1
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Garaci E, Paci M, Matteucci C, Costantini C, Puccetti P, Romani L. Phenotypic drug discovery: a case for thymosin alpha-1. Front Med (Lausanne) 2024; 11:1388959. [PMID: 38903817 PMCID: PMC11187271 DOI: 10.3389/fmed.2024.1388959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
Phenotypic drug discovery (PDD) involves screening compounds for their effects on cells, tissues, or whole organisms without necessarily understanding the underlying molecular targets. PDD differs from target-based strategies as it does not require knowledge of a specific drug target or its role in the disease. This approach can lead to the discovery of drugs with unexpected therapeutic effects or applications and allows for the identification of drugs based on their functional effects, rather than through a predefined target-based approach. Ultimately, disease definitions are mostly symptom-based rather than mechanism-based, and the therapeutics should be likewise. In recent years, there has been a renewed interest in PDD due to its potential to address the complexity of human diseases, including the holistic picture of multiple metabolites engaging with multiple targets constituting the central hub of the metabolic host-microbe interactions. Although PDD presents challenges such as hit validation and target deconvolution, significant achievements have been reached in the era of big data. This article explores the experiences of researchers testing the effect of a thymic peptide hormone, thymosin alpha-1, in preclinical and clinical settings and discuss how its therapeutic utility in the precision medicine era can be accommodated within the PDD framework.
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Affiliation(s)
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Paolo Puccetti
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- San Raffaele Sulmona, L’Aquila, Italy
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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2
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Michon M, Müller-Schiffmann A, Lingappa AF, Yu SF, Du L, Deiter F, Broce S, Mallesh S, Crabtree J, Lingappa UF, Macieik A, Müller L, Ostermann PN, Andrée M, Adams O, Schaal H, Hogan RJ, Tripp RA, Appaiah U, Anand SK, Campi TW, Ford MJ, Reed JC, Lin J, Akintunde O, Copeland K, Nichols C, Petrouski E, Moreira AR, Jiang IT, DeYarman N, Brown I, Lau S, Segal I, Goldsmith D, Hong S, Asundi V, Briggs EM, Phyo NS, Froehlich M, Onisko B, Matlack K, Dey D, Lingappa JR, Prasad DM, Kitaygorodskyy A, Solas D, Boushey H, Greenland J, Pillai S, Lo MK, Montgomery JM, Spiropoulou CF, Korth C, Selvarajah S, Paulvannan K, Lingappa VR. A pan-respiratory antiviral chemotype targeting a transient host multi-protein complex. Open Biol 2024; 14:230363. [PMID: 38889796 DOI: 10.1098/rsob.230363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024] Open
Abstract
We present a novel small molecule antiviral chemotype that was identified by an unconventional cell-free protein synthesis and assembly-based phenotypic screen for modulation of viral capsid assembly. Activity of PAV-431, a representative compound from the series, has been validated against infectious viruses in multiple cell culture models for all six families of viruses causing most respiratory diseases in humans. In animals, this chemotype has been demonstrated efficacious for porcine epidemic diarrhoea virus (a coronavirus) and respiratory syncytial virus (a paramyxovirus). PAV-431 is shown to bind to the protein 14-3-3, a known allosteric modulator. However, it only appears to target the small subset of 14-3-3 which is present in a dynamic multi-protein complex whose components include proteins implicated in viral life cycles and in innate immunity. The composition of this target multi-protein complex appears to be modified upon viral infection and largely restored by PAV-431 treatment. An advanced analog, PAV-104, is shown to be selective for the virally modified target, thereby avoiding host toxicity. Our findings suggest a new paradigm for understanding, and drugging, the host-virus interface, which leads to a new clinical therapeutic strategy for treatment of respiratory viral disease.
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Affiliation(s)
- Maya Michon
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | - Li Du
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | - Fred Deiter
- Veterans Administration Medical Center, San Francisco, CA, USA
| | - Sean Broce
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Jackelyn Crabtree
- University of Georgia, Animal Health Research Center, Athens, GA, 28130 USA
| | | | | | - Lisa Müller
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | | | - Marcel Andrée
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Ortwin Adams
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | - Robert J Hogan
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | - Ralph A Tripp
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
| | | | | | | | | | | | - Jim Lin
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Ian Brown
- Prosetta Biosciences, San Francisco, CA, USA
| | - Sharon Lau
- Prosetta Biosciences, San Francisco, CA, USA
| | - Ilana Segal
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Shi Hong
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Jaisri R Lingappa
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
| | | | | | | | - Homer Boushey
- University of California, San Francisco, CA, 94143, USA
| | - John Greenland
- Veterans Administration Medical Center, San Francisco, CA, USA
- University of California, San Francisco, CA, 94143, USA
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, 94118-4417 USA
- University of California, San Francisco, CA, 94143, USA
| | - Michael K Lo
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M Montgomery
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carsten Korth
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, 40225 Germany
| | | | | | - Vishwanath R Lingappa
- Prosetta Biosciences, San Francisco, CA, USA
- University of California, San Francisco, CA, 94143, USA
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3
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Levitskaya Z, Ser Z, Koh H, Mei WS, Chee S, Sobota RM, Ghadessy JF. Engineering cell-free systems by chemoproteomic-assisted phenotypic screening. RSC Chem Biol 2024; 5:372-385. [PMID: 38576719 PMCID: PMC10989505 DOI: 10.1039/d4cb00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/16/2024] [Indexed: 04/06/2024] Open
Abstract
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.
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Affiliation(s)
- Zarina Levitskaya
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Zheng Ser
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Hiromi Koh
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Wang Shi Mei
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Sharon Chee
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Radoslaw Mikolaj Sobota
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - John F Ghadessy
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
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4
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Michon M, Müller-Schiffmann A, Lingappa AF, Yu SF, Du L, Deiter F, Broce S, Mallesh S, Crabtree J, Lingappa UF, Macieik A, Müller L, Ostermann PN, Andrée M, Adams O, Schaal H, Hogan RJ, Tripp RA, Appaiah U, Anand SK, Campi TW, Ford MJ, Reed JC, Lin J, Akintunde O, Copeland K, Nichols C, Petrouski E, Moreira AR, Jiang IT, DeYarman N, Brown I, Lau S, Segal I, Goldsmith D, Hong S, Asundi V, Briggs EM, Phyo NS, Froehlich M, Onisko B, Matlack K, Dey D, Lingappa JR, Prasad MD, Kitaygorodskyy A, Solas D, Boushey H, Greenland J, Pillai S, Lo MK, Montgomery JM, Spiropoulou CF, Korth C, Selvarajah S, Paulvannan K, Lingappa VR. A Pan-Respiratory Antiviral Chemotype Targeting a Host Multi-Protein Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2021.01.17.426875. [PMID: 34931190 PMCID: PMC8687465 DOI: 10.1101/2021.01.17.426875] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a novel small molecule antiviral chemotype that was identified by an unconventional cell-free protein synthesis and assembly-based phenotypic screen for modulation of viral capsid assembly. Activity of PAV-431, a representative compound from the series, has been validated against infectious virus in multiple cell culture models for all six families of viruses causing most respiratory disease in humans. In animals this chemotype has been demonstrated efficacious for Porcine Epidemic Diarrhea Virus (a coronavirus) and Respiratory Syncytial Virus (a paramyxovirus). PAV-431 is shown to bind to the protein 14-3-3, a known allosteric modulator. However, it only appears to target the small subset of 14-3-3 which is present in a dynamic multi-protein complex whose components include proteins implicated in viral lifecycles and in innate immunity. The composition of this target multi-protein complex appears to be modified upon viral infection and largely restored by PAV-431 treatment. Our findings suggest a new paradigm for understanding, and drugging, the host-virus interface, which leads to a new clinical therapeutic strategy for treatment of respiratory viral disease.
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Affiliation(s)
- Maya Michon
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Fred Deiter
- Veterans Administration Medical Center, San Francisco, CA, USA
| | - Sean Broce
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Jackelyn Crabtree
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | | | | | - Lisa Müller
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | | | - Marcel Andrée
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Ortwin Adams
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, Düsseldorf, Germany
| | - Robert J. Hogan
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | - Ralph A. Tripp
- University of Georgia, Animal Health Research Center, Athens, GA, USA
| | | | | | | | | | - Jonathan C. Reed
- Dept. of Global Health, University of Washington, Seattle, WA, USA
| | - Jim Lin
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Ian Brown
- Prosetta Biosciences, San Francisco, CA, USA
| | - Sharon Lau
- Prosetta Biosciences, San Francisco, CA, USA
| | - Ilana Segal
- Prosetta Biosciences, San Francisco, CA, USA
| | | | - Shi Hong
- Prosetta Biosciences, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - John Greenland
- Veterans Administration Medical Center, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
| | - Michael K. Lo
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Carsten Korth
- Institute of Neuropathology, Heinrich Heine University, Düsseldorf, Germany
| | | | | | - Vishwanath R. Lingappa
- Prosetta Biosciences, San Francisco, CA, USA
- University of California, San Francisco, CA, USA
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5
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Cadena IA, Buchanan MR, Harris CG, Jenne MA, Rochefort WE, Nelson D, Fogg KC. Engineering high throughput screening platforms of cervical cancer. J Biomed Mater Res A 2023; 111:747-764. [PMID: 36861788 DOI: 10.1002/jbm.a.37522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
Cervical cancer is the second leading cause of cancer-related death in women under 40 and is one of the few cancers to have an increased incidence rate and decreased survival rate over the last 10 years. One in five patients will have recurrent and/or distant metastatic disease and these patients face a 5-year survival rate of less than 17%. Thus, there is a pressing need to develop new anticancer therapeutics for this underserved patient population. However, the development of new anticancer drugs remains a challenge, as only 7% of novel anticancer drugs are approved for clinical use. To facilitate identification of novel and effective anticancer drugs for cervical cancer, we developed a multilayer multicellular platform of human cervical cancer cell lines and primary human microvascular endothelial cells that interfaces with high throughput drug screening methods to evaluate the anti-metastatic and anti-angiogenic drug efficacy simultaneously. Through the use of design of experiments statistical optimization, we identified the specific concentrations of collagen I, fibrinogen, fibronectin, GelMA, and PEGDA in each hydrogel layer that maximized both cervical cancer invasion and endothelial microvessel length. We then validated the optimized platform and assessed its viscoelastic properties. Finally, using this optimized platform, we conducted a targeted drug screen of four clinically relevant drugs on two cervical cancer cell lines. Overall, this work provides a valuable platform that can be used to screen large compound libraries for mechanistic studies, drug discovery, and precision oncology for cervical cancer patients.
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Affiliation(s)
- Ines A Cadena
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Mina R Buchanan
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Conor G Harris
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Molly A Jenne
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Willie E Rochefort
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
| | - Dylan Nelson
- College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlin C Fogg
- School of Chemical, Biological, and Environmental Engineering, Oregon State University, Corvallis, Oregon, USA
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6
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Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov 2022; 21:899-914. [DOI: 10.1038/s41573-022-00472-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/29/2022]
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7
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Wlodkowic D. Future prospects of accelerating neuroactive drug discovery with high-throughput behavioral phenotyping. Expert Opin Drug Discov 2022; 17:305-308. [PMID: 35081850 DOI: 10.1080/17460441.2022.2031971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Melbourne, Australia
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8
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Selvaraj C, Chandra I, Singh SK. Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries. Mol Divers 2021; 26:1893-1913. [PMID: 34686947 PMCID: PMC8536481 DOI: 10.1007/s11030-021-10326-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/24/2021] [Indexed: 12/27/2022]
Abstract
The global spread of COVID-19 has raised the importance of pharmaceutical drug development as intractable and hot research. Developing new drug molecules to overcome any disease is a costly and lengthy process, but the process continues uninterrupted. The critical point to consider the drug design is to use the available data resources and to find new and novel leads. Once the drug target is identified, several interdisciplinary areas work together with artificial intelligence (AI) and machine learning (ML) methods to get enriched drugs. These AI and ML methods are applied in every step of the computer-aided drug design, and integrating these AI and ML methods results in a high success rate of hit compounds. In addition, this AI and ML integration with high-dimension data and its powerful capacity have taken a step forward. Clinical trials output prediction through the AI/ML integrated models could further decrease the clinical trials cost by also improving the success rate. Through this review, we discuss the backend of AI and ML methods in supporting the computer-aided drug design, along with its challenge and opportunity for the pharmaceutical industry. From the available information or data, the AI and ML based prediction for the high throughput virtual screening. After this integration of AI and ML, the success rate of hit identification has gained a momentum with huge success by providing novel drugs.
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Affiliation(s)
- Chandrabose Selvaraj
- CADD and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India.
| | - Ishwar Chandra
- CADD and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India
| | - Sanjeev Kumar Singh
- CADD and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India.
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9
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Lewis RA, Devi J, Green K, Li J, Hopkins A, Hayles J, Nurse P, Errington J, Allenby NEE. Screening and Purification of Natural Products from Actinomycetes that Induce a "Rounded" Morphological Phenotype in Fission Yeast. NATURAL PRODUCTS AND BIOPROSPECTING 2021; 11:431-445. [PMID: 33881756 PMCID: PMC8275771 DOI: 10.1007/s13659-021-00304-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
This study was designed to identify and investigate bioactive natural product compounds that alter the cellular shape of the fission yeast Schizosaccharomyces pombe and induce a "rounded" or "small" cellular morphological phenotype. Bioassays using a range of antifungal agents against a multidrug-sensitive fission yeast strain, SAK950 showed that many induced a "rounded" phenotype. We then investigated whether 46 of the actinomycete strains identified in our previous study as inducing a similar phenotype produced antifungal agents of similar classes. We show that five of the strains produced streptothricin and that 26 strains produced polyenes, including fungichromin, filipin and candicidin, the last of which was produced by 24 strains. A taxonomic study of the strains indicated that the majority of the candicidin only producers were Streptomyces hydrogenans and S. albidoflavus whilst those that additionally produced streptothricin were related to S. enissocaesilis. A follow-up study to investigate the natural products made by related strains indicated that they followed a similar pattern. The identification of several compounds from the actinomycete strains similar to the antifungal agents initially tested confirm the validity of an approach using the S. pombe morphological phenotype and actinomycete taxonomy as a predictive tool for natural product identification.
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Affiliation(s)
- Richard Alexander Lewis
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK.
| | - Jenileima Devi
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Katherine Green
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Juanjuan Li
- University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Adam Hopkins
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Jacqueline Hayles
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paul Nurse
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jeff Errington
- Demuris Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
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10
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Molina L, Williams DE, Andersen RJ, Golsteyn RM. Isolation of a natural product with anti-mitotic activity from a toxic Canadian prairie plant. Heliyon 2021; 7:e07131. [PMID: 34095597 PMCID: PMC8167235 DOI: 10.1016/j.heliyon.2021.e07131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/09/2021] [Accepted: 05/19/2021] [Indexed: 11/18/2022] Open
Abstract
We are investigating plants from the prairie ecological zone of Canada to identify natural products that inhibit mitosis in cancer cells. Investigation of plant parts from the Canadian plant species Hymenoxys richardsonii (Asteraceae) revealed that leaf extracts (PP-360A) had anti-mitotic activity on human cancer cell lines. Cells treated with leaf extracts acquired a rounded morphology, similar to that of cells in mitosis. We demonstrated that the rounded cells contained mitotic spindles and phospho-histone H3 using the techniques of immunofluorescence microscopy. By biology-guided fractionation of H. richardsonii leaves, we isolated a sesquiterpene lactone named hymenoratin, which had not been previously assigned a biological activity. Cells treated with hymenoratin have phospho-histone H3 positive chromosomes, a mitotic spindle, and enter a prolonged mitotic arrest in which the spindles become distorted. By Western blot analysis, hymenoratin treated cells acquire high levels of cyclin B and dephosphorylated Cdk1. There is a growing body of evidence that select members of the sesquiterpene lactone chemical family have anti-mitotic activity.
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Affiliation(s)
- Layla Molina
- Natural Product and Cancer Cell Laboratories, University of Lethbridge, Lethbridge, AB, T1K 3M4 Canada
| | - David E Williams
- Department of Earth, Ocean, Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Raymond J Andersen
- Department of Earth, Ocean, Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Roy M Golsteyn
- Natural Product and Cancer Cell Laboratories, University of Lethbridge, Lethbridge, AB, T1K 3M4 Canada
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11
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Alonso F, Galilea A, Mañez PA, Acebedo SL, Cabrera GM, Otero M, Barquero AA, Ramírez JA. Beyond Pseudo-natural Products: Sequential Ugi/Pictet-Spengler Reactions Leading to Steroidal Pyrazinoisoquinolines That Trigger Caspase-Independent Death in HepG2 Cells. ChemMedChem 2021; 16:1945-1955. [PMID: 33682316 DOI: 10.1002/cmdc.202100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/27/2021] [Indexed: 01/05/2023]
Abstract
In this work, we describe how stereochemically complex polycyclic compounds can be generated by applying a synthetic sequence comprising an intramolecular Ugi reaction followed by a Pictet-Spengler cyclization on steroid-derived scaffolds. The resulting compounds, which combine a fragment derived from a natural product and a scaffold not found in nature. are both structurally distinct and globally similar to natural products at the same time, and interrogate an alternative region of the chemical space. One of the new compounds showed significant antiproliferative activity on HepG2 cells through a caspase-independent cell-death mechanism, an appealing feature when new antitumor compounds are searched.
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Affiliation(s)
- Fernando Alonso
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Agustín Galilea
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Pau Arroyo Mañez
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Departamento de Química Orgánica de la Facultad de Farmacia, Universitat de València, Valencia, 46100, Spain
| | - Sofía L Acebedo
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Gabriela M Cabrera
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
| | - Marcelo Otero
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, CONICET - Universidad de Buenos Aires and Instituto de Física de Buenos Aires (IFIBA), Ciudad Universitaria, Buenos Aires, 1428, Argentina
| | - Andrea A Barquero
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Departamento de Química Biológica, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Instituto de Quimica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina
| | - Javier A Ramírez
- Departamento de Química Orgánica, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina.,Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), CONICET - Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, 1428, Argentina)
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12
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Jörg M, Madden KS. The right tools for the job: the central role for next generation chemical probes and chemistry-based target deconvolution methods in phenotypic drug discovery. RSC Med Chem 2021; 12:646-665. [PMID: 34124668 PMCID: PMC8152813 DOI: 10.1039/d1md00022e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
The reconnection of the scientific community with phenotypic drug discovery has created exciting new possibilities to develop therapies for diseases with highly complex biology. It promises to revolutionise fields such as neurodegenerative disease and regenerative medicine, where the development of new drugs has consistently proved elusive. Arguably, the greatest challenge in readopting the phenotypic drug discovery approach exists in establishing a crucial chain of translatability between phenotype and benefit to patients in the clinic. This remains a key stumbling block for the field which needs to be overcome in order to fully realise the potential of phenotypic drug discovery. Excellent quality chemical probes and chemistry-based target deconvolution techniques will be a crucial part of this process. In this review, we discuss the current capabilities of chemical probes and chemistry-based target deconvolution methods and evaluate the next advances necessary in order to fully support phenotypic screening approaches in drug discovery.
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Affiliation(s)
- Manuela Jörg
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
| | - Katrina S Madden
- School of Natural and Environmental Sciences, Newcastle University Bedson Building Newcastle upon Tyne NE1 7RU UK
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville Victoria 3052 Australia
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13
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Shabajee P, Gaudeau A, Legros C, Dorval T, Stéphan JP. [From high content screening to target deconvolution: New insights for phenotypic approaches]. Med Sci (Paris) 2021; 37:249-257. [PMID: 33739272 DOI: 10.1051/medsci/2021013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The advent of the molecular biology and the completion of the human genome sequencing prompted the pharmaceutical industry to progressively implement target-centric drug discovery strategies. However, concerns regarding the research and development productivity during the last ten years, combined with technological developments in high-content screening, automation, image analysis and artificial intelligence triggered a renewed interest for the phenotypic drug discovery approaches. Target-centric and phenotypic approaches are more and more considered complementary, hence, positioning the target deconvolution on the critical path. This review analyzes the evolution of the target-centric and phenotypic approaches, focusing more specifically on the high-content screening and the target deconvolution technologies currently available.
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Affiliation(s)
- Preety Shabajee
- Pôle d'expertise Criblage pharmacologique, chimiothèque et biobanques, Institut de Recherches Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Albane Gaudeau
- Pôle d'expertise Criblage pharmacologique, chimiothèque et biobanques, Institut de Recherches Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Céline Legros
- Pôle d'expertise Criblage pharmacologique, chimiothèque et biobanques, Institut de Recherches Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Thierry Dorval
- Pôle d'expertise Criblage pharmacologique, chimiothèque et biobanques, Institut de Recherches Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Jean-Philippe Stéphan
- Pôle d'expertise Criblage pharmacologique, chimiothèque et biobanques, Institut de Recherches Servier, 125, Chemin de Ronde, 78290 Croissy-sur-Seine, France
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14
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Malandraki-Miller S, Riley PR. Use of artificial intelligence to enhance phenotypic drug discovery. Drug Discov Today 2021; 26:887-901. [PMID: 33484947 DOI: 10.1016/j.drudis.2021.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/28/2020] [Accepted: 01/15/2021] [Indexed: 01/17/2023]
Abstract
Research and development (R&D) productivity across the pharmaceutical industry has received close scrutiny over the past two decades, especially taking into consideration reports of attrition rates and the colossal cost for drug development. The respective merits of the two main drug discovery approaches, phenotypic and target based, have divided opinion across the research community, because each hold different advantages for identifying novel molecular entities with a successful path to the market. Nevertheless, both have low translatability in the clinic. Artificial intelligence (AI) and adoption of machine learning (ML) tools offer the promise of revolutionising drug development, and overcoming obstacles in the drug discovery pipeline. Here, we assess the potential of target-driven and phenotypic-based approaches and offer a holistic description of the current state of the field, from both a scientific and industry perspective. With the emerging partnerships between AI/ML and pharma still in their relative infancy, we investigate the potential and current limitations with a particular focus on phenotypic drug discovery. Finally, we emphasise the value of public-private partnerships (PPPs) and cross-disciplinary collaborations to foster innovation and facilitate efficient drug discovery programmes.
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Affiliation(s)
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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15
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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16
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High-throughput animal tracking in chemobehavioral phenotyping: Current limitations and future perspectives. Behav Processes 2020; 180:104226. [DOI: 10.1016/j.beproc.2020.104226] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
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17
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Hartman GD, Kuduk SD, Espiritu C, Lam AM. P450s under Restriction (PURE) Screen Using HepaRG and Primary Human Hepatocytes for Discovery of Novel HBV Antivirals. ACS Med Chem Lett 2020; 11:1919-1927. [PMID: 33062174 DOI: 10.1021/acsmedchemlett.9b00630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Herein is reported a novel screening paradigm PURE (P450s under restriction) for the identification and optimization of hits as part of a hepatitis B virus (HBV) antiviral discovery program. To closely represent in vivo hepatocytes, differentiated HepaRG cells (dHRGs) and primary human hepatocytes (PHHs) were used as the basis for an HBV infection system. However, a significant challenge arose during potency evaluation in using cultured dHRGs and PHHs as screening platforms because, as with hepatocytes in vivo, these cells express active cytochrome P450 enzymes and thus can metabolize test compounds. The observed antiviral effects may be the cumulative result of a dynamic pool of parent compound and metabolites thus confounding structure activity relationship (SAR) interpretation and subsequent optimization design initiatives. We show here that PURE methodology restricts metabolism of HBV-infected dHRGs and PHHs and thus provides highly informative potency data for decision-making on key representative antiviral compounds.
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Affiliation(s)
- George D. Hartman
- Novira Therapeutics, a Janssen Pharmaceutical Company, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Scott D. Kuduk
- Novira Therapeutics, a Janssen Pharmaceutical Company, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Christine Espiritu
- Novira Therapeutics, a Janssen Pharmaceutical Company, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Angela M. Lam
- Novira Therapeutics, a Janssen Pharmaceutical Company, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
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18
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Noordin MAM, Noor MM, Aizat WM. The Impact of Plant Bioactive Compounds on Aging and Fertility of Diverse Organisms: A Review. Mini Rev Med Chem 2020; 20:1287-1299. [DOI: 10.2174/1389557520666200429101942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/22/2022]
Abstract
It is expected that in 2050, there will be more than 20% of senior citizens aged over 60 years
worldwide. Such alarming statistics require immediate attention to improve the health of the aging
population. Since aging is closely related to the loss of antioxidant defense mechanisms, this situation
eventually leads to numerous health problems, including fertility reduction. Furthermore, plant extracts
have been used in traditional medicine as potent antioxidant sources. Although many experiments had
reported the impact of various bioactive compounds on aging or fertility, there is a lack of review papers
that combine both subjects. In this review, we have collected and discussed various bioactive
compounds from 26 different plant species known to affect both longevity and fertility. These compounds,
including phenolics and terpenes, are mostly involved in the antioxidant defense mechanisms
of diverse organisms such as rats, mites, fruit flies, roundworms, and even roosters. A human clinical
trial should be considered in the future to measure the effects of these bioactive compounds on human
health and longevity. Ultimately, these plant-derived compounds could be developed into health supplements
or potential medical drugs to ensure a healthy aging population.
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Affiliation(s)
- Muhammad Akram Mohd Noordin
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia
| | - Mahanem Mat Noor
- Centre for Biotechnology and Functional Food, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 Bangi, Selangor, Malaysia
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19
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Abstract
There is a great need for innovative new medicines to treat unmet medical needs. The discovery and development of innovative new medicines is extremely difficult, costly, and inefficient. In the last decade, phenotypic drug discovery (PDD) was reintroduced as a strategy to provide first-in-class medicines. PDD uses empirical, target-agnostic lead generation to identify pharmacologically active molecules and novel therapeutics which work through unprecedented drug mechanisms. The economic and scientific value of PDD is exemplified through game-changing medicines for hepatitis C virus, spinal muscular atrophy, and cystic fibrosis. In this short review, recent advances are noted for the implementation and de-risking of PDD (for compound library selection, biomarker development, mechanism identification, and safety studies) and the potential for artificial intelligence. A significant barrier in the decision to implement PDD is balancing the potential impact of a novel mechanism of drug action with an under-defined scientific path forward, with the desire to provide infrastructure and metrics to optimize return on investment, which a known mechanism provides. A means to address this knowledge gap in the future is to empower precompetitive research utilizing the empirical concepts of PDD to identify new mechanisms and pharmacologically active compounds.
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20
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Yang L, Bui L, Hanjaya-Putra D, Bruening ML. Membrane-Based Affinity Purification to Identify Target Proteins of a Small-Molecule Drug. Anal Chem 2020; 92:11912-11920. [DOI: 10.1021/acs.analchem.0c02316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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A Phenotarget Approach for Identifying an Alkaloid Interacting with the Tuberculosis Protein Rv1466. Mar Drugs 2020; 18:md18030149. [PMID: 32150903 PMCID: PMC7143284 DOI: 10.3390/md18030149] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/11/2020] [Accepted: 02/20/2020] [Indexed: 01/10/2023] Open
Abstract
In recent years, there has been a revival of interest in phenotypic-based drug discovery (PDD) due to target-based drug discovery (TDD) falling below expectations. Both PDD and TDD have their unique advantages and should be used as complementary methods in drug discovery. The PhenoTarget approach combines the strengths of the PDD and TDD approaches. Phenotypic screening is conducted initially to detect cellular active components and the hits are then screened against a panel of putative targets. This PhenoTarget protocol can be equally applied to pure compound libraries as well as natural product fractions. Here we described the use of the PhenoTarget approach to identify an anti-tuberculosis lead compound. Fractions from Polycarpa aurata were identified with activity against Mycobacterium tuberculosis H37Rv. Native magnetic resonance mass spectrometry (MRMS) against a panel of 37 proteins from Mycobacterium proteomes showed that a fraction from a 95% ethanol re-extraction specifically formed a protein-ligand complex with Rv1466, a putative uncharacterized Mycobacterium tuberculosis protein. The natural product responsible was isolated and characterized to be polycarpine. The molecular weight of the ligand bound to Rv1466, 233 Da, was half the molecular weight of polycarpine less one proton, indicating that polycarpine formed a covalent bond with Rv1466.
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22
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Abstract
The value of innovation in medicines is clear. Despite all of the progress in the twenty-first century, there are still many unmet medical needs and opportunities to improve healthcare. The challenges for pharmaceutical companies include ways in which to stay competitive and flexible in an environment of constant knowledge growth and increasingly sophisticated technologies, and ways to generate sufficient revenues to sustain their own growth. To that end, pharmaceutical companies are compelled to adapt different business models in the face of new challenges. The industry is plagued with long research and development (R&D) cycles and low success rates for innovative treatments; something has to change. The need to collaborate externally across the process of discovery, development, manufacturing and commercialization is a must. Furthermore, collaborations have increased in frequency and scope, expanding the opportunities to access global scientific talent in academia, research institutes and biotechnology companies. Despite the perception that pharma companies are 'closed' or tightly controlled industries, open innovation is already well established in the pharmaceutical sector and used to supplement R&D in the process of bringing new medicines for patients faster, and at a lower cost. Over the years, each pharma company has tailored the open-innovation concept to develop its own model based on particular needs and offerings. Independently of the model, the creation of successful partnerships in external innovation requires reaching out and connecting beyond the traditional organizational boundaries. Substantial internal cultural changes are required to implement open-innovation strategies that should co-exist without competing with the traditional ways of operating. Major changes bring challenges but create multiple opportunities for scientists and organizations. High-quality drug discovery requires continuous learning and an open way of thinking to adopt novel operational models and to implement efficient collaborations.
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23
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24
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Friese A, Ursu A, Hochheimer A, Schöler HR, Waldmann H, Bruder JM. The Convergence of Stem Cell Technologies and Phenotypic Drug Discovery. Cell Chem Biol 2019; 26:1050-1066. [PMID: 31231030 DOI: 10.1016/j.chembiol.2019.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 04/04/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
Abstract
Recent advances in induced pluripotent stem cell technologies and phenotypic screening shape the future of bioactive small-molecule discovery. In this review we analyze the impact of small-molecule phenotypic screens on drug discovery as well as on the investigation of human development and disease biology. We further examine the role of 3D spheroid/organoid structures, microfluidic systems, and miniaturized on-a-chip systems for future discovery strategies. In highlighting representative examples, we analyze how recent achievements can translate into future therapies. Finally, we discuss remaining challenges that need to be overcome for the adaptation of the next generation of screening approaches.
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Affiliation(s)
- Alexandra Friese
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Andrei Ursu
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany
| | - Andreas Hochheimer
- ISAR Bioscience GmbH, Institute for Stem Cell & Applied Regenerative Medicine Research, 82152 Planegg, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstrasse 3, 48149 Münster, Germany.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 4a, 44227 Dortmund, Germany.
| | - Jan M Bruder
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.
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25
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Towards High-Throughput Chemobehavioural Phenomics in Neuropsychiatric Drug Discovery. Mar Drugs 2019; 17:md17060340. [PMID: 31174272 PMCID: PMC6627923 DOI: 10.3390/md17060340] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/19/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022] Open
Abstract
Identifying novel marine-derived neuroactive chemicals with therapeutic potential is difficult due to inherent complexities of the central nervous system (CNS), our limited understanding of the molecular foundations of neuro-psychiatric conditions, as well as the limited applications of effective high-throughput screening models that recapitulate functionalities of the intact CNS. Furthermore, nearly all neuro-modulating chemicals exhibit poorly characterized pleiotropic activities often referred to as polypharmacology. The latter renders conventional target-based in vitro screening approaches very difficult to accomplish. In this context, chemobehavioural phenotyping using innovative small organism models such as planarians and zebrafish represent powerful and highly integrative approaches to study the impact of new chemicals on central and peripheral nervous systems. In contrast to in vitro bioassays aimed predominantly at identification of chemicals acting on single targets, phenotypic chemobehavioural analysis allows for complex multi-target interactions to occur in combination with studies of polypharmacological effects of chemicals in a context of functional and intact milieu of the whole organism. In this review, we will outline recent advances in high-throughput chemobehavioural phenotyping and provide a future outlook on how those innovative methods can be utilized for rapidly screening and characterizing marine-derived compounds with prospective applications in neuropharmacology and psychosomatic medicine.
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26
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Ribeiro da Cunha B, Fonseca LP, Calado CRC. Antibiotic Discovery: Where Have We Come from, Where Do We Go? Antibiotics (Basel) 2019; 8:antibiotics8020045. [PMID: 31022923 PMCID: PMC6627412 DOI: 10.3390/antibiotics8020045] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 12/15/2022] Open
Abstract
Given the increase in antibiotic-resistant bacteria, alongside the alarmingly low rate of newly approved antibiotics for clinical usage, we are on the verge of not having effective treatments for many common infectious diseases. Historically, antibiotic discovery has been crucial in outpacing resistance and success is closely related to systematic procedures—platforms—that have catalyzed the antibiotic golden age, namely the Waksman platform, followed by the platforms of semi-synthesis and fully synthetic antibiotics. Said platforms resulted in the major antibiotic classes: aminoglycosides, amphenicols, ansamycins, beta-lactams, lipopeptides, diaminopyrimidines, fosfomycins, imidazoles, macrolides, oxazolidinones, streptogramins, polymyxins, sulphonamides, glycopeptides, quinolones and tetracyclines. During the genomics era came the target-based platform, mostly considered a failure due to limitations in translating drugs to the clinic. Therefore, cell-based platforms were re-instituted, and are still of the utmost importance in the fight against infectious diseases. Although the antibiotic pipeline is still lackluster, especially of new classes and novel mechanisms of action, in the post-genomic era, there is an increasingly large set of information available on microbial metabolism. The translation of such knowledge into novel platforms will hopefully result in the discovery of new and better therapeutics, which can sway the war on infectious diseases back in our favor.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL); Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Luís P Fonseca
- Institute for Bioengineering and Biosciences (IBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL); Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Cecília R C Calado
- Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa (IPL); R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal.
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27
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Peón A, Li H, Ghislat G, Leung KS, Wong MH, Lu G, Ballester PJ. MolTarPred: A web tool for comprehensive target prediction with reliability estimation. Chem Biol Drug Des 2019; 94:1390-1401. [PMID: 30916462 DOI: 10.1111/cbdd.13516] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/07/2019] [Accepted: 03/03/2019] [Indexed: 12/17/2022]
Abstract
Molecular target prediction can provide a starting point to understand the efficacy and side effects of phenotypic screening hits. Unfortunately, the vast majority of in silico target prediction methods are not available as web tools. Furthermore, these are limited in the number of targets that can be predicted, do not estimate which target predictions are more reliable and/or lack comprehensive retrospective validations. We present MolTarPred ( http://moltarpred.marseille.inserm.fr/), a user-friendly web tool for predicting protein targets of small organic compounds. It is powered by a large knowledge base comprising 607,659 compounds and 4,553 macromolecular targets collected from the ChEMBL database. In about 1 min, the predicted targets for the supplied molecule will be listed in a table. The chemical structures of the query molecule and the most similar compounds annotated with the predicted target will also be shown to permit visual inspection and comparison. Practical examples of the use of MolTarPred are showcased. MolTarPred is a new resource for scientists that require a more complete knowledge of the polypharmacology of a molecule. The introduction of a reliability score constitutes an attractive functionality of MolTarPred, as it permits focusing experimental confirmatory tests on the most reliable predictions, which leads to higher prospective hit rates.
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Affiliation(s)
- Antonio Peón
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068, Inserm, Marseille, France.,UMR7258, CNRS, Marseille, France.,Institut Paoli-Calmettes, Marseille, France.,UM 105, Aix-Marseille University, Marseille, France
| | - Hongjian Li
- SDIVF R&D Centre, Hong Kong Science Park, Sha Tin, New Territories, Hong Kong.,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong
| | - Pedro J Ballester
- Centre de Recherche en Cancérologie de Marseille (CRCM), U1068, Inserm, Marseille, France.,UMR7258, CNRS, Marseille, France.,Institut Paoli-Calmettes, Marseille, France.,UM 105, Aix-Marseille University, Marseille, France
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28
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Li Z, Sun H, Turek J, Jalal S, Childress M, Nolte DD. Doppler fluctuation spectroscopy of intracellular dynamics in living tissue. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2019; 36:665-677. [PMID: 31044988 PMCID: PMC6791373 DOI: 10.1364/josaa.36.000665] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 05/26/2023]
Abstract
Intracellular dynamics in living tissue are dominated by active transport driven by bioenergetic processes far from thermal equilibrium. Intracellular constituents typically execute persistent walks. In the limit of long mean free paths, the persistent walks are ballistic, exhibiting a "Doppler edge" in light scattering fluctuation spectra. At shorter transport lengths, the fluctuations are described by lifetime-broadened Doppler spectra. Dynamic light scattering from transport in the ballistic, diffusive, or the crossover regimes is derived analytically, including the derivation of autocorrelation functions through a driven damped harmonic oscillator analog for light scattering from persistent walks. The theory is validated through Monte Carlo simulations. Experimental evidence for the Doppler edge in three-dimensional (3D) living tissue is obtained using biodynamic imaging based on low-coherence interferometry and digital holography.
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Affiliation(s)
- Zhe Li
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, Indiana 47907, USA
| | - Hao Sun
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, Indiana 47907, USA
| | - John Turek
- Department of Basic Medical Sciences, Purdue University, 625 Harrison Street, West Lafayette, Indiana 47907, USA
| | - Shadia Jalal
- Department of Medicine, IU School of Medicine, 535 Barnhill Drive, Indianapolis, Indiana 46202, USA
| | - Michael Childress
- Department of Veterinary Clinical Sciences, Purdue University 625 Harrison Street, West Lafayette, Indiana 47907, USA
| | - David D. Nolte
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, Indiana 47907, USA
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A11, a novel diaryl acylhydrazone derivative, exerts neuroprotection against ischemic injury in vitro and in vivo. Acta Pharmacol Sin 2019; 40:160-169. [PMID: 29925921 DOI: 10.1038/s41401-018-0028-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/08/2018] [Accepted: 04/09/2018] [Indexed: 12/21/2022] Open
Abstract
There is an urgent need to develop effective therapies for ischemic stroke, but the complicated pathological processes after ischemia make doing so difficult. In the current study, we identified a novel diaryl acylhydrazone derivative, A11, which has multiple neuroprotective properties in ischemic stroke models. First, A11 was demonstrated to induce neuroprotection against ischemic injury in a dose-dependent manner (from 0.3 to 3 μM) in three in vitro experimental ischemic stroke models: oxygen glucose deprivation (OGD), hydrogen peroxide, and glutamate-stimulated neuronal cell injury models. Moreover, A11 was able to potently alleviate three critical pathological changes, apoptosis, oxidative stress, and mitochondrial dysfunction, following ischemic insult in neuronal cells. Further analysis revealed that A11 upregulated the phosphorylation levels of protein kinase B (AKT) and extracellular signal-regulated kinase (ERK) in OGD-exposed neuronal cells, suggesting joint activation of the phosphoinositide 3-kinase (PI3K)/AKT and mitogen-activated protein kinase (MEK)/ERK pathways. In rats with middle cerebral artery occlusion, single-dose administration of A11 (3 mg/kg per day, i.v.) at the onset of reperfusion significantly reduced the infarct volumes and ameliorated neurological deficits. Our study, for the first time, reports the anti-ischemic effect of diaryl acylhydrazone chemical entities, especially A11, which acts on multiple ischemia-associated pathological processes. Our results may provide new clues for the development of an effective therapeutic agent for ischemic stroke.
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The power of combining phenotypic and target-focused drug discovery. Drug Discov Today 2019; 24:526-532. [DOI: 10.1016/j.drudis.2018.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/10/2018] [Accepted: 10/16/2018] [Indexed: 01/09/2023]
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31
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Brown DG, Boström J. Where Do Recent Small Molecule Clinical Development Candidates Come From? J Med Chem 2018; 61:9442-9468. [DOI: 10.1021/acs.jmedchem.8b00675] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Dean G. Brown
- Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jonas Boström
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Pepparedsleden 1, Gothenburg SE-431 83, Sweden
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32
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Zhao Z, Rajagopalan R, Zweifach A. A Novel Multiple-Read Screen for Metabolically Active Compounds Based on a Genetically Encoded FRET Sensor for ATP. SLAS DISCOVERY 2018; 23:907-918. [PMID: 29898642 DOI: 10.1177/2472555218780636] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Both glycolysis and mitochondrial energetics are targets of interest for developing antiproliferative cancer therapeutics. We developed a novel multiple-read assay based on long-term expression in K562 cells of a genetically encoded intramolecular Förster resonance energy transfer sensor for adenosine triphosphate (ATP). The assay, conducted in a fluorescent plate reader, can identify compounds that inhibit oxidative phosphorylation-dependent ATP production, glycolysis, or both after short-term treatment. We screened a National Cancer Institute (NCI) compound library, identifying inhibitors of oxidative phosphorylation-dependent ATP production and glycolysis. Three glycolysis inhibitors blocked hexokinase activity, demonstrating that our assay can serve as the initial step in a workflow to identify compounds that inhibit glycolysis via a defined desired mechanism. Finally, upon reviewing the literature, we found surprisingly little evidence that inhibiting glycolysis with small molecules is antiproliferative. Using NCI data on proliferation of K562 cells, we found that inhibitors of oxidative phosphorylation-dependent ATP production were no more antiproliferative than the overall library, whereas all glycolysis inhibitors were in the top third of most effective antiproliferative compounds. Our results thus present a powerful new way to screen for compounds that affect cellular metabolism and also provide important support for the idea that blocking glycosis is antiproliferative.
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Affiliation(s)
- Ziyan Zhao
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Rahul Rajagopalan
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Adam Zweifach
- 1 Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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33
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Choi H, Li Z, Sun H, Merrill D, Turek J, Childress M, Nolte D. Biodynamic digital holography of chemoresistance in a pre-clinical trial of canine B-cell lymphoma. BIOMEDICAL OPTICS EXPRESS 2018; 9:2214-2228. [PMID: 29760982 PMCID: PMC5946783 DOI: 10.1364/boe.9.002214] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 05/08/2023]
Abstract
Biodynamic digital holography was used to obtain phenotypic profiles of canine non-Hodgkin B-cell lymphoma biopsies treated with standard-of-care chemotherapy. Biodynamic signatures from the living 3D tissues were extracted using fluctuation spectroscopy from intracellular Doppler light scattering in response to the molecular mechanisms of action of therapeutic drugs that modify a range of internal cellular motions. The standard-of-care to treat B-cell lymphoma in both humans and dogs is a combination CHOP therapy that consists of doxorubicin, prednisolone, cyclophosphamide and vincristine. The proportion of dogs experiencing durable cancer remission following CHOP chemotherapy was 68%, with 13 out of 19 dogs responding favorably to therapy and 6 dogs failing to have progression-free survival times greater than 100 days. Biodynamic signatures were found that correlate with inferior survival times, and biomarker selection was optimized to identify specific Doppler signatures related to chemoresistance. A machine learning classifier was constructed based on feature vector correlations and linear separability in high-dimensional feature space. Hold-out validation predicted patient response to therapy with 84% accuracy. These results point to the potential for biodynamic profiling to contribute to personalized medicine by aiding the selection of chemotherapy for cancer patients.
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Affiliation(s)
- Honggu Choi
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, IN 47907, USA
| | - Zhe Li
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, IN 47907, USA
| | - Hao Sun
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, IN 47907, USA
| | - Dan Merrill
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, IN 47907, USA
| | - John Turek
- College of Veterinary Medicine Purdue University, 625 Harrison St, West Lafayette, IN 47907, USA
| | - Michael Childress
- College of Veterinary Medicine Purdue University, 625 Harrison St, West Lafayette, IN 47907, USA
| | - David Nolte
- Department of Physics and Astronomy, Purdue University, 525 Northwestern Ave, West Lafayette, IN 47907, USA
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34
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Rodenhizer D, Dean T, D'Arcangelo E, McGuigan AP. The Current Landscape of 3D In Vitro Tumor Models: What Cancer Hallmarks Are Accessible for Drug Discovery? Adv Healthc Mater 2018; 7:e1701174. [PMID: 29350495 DOI: 10.1002/adhm.201701174] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/16/2017] [Indexed: 12/11/2022]
Abstract
Cancer prognosis remains a lottery dependent on cancer type, disease stage at diagnosis, and personal genetics. While investment in research is at an all-time high, new drugs are more likely to fail in clinical trials today than in the 1970s. In this review, a summary of current survival statistics in North America is provided, followed by an overview of the modern drug discovery process, classes of models used throughout different stages, and challenges associated with drug development efficiency are highlighted. Then, an overview of the cancer hallmarks that drive clinical progression is provided, and the range of available clinical therapies within the context of these hallmarks is categorized. Specifically, it is found that historically, the development of therapies is limited to a subset of possible targets. This provides evidence for the opportunities offered by novel disease-relevant in vitro models that enable identification of novel targets that facilitate interactions between the tumor cells and their surrounding microenvironment. Next, an overview of the models currently reported in literature is provided, and the cancer biology they have been used to explore is highlighted. Finally, four priority areas are suggested for the field to accelerate adoption of in vitro tumour models for cancer drug discovery.
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Affiliation(s)
- Darren Rodenhizer
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto 200 College Street Toronto M5S 3E5 Canada
| | - Teresa Dean
- Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto 200 College Street Toronto M5S 3E5 Canada
| | - Elisa D'Arcangelo
- Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto 200 College Street Toronto M5S 3E5 Canada
| | - Alison P. McGuigan
- Department of Chemical Engineering and Applied Chemistry & Institute of Biomaterials and Biomedical EngineeringUniversity of Toronto 200 College Street Toronto M5S 3E5 Canada
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35
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Orellana A, García-González V, López R, Pascual-Guiral S, Lozoya E, Díaz J, Casals D, Barrena A, Paris S, Andrés M, Segarra V, Vilella D, Malhotra R, Eastwood P, Planagumà A, Miralpeix M, Nueda A. Application of a phenotypic drug discovery strategy to identify biological and chemical starting points for inhibition of TSLP production in lung epithelial cells. PLoS One 2018; 13:e0189247. [PMID: 29320511 PMCID: PMC5761851 DOI: 10.1371/journal.pone.0189247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 11/24/2017] [Indexed: 11/18/2022] Open
Abstract
Thymic stromal lymphopoietin (TSLP) is a cytokine released by human lung epithelium in response to external insult. Considered as a master switch in T helper 2 lymphocyte (Th2) mediated responses, TSLP is believed to play a key role in allergic diseases including asthma. The aim of this study was to use a phenotypic approach to identify new biological and chemical starting points for inhibition of TSLP production in human bronchial epithelial cells (NHBE), with the objective of reducing Th2-mediated airway inflammation. To this end, a phenotypic screen was performed using poly I:C / IL-4 stimulated NHBE cells interrogated with a 44,974 compound library. As a result, 85 hits which downregulated TSLP protein and mRNA levels were identified and a representative subset of 7 hits was selected for further characterization. These molecules inhibited the activity of several members of the MAPK, PI3K and tyrosine kinase families and some of them have been reported as modulators of cellular phenotypic endpoints like cell-cell contacts, microtubule polymerization and caspase activation. Characterization of the biological profile of the hits suggested that mTOR could be a key activity involved in the regulation of TSLP production in NHBE cells. Among other targeted kinases, inhibition of p38 MAPK and JAK kinases showed different degrees of correlation with TSLP downregulation, while Syk kinase did not seem to be related. Overall, inhibition of TSLP production by the selected hits, rather than resulting from inhibition of single isolated targets, appeared to be due to a combination of activities with different levels of relevance. Finally, a hit expansion exercise yielded additional active compounds that could be amenable to further optimization, providing an opportunity to dissociate TSLP inhibition from other non-desired activities. This study illustrates the potential of phenotypic drug discovery to complement target based approaches by providing new chemistry and biology leads.
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Affiliation(s)
- Adelina Orellana
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Rosa López
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Estrella Lozoya
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Julia Díaz
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Daniel Casals
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Antolín Barrena
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Stephane Paris
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Miriam Andrés
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Victor Segarra
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Dolors Vilella
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Rajneesh Malhotra
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Paul Eastwood
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | - Anna Planagumà
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Arsenio Nueda
- Almirall R&D Center, Almirall S.A., Sant Feliu de Llobregat, Barcelona, Spain
- * E-mail:
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36
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Kato AS, Witkin JM. Protein complexes as psychiatric and neurological drug targets. Biochem Pharmacol 2018; 151:263-281. [PMID: 29330067 DOI: 10.1016/j.bcp.2018.01.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/05/2018] [Indexed: 12/25/2022]
Abstract
The need for improved medications for psychiatric and neurological disorders is clear. Difficulties in finding such drugs demands that all strategic means be utilized for their invention. The discovery of forebrain specific AMPA receptor antagonists, which selectively block the specific combinations of principal and auxiliary subunits present in forebrain regions but spare targets in the cerebellum, was recently disclosed. This discovery raised the possibility that other auxiliary protein systems could be utilized to help identify new medicines. Discussion of the TARP-dependent AMPA receptor antagonists has been presented elsewhere. Here we review the diversity of protein complexes of neurotransmitter receptors in the nervous system to highlight the broad range of protein/protein drug targets. We briefly outline the structural basis of protein complexes as drug targets for G-protein-coupled receptors, voltage-gated ion channels, and ligand-gated ion channels. This review highlights heterodimers, subunit-specific receptor constructions, multiple signaling pathways, and auxiliary proteins with an emphasis on the later. We conclude that the use of auxiliary proteins in chemical compound screening could enhance the detection of specific, targeted drug searches and lead to novel and improved medicines for psychiatric and neurological disorders.
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Affiliation(s)
- Akihiko S Kato
- Neuroscience Discovery, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, USA.
| | - Jeffrey M Witkin
- Neuroscience Discovery, Lilly Research Labs, Eli Lilly and Company, Indianapolis, IN, USA
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37
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Abstract
No therapies have been shown to improve outcomes in patients with acute kidney injury (AKI). Given the high morbidity and mortality associated with AKI this represents an important unmet medical need. A common feature of all of the therapeutic development efforts for AKI is that none were driven by target selection or preclinical modeling that was based primarily on human data. This is important when considering a heterogeneous and dynamic condition such as AKI, in which in the absence of more accurate molecular classifications, clinical cohorts are likely to include patients with different types of injury at different stages in the injury and repair continuum. The National Institutes of Health precision medicine initiative offers an opportunity to address this. By creating a molecular tissue atlas of AKI, defining patient subgroups, and identifying critical cells and pathways involved in human AKI, this initiative has the potential to transform our current approach to therapeutic discovery. In this review, we discuss the opportunities and challenges that this initiative presents, with a specific focus on AKI, what additional efforts will be needed to apply these discoveries to therapeutic development, and how we believe this effort might lead to the development of new therapeutics for subsets of patients with AKI.
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Affiliation(s)
- Mark de Caestecker
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Raymond Harris
- Nephrology Division, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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38
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Strange K. Drug Discovery in Fish, Flies, and Worms. ILAR J 2017; 57:133-143. [PMID: 28053067 DOI: 10.1093/ilar/ilw034] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 10/21/2016] [Indexed: 12/22/2022] Open
Abstract
Nonmammalian model organisms such as the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the zebrafish Danio rerio provide numerous experimental advantages for drug discovery including genetic and molecular tractability, amenability to high-throughput screening methods and reduced experimental costs and increased experimental throughput compared to traditional mammalian models. An interdisciplinary approach that strategically combines the study of nonmammalian and mammalian animal models with diverse experimental tools has and will continue to provide deep molecular and genetic understanding of human disease and will significantly enhance the discovery and application of new therapies to treat those diseases. This review will provide an overview of C. elegans, Drosophila, and zebrafish biology and husbandry and will discuss how these models are being used for phenotype-based drug screening and for identification of drug targets and mechanisms of action. The review will also describe how these and other nonmammalian model organisms are uniquely suited for the discovery of drug-based regenerative medicine therapies.
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Affiliation(s)
- Kevin Strange
- Kevin Strange, Ph.D., is President and CEO of the MDI Biological Laboratory and CEO of Novo Biosciences, Inc
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39
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Segatto NV, Remião MH, Schachtschneider KM, Seixas FK, Schook LB, Collares T. The Oncopig Cancer Model as a Complementary Tool for Phenotypic Drug Discovery. Front Pharmacol 2017; 8:894. [PMID: 29259556 PMCID: PMC5723300 DOI: 10.3389/fphar.2017.00894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/22/2017] [Indexed: 12/14/2022] Open
Abstract
The screening of potential therapeutic compounds using phenotypic drug discovery (PDD) is being embraced once again by researchers and pharmaceutical companies as an approach to enhance the development of new effective therapeutics. Before the genomics and molecular biology era and the consecutive emergence of targeted-drug discovery approaches, PDD was the most common platform used for drug discovery. PDD, also known as phenotypic screening, consists of screening potential compounds in either in vitro cellular or in vivo animal models to identify compounds resulting in a desirable phenotypic change. Using this approach, the biological targets of the compounds are not taken into consideration. Suitable animal models are crucial for the continued validation and discovery of new drugs, as compounds displaying promising results in phenotypic in vitro cell-based and in vivo small animal model screenings often fail in clinical trials. Indeed, this is mainly a result of differential anatomy, physiology, metabolism, immunology, and genetics between humans and currently used pre-clinical small animal models. In contrast, pigs are more predictive of therapeutic treatment outcomes in humans than rodents. In addition, pigs provide an ideal platform to study cancer due to their similarities with humans at the anatomical, physiological, metabolic, and genetic levels. Here we provide a mini-review on the reemergence of PDD in drug development, highlighting the potential of porcine cancer models for improving pre-clinical drug discovery and testing. We also present precision medicine based genetically defined swine cancer models developed to date and their potential as biomedical models.
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Affiliation(s)
- Natalia V. Segatto
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Mariana H. Remião
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | | | - Fabiana K. Seixas
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Champaign, IL, United States
| | - Tiago Collares
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
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40
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Yin C, Fufa T, Chandrasekar G, Aeluri M, Zaky V, Abdelhady S, Rodríguez AB, Jakobsson J, Varnoosfaderani FS, Mahalingam J, Liu J, Larsson O, Hovatta O, Gaunitz F, Göndör A, Andäng M, Kitambi SS. Phenotypic Screen Identifies a Small Molecule Modulating ERK2 and Promoting Stem Cell Proliferation. Front Pharmacol 2017; 8:726. [PMID: 29114221 PMCID: PMC5660848 DOI: 10.3389/fphar.2017.00726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/27/2017] [Indexed: 11/20/2022] Open
Abstract
Stem cells display a fundamentally different mechanism of proliferation control when compared to somatic cells. Uncovering these mechanisms would maximize the impact in drug discovery with a higher translational applicability. The unbiased approach used in phenotype-based drug discovery (PDD) programs can offer a unique opportunity to identify such novel biological phenomenon. Here, we describe an integrated phenotypic screening approach, employing a combination of in vitro and in vivo PDD models to identify a small molecule increasing stem cell proliferation. We demonstrate that a combination of both in vitro and in vivo screening models improves hit identification and reproducibility of effects across various PDD models. Using cell viability and colony size phenotype measurement we characterize the structure activity relationship of the lead molecule, and identify that the small molecule inhibits phosphorylation of ERK2 and promotes stem cell proliferation. This study demonstrates a PDD approach that employs combinatorial models to identify compounds promoting stem cell proliferation.
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Affiliation(s)
- Chang Yin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Temesgen Fufa
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Gayathri Chandrasekar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Madhu Aeluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
| | - Verina Zaky
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Shaimaa Abdelhady
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Antonio B Rodríguez
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Jakobsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Jianping Liu
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Olle Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Outi Hovatta
- Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Frank Gaunitz
- Klinik und Poliklinik für Neurochirurgie, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Anita Göndör
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Michael Andäng
- Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Hyderabad, India
| | - Satish S Kitambi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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41
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Warchal SJ, Dawson JC, Carragher NO. Development of the Theta Comparative Cell Scoring Method to Quantify Diverse Phenotypic Responses Between Distinct Cell Types. Assay Drug Dev Technol 2017; 14:395-406. [PMID: 27552144 PMCID: PMC5015429 DOI: 10.1089/adt.2016.730] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this article, we have developed novel data visualization tools and a Theta comparative cell scoring (TCCS) method, which supports high-throughput in vitro pharmacogenomic studies across diverse cellular phenotypes measured by multiparametric high-content analysis. The TCCS method provides a univariate descriptor of divergent compound-induced phenotypic responses between distinct cell types, which can be used for correlation with genetic, epigenetic, and proteomic datasets to support the identification of biomarkers and further elucidate drug mechanism-of-action. Application of these methods to compound profiling across high-content assays incorporating well-characterized cells representing known molecular subtypes of disease supports the development of personalized healthcare strategies without prior knowledge of a drug target. We present proof-of-principle data quantifying distinct phenotypic response between eight breast cancer cells representing four disease subclasses. Application of the TCCS method together with new advances in next-generation sequencing, induced pluripotent stem cell technology, gene editing, and high-content phenotypic screening are well placed to advance the identification of predictive biomarkers and personalized medicine approaches across a broader range of disease types and therapeutic classes.
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Affiliation(s)
- Scott J Warchal
- Institute of Genetics and Molecular Medicine, Cancer Research UK Edinburgh Centre, University of Edinburgh , Edinburgh, United Kingdom
| | - John C Dawson
- Institute of Genetics and Molecular Medicine, Cancer Research UK Edinburgh Centre, University of Edinburgh , Edinburgh, United Kingdom
| | - Neil O Carragher
- Institute of Genetics and Molecular Medicine, Cancer Research UK Edinburgh Centre, University of Edinburgh , Edinburgh, United Kingdom
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42
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Moffat JG, Vincent F, Lee JA, Eder J, Prunotto M. Opportunities and challenges in phenotypic drug discovery: an industry perspective. Nat Rev Drug Discov 2017; 16:531-543. [PMID: 28685762 DOI: 10.1038/nrd.2017.111] [Citation(s) in RCA: 484] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phenotypic drug discovery (PDD) approaches do not rely on knowledge of the identity of a specific drug target or a hypothesis about its role in disease, in contrast to the target-based strategies that have been widely used in the pharmaceutical industry in the past three decades. However, in recent years, there has been a resurgence in interest in PDD approaches based on their potential to address the incompletely understood complexity of diseases and their promise of delivering first-in-class drugs, as well as major advances in the tools for cell-based phenotypic screening. Nevertheless, PDD approaches also have considerable challenges, such as hit validation and target deconvolution. This article focuses on the lessons learned by researchers engaged in PDD in the pharmaceutical industry and considers the impact of 'omics' knowledge in defining a cellular disease phenotype in the era of precision medicine, introducing the concept of a chain of translatability. We particularly aim to identify features and areas in which PDD can best deliver value to drug discovery portfolios and can contribute to the identification and the development of novel medicines, and to illustrate the challenges and uncertainties that are associated with PDD in order to help set realistic expectations with regard to its benefits and costs.
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Affiliation(s)
- John G Moffat
- Biochemical &Cellular Pharmacology, Genentech, South San Francisco, California 94080, USA
| | - Fabien Vincent
- Discovery Sciences, Primary Pharmacology Group, Pfizer, Groton, Connecticut 06340, USA
| | - Jonathan A Lee
- Department of Quantitative Biology, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Jörg Eder
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Marco Prunotto
- Phenotype and Target ID, Chemical Biology, pRED, Roche, 4070 Basel, Switzerland. Present address: Office of Innovation, Immunology, Infectious Diseases &Ophthalmology (I2O), Roche Late Stage Development, 124 Grenzacherstrasse, 4070 Basel, Switzerland
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43
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Mello JDFRE, Gomes RA, Vital-Fujii DG, Ferreira GM, Trossini GHG. Fragment-based drug discovery as alternative strategy to the drug development for neglected diseases. Chem Biol Drug Des 2017; 90:1067-1078. [PMID: 28547936 DOI: 10.1111/cbdd.13030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/12/2017] [Accepted: 05/08/2017] [Indexed: 12/24/2022]
Abstract
Neglected diseases (NDs) affect large populations and almost whole continents, representing 12% of the global health burden. In contrast, the treatment available today is limited and sometimes ineffective. Under this scenery, the Fragment-Based Drug Discovery emerged as one of the most promising alternatives to the traditional methods of drug development. This method allows achieving new lead compounds with smaller size of fragment libraries. Even with the wide Fragment-Based Drug Discovery success resulting in new effective therapeutic agents against different diseases, until this moment few studies have been applied this approach for NDs area. In this article, we discuss the basic Fragment-Based Drug Discovery process, brief successful ideas of general applications and show a landscape of its use in NDs, encouraging the implementation of this strategy as an interesting way to optimize the development of new drugs to NDs.
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Affiliation(s)
- Juliana da Fonseca Rezende E Mello
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Renan Augusto Gomes
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Drielli Gomes Vital-Fujii
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Glaucio Monteiro Ferreira
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-graduação em Toxicologia e Análises Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Gustavo Henrique Goulart Trossini
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-graduação em Toxicologia e Análises Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
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Peón A, Naulaerts S, Ballester PJ. Predicting the Reliability of Drug-target Interaction Predictions with Maximum Coverage of Target Space. Sci Rep 2017; 7:3820. [PMID: 28630414 PMCID: PMC5476590 DOI: 10.1038/s41598-017-04264-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/26/2017] [Indexed: 02/05/2023] Open
Abstract
Many computational methods to predict the macromolecular targets of small organic molecules have been presented to date. Despite progress, target prediction methods still have important limitations. For example, the most accurate methods implicitly restrict their predictions to a relatively small number of targets, are not systematically validated on drugs (whose targets are harder to predict than those of non-drug molecules) and often lack a reliability score associated with each predicted target. Here we present a systematic validation of ligand-centric target prediction methods on a set of clinical drugs. These methods exploit a knowledge-base covering 887,435 known ligand-target associations between 504,755 molecules and 4,167 targets. Based on this dataset, we provide a new estimate of the polypharmacology of drugs, which on average have 11.5 targets below IC50 10 µM. The average performance achieved across clinical drugs is remarkable (0.348 precision and 0.423 recall, with large drug-dependent variability), especially given the unusually large coverage of the target space. Furthermore, we show how a sparse ligand-target bioactivity matrix to retrospectively validate target prediction methods could underestimate prospective performance. Lastly, we present and validate a first-in-kind score capable of accurately predicting the reliability of target predictions.
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Affiliation(s)
- Antonio Peón
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France
- CNRS, UMR7258, Marseille, F-13009, France
- Institut Paoli-Calmettes, Marseille, F-13009, France
- Aix-Marseille University, UM 105, F-13284, Marseille, France
| | - Stefan Naulaerts
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France
- CNRS, UMR7258, Marseille, F-13009, France
- Institut Paoli-Calmettes, Marseille, F-13009, France
- Aix-Marseille University, UM 105, F-13284, Marseille, France
| | - Pedro J Ballester
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France.
- CNRS, UMR7258, Marseille, F-13009, France.
- Institut Paoli-Calmettes, Marseille, F-13009, France.
- Aix-Marseille University, UM 105, F-13284, Marseille, France.
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Hukriede N, Vogt A, de Caestecker M. Drug Discovery to Halt the Progression of Acute Kidney Injury to Chronic Kidney Disease: A Case for Phenotypic Drug Discovery in Acute Kidney Injury. Nephron Clin Pract 2017; 137:268-272. [PMID: 28614822 DOI: 10.1159/000476079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/24/2017] [Indexed: 12/29/2022] Open
Abstract
The cellular responses that occur following acute kidney injury (AKI) are complex and dynamic, involving multiple cells types and molecular pathways. For this reason, early selection of defined molecular targets for therapeutic intervention is unlikely to be effective in complex in vivo models of AKI, let alone Phase 3 clinical trials in patients with even more complex AKI pathobiology. Phenotypic screening using zebrafish provides an attractive alternative that does not require prior knowledge of molecular targets and may identify compounds that modify multiple targets that might be missed in more traditional target-based screens. In this review, we discuss results of an academic drug discovery campaign that used zebrafish as a primary screening tool to discover compounds with favorable absorption, metabolism, and toxicity that enhance repair when given late after injury in multiple models of AKI. We discuss how this screening campaign is being integrated into a more comprehensive, phenotypic, and target-based screen for lead compound optimization.
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Affiliation(s)
- Neil Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
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46
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Haak AJ, Girtman MA, Ali MF, Carmona EM, Limper AH, Tschumperlin DJ. Phenylpyrrolidine structural mimics of pirfenidone lacking antifibrotic activity: A new tool for mechanism of action studies. Eur J Pharmacol 2017; 811:87-92. [PMID: 28576410 DOI: 10.1016/j.ejphar.2017.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/24/2017] [Accepted: 05/29/2017] [Indexed: 12/21/2022]
Abstract
Pirfenidone recently received FDA approval as one of the first two drugs designed to treat idiopathic pulmonary fibrosis. While the clinical data continues to support the efficacy of pirfenidone, the specific molecular mechanism of action of this drug has not been fully defined. From a chemical perspective the comparatively simple and lipophilic structure of pirfenidone combined with its administration at high doses, both experimentally and clinically, complicates some of the basic tenants of drug action and drug design. Our objective here was to identify a commercially available structural mimic of pirfenidone which retains key aspects of its physical chemical properties but does not display any of its antifibrotic effects. We tested these molecules using lung fibroblasts derived from patients with idiopathic pulmonary fibrosis and found phenylpyrrolidine based analogs of pirfenidone that were non-toxic and lacked antifibrotic activity even when applied at millimolar concentrations. Based on our findings, these molecules represent pharmacological tools for future studies delineating pirfenidone's mechanism of action.
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Affiliation(s)
- Andrew J Haak
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, United States
| | - Megan A Girtman
- Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Mohamed F Ali
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Eva M Carmona
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States; Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Andrew H Limper
- Thoracic Diseases Research Unit, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States; Division of Pulmonary Critical Care and Internal Medicine, Department of Medicine, Mayo Clinic and Foundation, Rochester, MN 55905, United States
| | - Daniel J Tschumperlin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, United States.
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Waters S, Svensson P, Kullingsjö J, Pontén H, Andreasson T, Sunesson Y, Ljung E, Sonesson C, Waters N. In Vivo Systems Response Profiling and Multivariate Classification of CNS Active Compounds: A Structured Tool for CNS Drug Discovery. ACS Chem Neurosci 2017; 8:785-797. [PMID: 27997108 DOI: 10.1021/acschemneuro.6b00371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
This paper describes the application of in vivo systems response profiling in CNS drug discovery by a process referred to as the Integrative Screening Process. The biological response profile, treated as an array, is used as major outcome for selection of candidate drugs. Dose-response data, including ex vivo brain monoaminergic biomarkers and behavioral descriptors, are systematically collected and analyzed by principal component analysis (PCA) and partial least-squares (PLS) regression, yielding multivariate characterization across compounds. The approach is exemplified by assessing a new class of CNS active compounds, the dopidines, compared to other monoamine modulating compounds including antipsychotics, antidepressants, and procognitive agents. Dopidines display a distinct phenotypic profile which has prompted extensive further preclinical and clinical investigations. In summary, in vivo profiles of CNS compounds are mapped, based on dose response studies in the rat. Applying a systematic and standardized work-flow, a database of in vivo systems response profiles is compiled, enabling comparisons and classification. This creates a framework for translational mapping, a crucial component in CNS drug discovery.
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Affiliation(s)
- Susanna Waters
- Department
of Pharmacology, Gothenburg University, SE-405 30 Gothenburg, Sweden
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
| | - Peder Svensson
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
| | - Johan Kullingsjö
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
| | - Henrik Pontén
- Department
of Pharmacology, Gothenburg University, SE-405 30 Gothenburg, Sweden
| | | | | | - Elisabeth Ljung
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
| | - Clas Sonesson
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
| | - Nicholas Waters
- Integrative Research Laboratories Sweden AB, Gothenburg SE-413 46, Sweden
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48
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O'Duibhir E, Carragher NO, Pollard SM. Accelerating glioblastoma drug discovery: Convergence of patient-derived models, genome editing and phenotypic screening. Mol Cell Neurosci 2017; 80:198-207. [PMID: 27825983 PMCID: PMC6128397 DOI: 10.1016/j.mcn.2016.11.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/05/2016] [Accepted: 11/02/2016] [Indexed: 12/27/2022] Open
Abstract
Patients diagnosed with glioblastoma (GBM) continue to face a bleak prognosis. It is critical that new effective therapeutic strategies are developed. GBM stem cells have molecular hallmarks of neural stem and progenitor cells and it is possible to propagate both non-transformed normal neural stem cells and GBM stem cells, in defined, feeder-free, adherent culture. These primary stem cell lines provide an experimental model that is ideally suited to cell-based drug discovery or genetic screens in order to identify tumour-specific vulnerabilities. For many solid tumours, including GBM, the genetic disruptions that drive tumour initiation and growth have now been catalogued. CRISPR/Cas-based genome editing technologies have recently emerged, transforming our ability to functionally annotate the human genome. Genome editing opens prospects for engineering precise genetic changes in normal and GBM-derived neural stem cells, which will provide more defined and reliable genetic models, with critical matched pairs of isogenic cell lines. Generation of more complex alleles such as knock in tags or fluorescent reporters is also now possible. These new cellular models can be deployed in cell-based phenotypic drug discovery (PDD). Here we discuss the convergence of these advanced technologies (iPS cells, neural stem cell culture, genome editing and high content phenotypic screening) and how they herald a new era in human cellular genetics that should have a major impact in accelerating glioblastoma drug discovery.
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Affiliation(s)
- Eoghan O'Duibhir
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK
| | - Neil O Carragher
- Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK.
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK; Institute of Genetics and Molecular Medicine, CRUK Edinburgh Centre, University of Edinburgh, UK.
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Abstract
The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.
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50
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Sun H, Merrill D, An R, Turek J, Matei D, Nolte DD. Biodynamic imaging for phenotypic profiling of three-dimensional tissue culture. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:16007. [PMID: 28301634 PMCID: PMC5221565 DOI: 10.1117/1.jbo.22.1.016007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/28/2016] [Indexed: 05/04/2023]
Abstract
Three-dimensional (3-D) tissue culture represents a more biologically relevant environment for testing new drugs compared to conventional two-dimensional cancer cell culture models. Biodynamic imaging is a high-content 3-D optical imaging technology based on low-coherence interferometry and digital holography that uses dynamic speckle as high-content image contrast to probe deep inside 3-D tissue. Speckle contrast is shown to be a scaling function of the acquisition time relative to the persistence time of intracellular transport and hence provides a measure of cellular activity. Cellular responses of 3-D multicellular spheroids to paclitaxel are compared among three different growth techniques: rotating bioreactor (BR), hanging-drop (HD), and nonadherent (U-bottom, UB) plate spheroids, compared with ex vivo living tissues. HD spheroids have the most homogeneous tissue, whereas BR spheroids display large sample-to-sample variability as well as spatial heterogeneity. The responses of BR-grown tumor spheroids to paclitaxel are more similar to those of ex vivo biopsies than the responses of spheroids grown using HD or plate methods. The rate of mitosis inhibition by application of taxol is measured through tissue dynamics spectroscopic imaging, demonstrating the ability to monitor antimitotic chemotherapy. These results illustrate the potential use of low-coherence digital holography for 3-D pharmaceutical screening applications.
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Affiliation(s)
- Hao Sun
- Purdue University, Department of Physics, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Daniel Merrill
- Purdue University, Department of Physics, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
| | - Ran An
- Animated Dynamics, Inc., 5770 Decatur Boulevard Suite A, Indianapolis, Indiana 46241, United States
| | - John Turek
- Purdue University, Department of Basic Medical Sciences, West Lafayette, 625 Harrison Street, Indiana 47907, United States
| | - Daniela Matei
- Northwestern University School of Medicine, 303 East SuperiorChicago, Illinois 60611, United States
| | - David D. Nolte
- Purdue University, Department of Physics, 525 Northwestern Avenue, West Lafayette, Indiana 47907, United States
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