, might yield promising clinical candidates that can be developed into new antitubercular drugs. In this review, we describe the application of different hit-identification strategies to InhA, which clearly illustrate the druggability of its active site through distinct binding mechanisms. We further characterize four classes of InhA inhibitors that show novel binding modes, and provide evidence of their successful target engagement as well as their in vivo activity.
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Affiliation(s)
- Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Raquel Fernandez
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Robert J Young
- GlaxoSmithKline Medicines Research Centre, Stevenage, Herfordshire SG1 2NY, UK
| | - Alfonso Mendoza
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
| | - Lourdes Encinas
- Diseases of the Developing World, Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Madrid, Spain.
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22
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C. elegans screening strategies to identify pro-longevity interventions. Mech Ageing Dev 2016; 157:60-9. [PMID: 27473404 DOI: 10.1016/j.mad.2016.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 02/07/2023]
Abstract
Drugs screenings in search of enhancers or suppressors of selected readout(s) are nowadays mainly carried out in single cells systems. These approaches are however limited when searching for compounds with effects at the organismal level. To overcome this drawback the use of different model organisms to carry out modifier screenings has exponentially grown in the past decade. Unique characteristics such as easy manageability, low cost, fast reproductive cycle, short lifespan, simple anatomy and genetic amenability, make the nematode Caenorhabditis elegans especially suitable for this purpose. Here we briefly review the different high-throughput and high-content screenings which exploited the nematode to identify new compounds extending healthy lifespan. In this context, we describe our recently developed screening strategy to search for pro-longevity interventions taking advantage of the very reproducible phenotypes observed in C. elegans upon different degrees of mitochondrial stress. Indeed, in Mitochondrial mutants, the processes induced to cope with mild mitochondrial alterations during development, and ultimately extending animal lifespan, lead to reduced size and induction of specific stress responses. Instead, upon strong mitochondrial dysfunction, worms arrest their development. Exploiting these automatically quantifiable phenotypic readouts, we developed a new screening approach using the Cellomics ArrayScanVTI-HCS Reader and identified a new pro-longevity drug.
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23
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Guenat S, Rouleau N, Bielmann C, Bedard J, Maurer F, Allaman-Pillet N, Nicod P, Bielefeld-Sévigny M, Beckmann JS, Bonny C, Bossé R, Roduit R. Homogeneous and Nonradioactive High-Throughput Screening Platform for the Characterization of Kinase Inhibitors in Cell Lysates. ACTA ACUST UNITED AC 2016; 11:1015-26. [PMID: 17092917 DOI: 10.1177/1087057106294697] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein kinases are directly implicated in many human diseases; therefore, kinase inhibitors show great promises as new therapeutic drugs. In an effort to facilitate the screening and the characterization of kinase inhibitors, a novel application of the AlphaScreen technology was developed to monitor JNK activity from (1) purified kinase preparations and (2) endogenous kinase from cell lysates preactivated with different cytokines. The authors confirmed that both adenosine triphosphate (ATP) competitive as well as peptide-based JNK inhibitors were able to block the activity of both recombinant and HepG2 endogenous JNK activity. Using the same luminescence technique adapted for binding studies, the authors characterized peptide inhibitor mechanisms by measuring the binding affinity of the inhibitors for JNK. Because of the versatility of the technology, this cell-based JNK kinase assay could be adapted to other kinases and would represent a powerful tool to evaluate endogenous kinase activity and test a large number of potential inhibitors in a more physiologically relevant environment.
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Affiliation(s)
- Sylvie Guenat
- Service of Medical Genetics, CHUV, Lausanne, Switzerland
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24
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Ryan SL, Baird AM, Vaz G, Urquhart AJ, Senge M, Richard DJ, O'Byrne KJ, Davies AM. Drug Discovery Approaches Utilizing Three-Dimensional Cell Culture. Assay Drug Dev Technol 2016; 14:19-28. [PMID: 26866750 DOI: 10.1089/adt.2015.670] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Historically, two-dimensional (2D) cell culture has been the preferred method of producing disease models in vitro. Recently, there has been a move away from 2D culture in favor of generating three-dimensional (3D) multicellular structures, which are thought to be more representative of the in vivo environment. This transition has brought with it an influx of technologies capable of producing these structures in various ways. However, it is becoming evident that many of these technologies do not perform well in automated in vitro drug discovery units. We believe that this is a result of their incompatibility with high-throughput screening (HTS). In this study, we review a number of technologies, which are currently available for producing in vitro 3D disease models. We assess their amenability with high-content screening and HTS and highlight our own work in attempting to address many of the practical problems that are hampering the successful deployment of 3D cell systems in mainstream research.
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Affiliation(s)
- Sarah-Louise Ryan
- 1 Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia .,2 Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Australia
| | - Anne-Marie Baird
- 1 Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia .,2 Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Australia .,3 Thoracic Oncology Research Group, Institute of Molecular Medicine , Trinity College Dublin, Dublin, Ireland
| | - Gisela Vaz
- 4 Medical Chemistry Research Group, Institute of Molecular Medicine , Trinity College Dublin, Dublin, Ireland
| | - Aaron J Urquhart
- 1 Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia .,2 Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Australia
| | - Mathias Senge
- 4 Medical Chemistry Research Group, Institute of Molecular Medicine , Trinity College Dublin, Dublin, Ireland
| | - Derek J Richard
- 1 Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Kenneth J O'Byrne
- 1 Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia .,3 Thoracic Oncology Research Group, Institute of Molecular Medicine , Trinity College Dublin, Dublin, Ireland .,5 Division of Cancer Services, Princess Alexandra Hospital , Brisbane, Australia
| | - Anthony M Davies
- 2 Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Australia .,6 Irish National Centre for High Content Screening and Analysis, Institute of Molecular Medicine , Trinity College Dublin, Dublin, Ireland
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25
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Maglioni S, Arsalan N, Franchi L, Hurd A, Opipari AW, Glick GD, Ventura N. An automated phenotype-based microscopy screen to identify pro-longevity interventions acting through mitochondria in C. elegans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1469-78. [PMID: 25979236 DOI: 10.1016/j.bbabio.2015.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/17/2015] [Accepted: 05/05/2015] [Indexed: 01/22/2023]
Abstract
Mitochondria are multifunctional organelles that play a central role in cellular homeostasis. Severe mitochondrial dysfunction leads to life-threatening diseases in humans and accelerates the aging process. Surprisingly, moderate reduction of mitochondrial function in different species has anti-aging effects. High-throughput screenings in the nematode Caenorhabditis elegans lead to the identification of several pro-longevity genetic and pharmacological interventions. Large-scale screens, however, are manual, subjective, time consuming and costly. These limitations could be reduced by the identification of automatically quantifiable biomarkers of healthy aging. In this study we exploit the distinct and reproducible phenotypes described in C. elegans upon different levels of mitochondrial alteration to develop an automated high-content strategy to identify new potential pro-longevity interventions. Utilizing the microscopy platform Cellomics ArrayScan Reader, we optimize a workflow to automatically and reliably quantify the discrete phenotypic readouts associated with different degrees of silencing of mitochondrial respiratory chain regulatory proteins, and validate the approach with mitochondrial-targeting drugs known to extend lifespan in C. elegans. Finally, we report that a new mitochondrial ATPase modulator matches our screening phenotypic criteria and extends nematode's lifespan thus providing the proof of principle that our strategy could be exploited to identify novel mitochondrial-targeted drugs with pro-longevity activity. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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Affiliation(s)
- Silvia Maglioni
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, 40225 Duesseldorf, Germany; IUF-Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Nayna Arsalan
- IUF-Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | | | | | | | | | - Natascia Ventura
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, 40225 Duesseldorf, Germany; IUF-Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany.
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26
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Wu SH, Yao CH, Hsieh CJ, Liu YW, Chao YS, Song JS, Lee JC. Development and application of a fluorescent glucose uptake assay for the high-throughput screening of non-glycoside SGLT2 inhibitors. Eur J Pharm Sci 2015; 74:40-4. [PMID: 25819489 DOI: 10.1016/j.ejps.2015.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/05/2015] [Accepted: 03/20/2015] [Indexed: 11/26/2022]
Abstract
Sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors are of current interest as a treatment for type 2 diabetes. Efforts have been made to discover phlorizin-related glycosides with good SGLT2 inhibitory activity. To increase structural diversity and better understand the role of non-glycoside SGLT2 inhibitors on glycemic control, we initiated a research program to identify non-glycoside hits from high-throughput screening. Here, we report the development of a novel, fluorogenic probe-based glucose uptake system based on a Cu(I)-catalyzed [3+2] cycloaddition. The safer processes and cheaper substances made the developed assay our first priority for large-scale primary screening as compared to the well-known [(14)C]-labeled α-methyl-D-glucopyranoside ([(14)C]-AMG) radioactive assay. This effort culminated in the identification of a benzimidazole, non-glycoside SGLT2 hit with an EC50 value of 0.62 μM by high-throughput screening of 41,000 compounds.
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Affiliation(s)
- Szu-Huei Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
| | - Chun-Hsu Yao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
| | - Chieh-Jui Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
| | - Yu-Wei Liu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
| | - Yu-Sheng Chao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC.
| | - Jinq-Chyi Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC.
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27
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Eddaoudi M, Sava DF, Eubank JF, Adil K, Guillerm V. Zeolite-like metal-organic frameworks (ZMOFs): design, synthesis, and properties. Chem Soc Rev 2014; 44:228-49. [PMID: 25341691 DOI: 10.1039/c4cs00230j] [Citation(s) in RCA: 482] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review highlights various design and synthesis approaches toward the construction of ZMOFs, which are metal-organic frameworks (MOFs) with topologies and, in some cases, features akin to traditional inorganic zeolites. The interest in this unique subset of MOFs is correlated with their exceptional characteristics arising from the periodic pore systems and distinctive cage-like cavities, in conjunction with modular intra- and/or extra-framework components, which ultimately allow for tailoring of the pore size, pore shape, and/or properties towards specific applications.
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Affiliation(s)
- Mohamed Eddaoudi
- Functional Materials Design, Discovery and Development Research Group (FMD3), Advanced Membranes and Porous Materials Center (AMPM), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
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28
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Laplatine L, Leroy L, Calemczuk R, Baganizi D, Marche PN, Roupioz Y, Livache T. Spatial resolution in prism-based surface plasmon resonance microscopy. OPTICS EXPRESS 2014; 22:22771-85. [PMID: 25321746 DOI: 10.1364/oe.22.022771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Several optical surface sensing techniques, such as Surface Plasmon Resonance (SPR), work by imaging the base of a prism by one of its faces. However, such a fundamental optical concern has not been fully analyzed and understood so far, and spatial resolution remains a critical and controversial issue. In SPR, the propagation length L(x) of the surface plasmon waves has been considered as the limiting factor. Here, we demonstrate that for unoptimized systems geometrical aberrations caused by the prism can be more limiting than the propagation length. By combining line-scan imaging mode with optimized prisms, we access the ultimate lateral resolution which is diffraction-limited by the object light diffusion. We describe several optimized configurations in water and discuss the trade-off between L(x) and sensitivity. The improvement of resolution is confirmed by imaging micro-structured PDMS stamps and individual living eukaryote cells and bacteria on field-of-view from 0.1 to 20 mm(2).
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29
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Wyhs N, Walker D, Giovinazzo H, Yegnasubramanian S, Nelson WG. Time-Resolved Fluorescence Resonance Energy Transfer Assay for Discovery of Small-Molecule Inhibitors of Methyl-CpG Binding Domain Protein 2. JOURNAL OF BIOMOLECULAR SCREENING 2014; 19:1060-9. [PMID: 24608100 PMCID: PMC4183726 DOI: 10.1177/1087057114526433] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/10/2014] [Indexed: 01/23/2023]
Abstract
Methylated DNA binding proteins such as Methyl-CpG Binding Domain Protein 2 (MBD2) can transduce DNA methylation alterations into a repressive signal by recruiting transcriptional co-repressor complexes. Interfering with MBD2 could lead to reactivation of tumor suppressor genes and therefore represents an attractive strategy for epigenetic therapy. We developed and compared fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET)-based high-throughput screening (HTS) assays to identify small-molecule inhibitors of the interaction between the methyl binding domain of MBD2 (MBD2-MBD) and methylated DNA. Although both assays performed well in 96-well format, the TR-FRET assay (Z' factor = 0.58) emerged as a superior screening strategy compared with FP (Z' factor = 0.08) when evaluated in an HTS 384-well plate format. Using TR-FRET, we screened the Sigma LOPAC library for MBD2-MBD inhibitors and identified four compounds that also validated in a dose-response series. This included two known DNA intercalators (mitoxantrone and idarubicin) among two other inhibitory compounds (NF449 and aurintricarboxylic acid). All four compounds also inhibited the binding of SP-1, a transcription factor with a GC-rich binding sequence, to a methylated oligonucleotide, demonstrating that the activity was nonspecific. Our results provide proof of principle for using TR-FRET-based HTS to identify small-molecule inhibitors of MBD2 and other DNA-protein interactions.
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Affiliation(s)
- Nicolas Wyhs
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Walker
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hugh Giovinazzo
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - William G Nelson
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Martell RE, Brooks DG, Wang Y, Wilcoxen K. Discovery of novel drugs for promising targets. Clin Ther 2014; 35:1271-81. [PMID: 24054704 DOI: 10.1016/j.clinthera.2013.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 06/27/2013] [Accepted: 08/13/2013] [Indexed: 11/18/2022]
Abstract
BACKGROUND Once a promising drug target is identified, the steps to actually discover and optimize a drug are diverse and challenging. OBJECTIVE The goal of this study was to provide a road map to navigate drug discovery. METHODS Review general steps for drug discovery and provide illustrating references. RESULTS A number of approaches are available to enhance and accelerate target identification and validation. Consideration of a variety of potential mechanisms of action of potential drugs can guide discovery efforts. The hit to lead stage may involve techniques such as high-throughput screening, fragment-based screening, and structure-based design, with informatics playing an ever-increasing role. Biologically relevant screening models are discussed, including cell lines, 3-dimensional culture, and in vivo screening. The process of enabling human studies for an investigational drug is also discussed. CONCLUSIONS Drug discovery is a complex process that has significantly evolved in recent years.
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Affiliation(s)
- Robert E Martell
- TESARO Inc, Waltham, Massachusetts; Tufts Medical Center, Boston, Massachusetts.
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31
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Abstract
High-throughput screening (HTS) is a key process used in drug discovery to identify hits from compound libraries that may become leads for medicinal chemistry optimization. This updated overview discusses the utilization of compound libraries, compounds derived from combinatorial and parallel synthesis campaigns and natural product sources; creation of mother and daughter plates; and compound storage, handling, and bar coding in HTS. The unit also presents an overview of established and emerging assay technologies (i.e., time-resolved fluorescence, fluorescence polarization, fluorescence-correlation spectroscopy, functional whole cell assays, and high-content assays) and their integration in automation hardware and IT systems. This revised unit provides updated descriptions of state-of-the-art instrumentation and technologies in this rapidly changing environment. The section on assay methodologies now also covers enzyme complementation assays and methods for high-throughput screening of ion channel activities. Finally, a section on criteria for assay robustness is included discussing the Z'-factor, which is now a widely accepted criterion for evaluation and validation of high throughput screening assays.
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Affiliation(s)
- Michael Entzeroth
- Experimental Therapeutics Centre, Agency for Science, Technology, and Research (A*STAR), Singapore
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32
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Shan J, Zheng JJ. Virtual ligand screening combined with NMR to identify Dvl PDZ domain inhibitors targeting the Wnt signaling. Methods Mol Biol 2012; 928:17-28. [PMID: 22956130 PMCID: PMC3964848 DOI: 10.1007/978-1-62703-008-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Virtual ligand screening is a powerful technique to identify potential hits of targets and to increase hit rates. Here, we describe how we used this technique combined with NMR (15)N HSQC experiments to obtain small molecules that bind to the PDZ domain of Dvl targeting the Wnt signaling pathway.
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Abstract
Despite an increased investment in research and development, there has been a steady decline in the number of drugs brought to market over the past 40 years. The tools of personalized medicine are refining diseases into molecular categories, and future therapeutics may be dictated by a patient's molecular profile relative to these categories. The adoption of a personalized medicine approach to drug development may improve the success rate by minimizing variability during each phase of the drug development process. This chapter describes the current paradigm of drug development and then discusses how molecular profiling/personalized medicine might be used to improve upon this paradigm.
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Affiliation(s)
- Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA, USA.
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34
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Jin S, Ellis E, Veetil JV, Yao H, Ye K. Visualization of human immunodeficiency virus protease inhibition using a novel Förster resonance energy transfer molecular probe. Biotechnol Prog 2011; 27:1107-14. [PMID: 21584951 DOI: 10.1002/btpr.628] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 03/23/2011] [Indexed: 11/11/2022]
Abstract
The in vivo high-throughput screening (HTS) of human immunodeficiency virus (HIV) protease inhibitors is a significant challenge because of the lack of reliable assays that allow the visualization of HIV targets within living cells. In this study, we developed a new molecular probe that utilizes the principles of Förster resonance energy transfer (FRET) to visualize HIV-1 protease inhibition within living cells. The probe is constructed by linking two fluorescent proteins: AcGFP1 (a mutant green fluorescent protein) and mCherry (a red fluorescent protein) with an HIV-1 protease cleavable p2/p7 peptide. The cleavage of the linker peptide by HIV-1 protease leads to separation of AcGFP1 from mCherry, quenching FRET between AcGFP1 and mCherry. Conversely, the addition of a protease inhibitor prevents the cleavage of the linker peptide by the protease, allowing FRET from AcGFP1 to mCherry. Thus, HIV-1 protease inhibition can be determined by measuring the FRET signal's change generated from the probe. Both in vitro and in vivo studies demonstrated the feasibility of applying the probe for quantitative analyses of HIV-1 protease inhibition. By cotransfecting HIV-1 protease and the probe expression plasmids into 293T cells, we showed that the inhibition of HIV-1 protease by inhibitors can be visualized or quantitatively determined within living cells through ratiometric FRET microscopy imaging measurement. It is expected that this new probe will allow high-content screening (HCS) of new anti-HIV drugs.
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Affiliation(s)
- Sha Jin
- Biomedical Engineering Program, College of Engineering, University of Arkansas, Fayetteville, AR 72701, USA.
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35
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Challenges and perspectives of chemical biology, a successful multidisciplinary field of natural sciences. Molecules 2011; 16:2672-87. [PMID: 21441869 PMCID: PMC6259834 DOI: 10.3390/molecules16032672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/09/2011] [Accepted: 03/15/2011] [Indexed: 12/17/2022] Open
Abstract
Objects, goals, and main methods as well as perspectives of chemical biology are discussed. This review is focused on the fundamental aspects of this emerging field of life sciences: chemical space, the small molecule library and chemical sensibilization (small molecule microassays).
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36
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An antigen microarray immunoassay for multiplex screening of mouse monoclonal antibodies. Nat Protoc 2010; 5:1932-44. [PMID: 21127487 DOI: 10.1038/nprot.2010.161] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mouse monoclonal antibody (mAb) technology still represents a key source of reagents for research and clinical diagnosis, although it is relatively inefficient and expensive and therefore unsuitable for high-throughput production against a vast repertoire of antigens. In this article, we describe a protocol that combines the immunization of individual mice with complex mixtures of influenza virus strains and a microarray-based immunoassay procedure to perform a parallel screening against the viral antigens. The protocol involves testing the supernatants of somatic cell hybrids against a capture substratum containing an array of different antigens. For each fusion experiment, we carried out more than 25,000 antigen-antibody reactivity tests in less than a week, a throughput that is two orders of magnitude higher than that of traditional antibody detection assays such as enzyme-linked immunosorbent assays and immunofluorescence. Using a limited number of mice, we can develop a vast repertoire of mAbs directed against nuclear and surface proteins of several human and avian influenza virus strains.
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37
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Wang Y, Jadhav A, Southal N, Huang R, Nguyen DT. A grid algorithm for high throughput fitting of dose-response curve data. CURRENT CHEMICAL GENOMICS 2010; 4:57-66. [PMID: 21331310 PMCID: PMC3040458 DOI: 10.2174/1875397301004010057] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/04/2010] [Accepted: 08/30/2010] [Indexed: 12/03/2022]
Abstract
We describe a novel algorithm, Grid algorithm, and the corresponding computer program for high throughput fitting of dose-response curves that are described by the four-parameter symmetric logistic dose-response model. The Grid algorithm searches through all points in a grid of four dimensions (parameters) and finds the optimum one that corresponds to the best fit. Using simulated dose-response curves, we examined the Grid program’s performance in reproducing the actual values that were used to generate the simulated data and compared it with the DRC package for the language and environment R and the XLfit add-in for Microsoft Excel. The Grid program was robust and consistently recovered the actual values for both complete and partial curves with or without noise. Both DRC and XLfit performed well on data without noise, but they were sensitive to and their performance degraded rapidly with increasing noise. The Grid program is automated and scalable to millions of dose-response curves, and it is able to process 100,000 dose-response curves from high throughput screening experiment per CPU hour. The Grid program has the potential of greatly increasing the productivity of large-scale dose-response data analysis and early drug discovery processes, and it is also applicable to many other curve fitting problems in chemical, biological, and medical sciences.
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Affiliation(s)
- Yuhong Wang
- National Institutes of Health, NIH Chemical Genomics Center, 9800 Medical Center Drive, Rockville, MD 20850, USA
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38
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Synthesis and biological evaluation of 2-amino-1-thiazolyl imidazoles as orally active anticancer agents. Invest New Drugs 2010; 30:164-75. [PMID: 20890633 DOI: 10.1007/s10637-010-9547-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 09/21/2010] [Indexed: 12/12/2022]
Abstract
Designed from a high throughput screened hit compound, novel 2-amino-1-thiazolyl imidazoles were synthesized and demonstrated cytotoxicity against human cancer cells. 1-(4-Phenylthiazol-2-yl)-4-(thiophen-2-yl)-1H-imidazol-2-amine (compound 2), a 2-amino-1-thiazolyl imidazole, inhibited tubulin polymerization, interacted with the colchicine-binding sites of tubulins, and caused cell cycle arrest at the G(2)/M phase in human gastric cancer cells. Disruption of the microtubule structure in cancer cells by compound 2 was also observed. Compound 2 concentration-dependently inhibited the proliferation of cancer cells in histocultured human gastric and colorectal tumors. Given orally, compound 2 prolonged the lifespans of leukemia mice intraperitoneally inoculated with the murine P388 leukemic cells. We report 2-amino-1-thiazolyl imidazoles as a novel class of orally active microtubule-destabilizing anticancer agents.
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39
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Voutchkova AM, Osimitz TG, Anastas PT. Toward a Comprehensive Molecular Design Framework for Reduced Hazard. Chem Rev 2010; 110:5845-82. [DOI: 10.1021/cr9003105] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Adelina M. Voutchkova
- Center for Green Chemistry and Green Engineering, Yale University, New Haven, Connecticut 06511, and Science Strategies LLC, 600 East Water St., Charlottesville, VA 22902
| | - Thomas G. Osimitz
- Center for Green Chemistry and Green Engineering, Yale University, New Haven, Connecticut 06511, and Science Strategies LLC, 600 East Water St., Charlottesville, VA 22902
| | - Paul T. Anastas
- Center for Green Chemistry and Green Engineering, Yale University, New Haven, Connecticut 06511, and Science Strategies LLC, 600 East Water St., Charlottesville, VA 22902
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40
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Abstract
Cell-based assays represent approximately half of all high-throughput screens currently performed. Here, we review in brief the history and status of high-throughput screening (HTS), and summarize some of the challenges and benefits associated with the use of cell-based assays in HTS. Approaches for successful experimental design and execution of cell-based screens are introduced, including strategies for assay development, implementation of primary and secondary screens, and target identification. In doing so, we hope to provide a comprehensive review of the cell-based HTS process and an introduction to the methodologies and techniques used.
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Affiliation(s)
- W Frank An
- Chemical Biology Platform, The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
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41
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Mueller R, Rodriguez AL, Dawson ES, Butkiewicz M, Nguyen TT, Oleszkiewicz S, Bleckmann A, Weaver CD, Lindsley CW, Conn PJ, Meiler J. Identification of Metabotropic Glutamate Receptor Subtype 5 Potentiators Using Virtual High-Throughput Screening. ACS Chem Neurosci 2010; 1:288-305. [PMID: 20414370 PMCID: PMC2857954 DOI: 10.1021/cn9000389] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 01/04/2010] [Indexed: 11/30/2022] Open
Abstract
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Selective potentiators of glutamate response at metabotropic glutamate receptor subtype 5 (mGluR5) have exciting potential for the development of novel treatment strategies for schizophrenia. A total of 1,382 compounds with positive allosteric modulation (PAM) of the mGluR5 glutamate response were identified through high-throughput screening (HTS) of a diverse library of 144,475 substances utilizing a functional assay measuring receptor-induced intracellular release of calcium. Primary hits were tested for concentration-dependent activity, and potency data (EC50 values) were used for training artificial neural network (ANN) quantitative structure−activity relationship (QSAR) models that predict biological potency from the chemical structure. While all models were trained to predict EC50, the quality of the models was assessed by using both continuous measures and binary classification. Numerical descriptors of chemical structure were used as input for the machine learning procedure and optimized in an iterative protocol. The ANN models achieved theoretical enrichment ratios of up to 38 for an independent data set not used in training the model. A database of ∼450,000 commercially available drug-like compounds was targeted in a virtual screen. A set of 824 compounds was obtained for testing based on the highest predicted potency values. Biological testing found 28.2% (232/824) of these compounds with various activities at mGluR5 including 177 pure potentiators and 55 partial agonists. These results represent an enrichment factor of 23 for pure potentiation of the mGluR5 glutamate response and 30 for overall mGluR5 modulation activity when compared with those of the original mGluR5 experimental screening data (0.94% hit rate). The active compounds identified contained 72% close derivatives of previously identified PAMs as well as 28% nontrivial derivatives of known active compounds.
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Affiliation(s)
| | | | - Eric S. Dawson
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-6600
| | | | | | | | | | | | - Craig W. Lindsley
- Department of Chemistry
- Department of Pharmacology
- Institute for Chemical Biology
| | | | - Jens Meiler
- Department of Chemistry
- Department of Pharmacology
- Institute for Chemical Biology
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-6600
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42
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Li WT, Hwang DR, Song JS, Chen CP, Chuu JJ, Hu CB, Lin HL, Huang CL, Huang CY, Tseng HY, Lin CC, Chen TW, Lin CH, Wang HS, Shen CC, Chang CM, Chao YS, Chen CT. Synthesis and Biological Activities of 2-Amino-1-arylidenamino Imidazoles as Orally Active Anticancer Agents. J Med Chem 2010; 53:2409-17. [DOI: 10.1021/jm901501s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen-Tai Li
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Der-Ren Hwang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Jen-Shin Song
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Ching-Ping Chen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Jiunn-Jye Chuu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chih-Bo Hu
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Heng-Liang Lin
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chen-Lung Huang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chiung-Yi Huang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Huan-Yi Tseng
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chu-Chung Lin
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Tung-Wei Chen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
- Institute of Biophotonics, National Yang Ming University, Shih-Pai, Taipei 11221, Taiwan, ROC
| | - Chi-Hung Lin
- Institute of Biophotonics, National Yang Ming University, Shih-Pai, Taipei 11221, Taiwan, ROC
| | - Hsin-Sheng Wang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chien-Chang Shen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chung-Ming Chang
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Yu-Sheng Chao
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
| | - Chiung-Tong Chen
- Division of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 35053, Taiwan, ROC
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43
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Cragg GM, Grothaus PG, Newman DJ. Impact of natural products on developing new anti-cancer agents. Chem Rev 2009; 109:3012-43. [PMID: 19422222 DOI: 10.1021/cr900019j] [Citation(s) in RCA: 887] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gordon M Cragg
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, NCI-Frederick, Fairview Center, Suite 206, P.O. Box B, Frederick, Maryland 21702-1201, USA
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44
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Goodell JR, McMullen JP, Zaborenko N, Maloney JR, Ho CX, Jensen KF, Porco JA, Beeler AB. Development of an automated microfluidic reaction platform for multidimensional screening: reaction discovery employing bicyclo[3.2.1]octanoid scaffolds. J Org Chem 2009; 74:6169-80. [PMID: 20560568 PMCID: PMC2976622 DOI: 10.1021/jo901073v] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An automated, silicon-based microreactor system has been developed for rapid, low-volume, multidimensional reaction screening. Use of the microfluidic platform to identify transformations of densely functionalized bicyclo[3.2.1]octanoid scaffolds will be described.
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Affiliation(s)
- John R. Goodell
- Contribution from the Department of Chemistry and Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
| | - Jonathan P. McMullen
- Department of Chemical Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue, 66-342, Cambridge, Massachusetts 02139
| | - Nikolay Zaborenko
- Department of Chemical Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue, 66-342, Cambridge, Massachusetts 02139
| | - Jason R. Maloney
- Contribution from the Department of Chemistry and Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
| | - Chuan-Xing Ho
- Contribution from the Department of Chemistry and Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
| | - Klavs F. Jensen
- Department of Chemical Engineering Massachusetts Institute of Technology 77 Massachusetts Avenue, 66-342, Cambridge, Massachusetts 02139
| | - John A. Porco
- Contribution from the Department of Chemistry and Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
| | - Aaron B. Beeler
- Contribution from the Department of Chemistry and Center for Chemical Methodology and Library Development (CMLD-BU), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215
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Abstract
High-throughput screening (HTS) covers a range of measurements, from primary screens of either large libraries (>250 K) or small, focused collections (100-1,000 s) of test compounds, to secondary screens used to characterize the mechanism of action of a relatively small number of compounds. Data analysis of assay results from HTS relies upon assay performance and the control wells used to define the assay system. This chapter discusses parameters that must be considered when defining controls and plate maps for primary and secondary assays in HTS. Control wells and plate maps are suggested, which can gene-rally be applied toward a variety of biochemical and cellular assays. The controls and plate-map options can be matched to the scale of the screening campaign; examples are primary screens with % inhibition or % activation as endpoints or secondary screens with IC(50) or EC(50) values as endpoints.
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46
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Nigsch F, Macaluso NJM, Mitchell JBO, Zmuidinavicius D. Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin Drug Metab Toxicol 2009; 5:1-14. [PMID: 19236225 DOI: 10.1517/17425250802660467] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Toxicology has the goal of ensuring the safety of humans, animals and the environment. Computational toxicology is an area of active development and great potential. There are tangible reasons for the emerging interest in this discipline from academia, industry, regulatory bodies and governments. RESULTS Pharmaceuticals, personal health care products, nutritional ingredients and products of the chemical industries are all potential hazards and need to be assessed. Toxicological tests for these products are costly, frequently use laboratory animals and are time-consuming. This delays end-user access to improved products or, conversely, the timely withdrawal of dangerous substances from the market. The aim of computational toxicology is to accelerate the assessment of potentially dangerous substances through in silico models. CONCLUSIONS In this review, we provide an overview of the development of models for computational toxicology. Addressing the significant divide between the experimental and computational worlds-believed to be a prime hindrance to computational toxicology-we briefly consider the fundamental issue of toxicological data and the assays they stem from. Different kinds of models that can be built using such data are presented: computational filters, models for specific toxicological endpoints and tools for the generation of testable hypotheses.
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Affiliation(s)
- Florian Nigsch
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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47
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Cavasotto CN, Phatak SS. Homology modeling in drug discovery: current trends and applications. Drug Discov Today 2009; 14:676-83. [PMID: 19422931 DOI: 10.1016/j.drudis.2009.04.006] [Citation(s) in RCA: 272] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 04/20/2009] [Accepted: 04/23/2009] [Indexed: 10/20/2022]
Abstract
As structural genomics (SG) projects continue to deposit representative 3D structures of proteins, homology modeling methods will play an increasing role in structure-based drug discovery. Although computational structure prediction methods provide a cost-effective alternative in the absence of experimental structures, developing accurate enough models still remains a big challenge. In this contribution, we report the current developments in this field, discuss in silico modeling limitations, and review the successful application of this technique to different stages of the drug discovery process.
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Affiliation(s)
- Claudio N Cavasotto
- School of Health Information Sciences, The University of Texas Health Science Center at Houston, 7000 Fannin, Suite 860B, Houston, TX 77030, United States.
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48
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Pais E, Cambridge JS, Johnson CS, Meiselman HJ, Fisher TC, Alexy T. A Novel High-Throughput Screening Assay for Sickle Cell Disease Drug Discovery. ACTA ACUST UNITED AC 2009; 14:330-6. [DOI: 10.1177/1087057109333975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Although the pathophysiology and molecular basis of sickle cell disease (SCD) were described more than half a century ago, an effective and safe therapy is not yet available. This may be explained by the lack of a suitable high-throughput technique that allows rapid screening of thousands of compounds for their antisickling effect. The authors have thus developed a novel high-throughput screening (HTS) assay based on detecting the ability of red blood cells (RBC) to traverse a column of tightly packed Sephacryl chromatography beads. When deoxygenated, sickle RBC are rigid and remain on the top of the column. However, when deoxygenated and treated with an effective antisickling agent, erythrocytes move through the Sephacryl media and produce a red dot on the bottom of the assay tubes. This approach has been adapted to wells in a 384-well microplate. Results can be obtained by optical scanning: The size of the red dot is proportional to the antisickling effect of the test molecule. The new assay is simple, inexpensive, reproducible, requires no special reagents, and should be readily adaptable to robotic HTS systems. It has the potential to identify novel drug candidates, allowing the development of new therapeutic options for individuals affected with SCD. ( Journal of Biomolecular Screening. 2009:330-336)
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Affiliation(s)
- Eszter Pais
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, Childrens Hospital, Los Angeles, California
| | - John S. Cambridge
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles
| | - Cage S. Johnson
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles
| | - Herbert J. Meiselman
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles
| | - Timothy C. Fisher
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles
| | - Tamas Alexy
- Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles,
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49
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Sieuwerts S, de Bok FAM, Mols E, de vos WM, Vlieg JETVH. A simple and fast method for determining colony forming units. Lett Appl Microbiol 2009; 47:275-8. [PMID: 18778376 DOI: 10.1111/j.1472-765x.2008.02417.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a flexible and fast colony forming unit quantification method that can be operated in a standard microbiology laboratory. METHODS AND RESULTS A miniaturized plating method is reported where droplets of bacterial cultures are spotted on agar plates. Subsequently, minicolony spots are imaged with a digital camera and quantified using a dedicated plug-in developed for the freeware program IMAGEJ. A comparison between conventional and minicolony plating of industrial micro-organisms including lactic acid bacteria, Eschericha coli and Saccharomyces cerevisiae showed that there was no significant difference in the results obtained with the methods. CONCLUSIONS The presented method allows downscaling of plating by 100-fold, is flexible, easy-to-use and is more labour-efficient and cost-efficient than conventional plating methods. SIGNIFICANCE AND IMPACT OF THE STUDY The method can be used for rapid assessment of viable counts of micro-organisms similar to conventional plating using standard laboratory equipment. It is faster and cheaper than conventional plating methods.
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Affiliation(s)
- S Sieuwerts
- Top Institute Food and Nutrition, Wageningen, The Netherlands
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50
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Thepchatri P, Min J, Ganesh T, Du Y, Lewis I, Kurtkaya S, Prussia A, Li L, Plemper RK, Fu H, Liotta DC, Snyder JP, Dingledine R, Sun A. Cancer and virus leads by HTS, chemical design and SEA data mining. Curr Top Med Chem 2009; 9:1159-71. [PMID: 19807668 PMCID: PMC4442615 DOI: 10.2174/156802609789753581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2008] [Accepted: 10/18/2008] [Indexed: 11/22/2022]
Abstract
A variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads and to accelerate the development of drug candidates. The Emory Chemical and Biology Discovery Center (ECBDC) has been an active participant in the NIH's high-throughput screening (HTS) endeavor to identify potent small molecule probes for poorly studied proteins. Several of Emory's projects relate to cancer or virus infection. We have chosen three successful examples including discovery of potent measles virus RNA-dependent RNA polymerase inhibitors, development of Heat Shock Protein 90 (Hsp90) blockers and identification of angiogenesis inhibitors using transgenic Zebrafish as a HTS model. In parallel with HTS, a unique component of the Emory virtual screening (VS) effort, namely, substructure enrichment analysis (SEA) program has been utilized in several cases.
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Affiliation(s)
- Pahk Thepchatri
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Jaeki Min
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Thota Ganesh
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Yuhong Du
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Pharmacology, Emory University, 1510 Clifton Road, Atlanta GA 30322
| | - Iestyn Lewis
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Pharmacology, Emory University, 1510 Clifton Road, Atlanta GA 30322
| | - Serdar Kurtkaya
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Andrew Prussia
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Lian Li
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
| | - Richard K. Plemper
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Emory Children’s Center, 2015 Uppergate Drive, Emory University School of Medicine, Atlanta, GA 30322
| | - Haian Fu
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Pharmacology, Emory University, 1510 Clifton Road, Atlanta GA 30322
| | - Dennis C. Liotta
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - James P. Snyder
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322
| | - Raymond Dingledine
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Pharmacology, Emory University, 1510 Clifton Road, Atlanta GA 30322
| | - Aiming Sun
- Chemical Biology Discovery Center, 1510 Clifton Road, Emory University, Atlanta, GA 30322
- Department of Pharmacology, Emory University, 1510 Clifton Road, Atlanta GA 30322
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