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Chen T, Sun T, Bian Y, Pei Y, Feng F, Chi H, Li Y, Tang X, Sang S, Du C, Chen Y, Chen Y, Sun H. The Design and Optimization of Monomeric Multitarget Peptides for the Treatment of Multifactorial Diseases. J Med Chem 2022; 65:3685-3705. [DOI: 10.1021/acs.jmedchem.1c01456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tingkai Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Tianyu Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yaoyao Bian
- College of Acupuncture and Massage, College of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Feng Feng
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Heng Chi
- Food and Pharmaceutical Research Institute, Jiangsu Food and Pharmaceuticals Science College, Huaian 223003, People’s Republic of China
| | - Yuan Li
- Department of Pharmaceutical Engineering, Jiangsu Food and Pharmaceuticals Science College, Huaian 223005, People’s Republic of China
| | - Xu Tang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Shenghu Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Chenxi Du
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Ying Chen
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, People’s Republic of China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, People’s Republic of China
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2
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A Human Retinal Pigment Epithelium-Based Screening Platform Reveals Inducers of Photoreceptor Outer Segments Phagocytosis. Stem Cell Reports 2020; 15:1347-1361. [PMID: 33242397 PMCID: PMC7724476 DOI: 10.1016/j.stemcr.2020.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/20/2022] Open
Abstract
Phagocytosis is a key function in various cells throughout the body. A deficiency in photoreceptor outer segment (POS) phagocytosis by the retinal pigment epithelium (RPE) causes vision loss in inherited retinal diseases and possibly age-related macular degeneration. To date, there are no effective therapies available aiming at recovering the lost phagocytosis function. Here, we developed a high-throughput screening assay based on RPE derived from human embryonic stem cells (hRPE) to reveal enhancers of POS phagocytosis. One of the hits, ramoplanin (RM), reproducibly enhanced POS phagocytosis and ensheathment in hRPE, and enhanced the expression of proteins known to regulate membrane dynamics and ensheathment in other cell systems. Additionally, RM rescued POS internalization defect in Mer receptor tyrosine kinase (MERTK) mutant hRPE, derived from retinitis pigmentosa patient induced pluripotent stem cells. Our platform, including a primary phenotypic screening phagocytosis assay together with orthogonal assays, establishes a basis for RPE-based therapy discovery aiming at a broad patient spectrum.
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3
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Gorshkov K, Pradhan M, Xu M, Yang S, Lee EM, Chen CZ, Shen M, Zheng W. Cell-Based No-Wash Fluorescence Assays for Compound Screens Using a Fluorescence Cytometry Plate Reader. J Pharmacol Exp Ther 2020; 374:500-511. [PMID: 32532853 PMCID: PMC7495342 DOI: 10.1124/jpet.120.265207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/01/2020] [Indexed: 11/22/2022] Open
Abstract
High-throughput cell-based fluorescent imaging assays often require removal of background fluorescent signal to obtain robust measurements. Processing high-density microplates to remove background signal is challenging because of equipment requirements and increasing variation after multiple plate wash steps. Here, we present the development of a wash-free cell-based fluorescence assay method for high-throughput screening using a laser scanning fluorescence plate cytometer. The cytometry data consisted of cell count and fluorescent intensity measurements for phenotypic screening. We obtained robust screening results by applying this assay methodology to the lysosomal storage disease Niemann-Pick disease type A. We further demonstrated that this cytometry method can be applied to the detection of cholesterol in Niemann-Pick disease type C. Lastly, we used the Mirrorball method to obtain preliminary results for the detection of Zika and Dengue viral envelope protein. The advantages of this assay format include 1) no plate washing, 2) 4-fold faster plate scan and analysis time, 3) high throughput, and 4) >10-fold smaller direct data files. In contrast, traditional imaging assays require multiple plate washes to remove the background signal, long plate scan and data analysis times, and large data files. Therefore, this versatile and broadly applicable Mirrorball-based method greatly improves the throughput and data quality of image-based screening by increasing sensitivity and efficiency while reducing assay artifacts.
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Affiliation(s)
- Kirill Gorshkov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Manisha Pradhan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Miao Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Shu Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Emily M Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
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4
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Antileishmanial activity evaluation of thiazolidine-2,4-dione against Leishmania infantum and Leishmania braziliensis. Parasitol Res 2020; 119:2263-2274. [PMID: 32462293 DOI: 10.1007/s00436-020-06706-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 01/04/2023]
Abstract
Leishmaniasis is responsible for approximately 65,000 annual deaths. Despite the mortality data, drugs available for the treatment of patients are insufficient and have moderate therapeutic efficacy in addition to serious adverse effects, which makes the development of new drugs urgent. To achieve this goal, the integration of kinetic and DSF assays against parasitic validated targets, along with phenotypic assays, can help the identification and optimization of bioactive compounds. Pteridine reductase 1 (PTR1), a validated target in Leishmania sp., is responsible for the reduction of folate and biopterin to tetrahydrofolate and tetrahydrobiopterin, respectively, both of which are essential for cell growth. In addition to the in vitro evaluation of 16 thiazolidine-2,4-dione derivatives against Leishmania major PTR1 (LmPTR1), using the differential scanning fluorimetry (ThermoFluor®), phenotypic assays were employed to evaluate the compound effect over Leishmania braziliensis (MHOM/BR/75/M2903) and Leishmania infantum (MHOM/BR/74/PP75) promastigotes viability. The ThermoFluor® results show that thiazolidine-2,4-dione derivatives have micromolar affinity to the target and equivalent activity on Leishmania cells. 2b is the most potent compound against L. infantum (EC50 = 23.45 ± 4.54 μM), whereas 2a is the most potent against L. braziliensis (EC50 = 44.16 ± 5.77 μM). This result suggests that lipophilic substituents on either-meta and/or-para positions of the benzylidene ring increase the potency against L. infantum. On the other hand, compound 2c (CE50 = 49.22 ± 7.71 μM) presented the highest selectivity index.
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5
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Hunt A, Kirsch DR. Decision making in the pharmaceutical industry - A tale of three antibiotics. Int J Pharm 2020; 581:119251. [PMID: 32209367 DOI: 10.1016/j.ijpharm.2020.119251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 11/28/2022]
Abstract
There is a mounting crisis in treatment of bacterial diseases. The appearance of nosocomial infections produced by multi-drug resistant bacteria is rapidly increasing and at the same time the pharmaceutical industry has been abandoning new antibiotic discovery. To help understand why, we investigated the decision-making processes behind three novel antibiotics that were initially discovered in the late 1980's and early 1990's: daptomycin, linezolid, and lysobactin. Each antibiotic was investigated by two highly qualified scientific organizations that came to opposing opinions regarding the clinical utility and commercial potential of the drug. After reviewing the literature and interviewing key scientific staff members working on each of these molecules, we have identified factors needed to generate positive development decisions. Organizational factors included decision timing, therapeutic area focus, organizational support for risk taking and the presence of a project champion. Technical factors included investment in the optimization of dosing for improved drug exposure, toxicological evaluation of the purified eutomer from a diastereomer and the failure to develop an effective research formulation.
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Affiliation(s)
- Avery Hunt
- Biotechnology Department, Harvard Extension School, 51 Brattle Street, Cambridge, MA, 02138, United States
| | - Donald R Kirsch
- Biotechnology Department, Harvard Extension School, 51 Brattle Street, Cambridge, MA, 02138, United States.
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6
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Drakakis G, Cortés-Ciriano I, Alexander-Dann B, Bender A. Elucidating Compound Mechanism of Action and Predicting Cytotoxicity Using Machine Learning Approaches, Taking Prediction Confidence into Account. ACTA ACUST UNITED AC 2020; 11:e73. [PMID: 31483099 DOI: 10.1002/cpch.73] [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] [Indexed: 02/06/2023]
Abstract
The modes of action (MoAs) of drugs frequently are unknown, because many are small molecules initially identified from phenotypic screens, giving rise to the need to elucidate their MoAs. In addition, the high attrition rate for candidate drugs in preclinical studies due to intolerable toxicity has motivated the development of computational approaches to predict drug candidate (cyto)toxicity as early as possible in the drug-discovery process. Here, we provide detailed instructions for capitalizing on bioactivity predictions to elucidate the MoAs of small molecules and infer their underlying phenotypic effects. We illustrate how these predictions can be used to infer the underlying antidepressive effects of marketed drugs. We also provide the necessary functionalities to model cytotoxicity data using single and ensemble machine-learning algorithms. Finally, we give detailed instructions on how to calculate confidence intervals for individual predictions using the conformal prediction framework. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Georgios Drakakis
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Isidro Cortés-Ciriano
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ben Alexander-Dann
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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7
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Zhou J, Jiang X, He S, Jiang H, Feng F, Liu W, Qu W, Sun H. Rational Design of Multitarget-Directed Ligands: Strategies and Emerging Paradigms. J Med Chem 2019; 62:8881-8914. [PMID: 31082225 DOI: 10.1021/acs.jmedchem.9b00017] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to the complexity of multifactorial diseases, single-target drugs do not always exhibit satisfactory efficacy. Recently, increasing evidence indicates that simultaneous modulation of multiple targets may improve both therapeutic safety and efficacy, compared with single-target drugs. However, few multitarget drugs are on market or in clinical trials, despite the best efforts of medicinal chemists. This article discusses the systematic establishment of target combination, lead generation, and optimization of multitarget-directed ligands (MTDLs). Moreover, we analyze some MTDLs research cases for several complex diseases in recent years and the physicochemical properties of 117 clinical multitarget drugs, with the aim to reveal the trends and insights of the potential use of MTDLs.
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Affiliation(s)
- Junting Zhou
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Xueyang Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Siyu He
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
| | - Hongli Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China.,Jiangsu Food and Pharmaceutical Science College , Huaian 223003 , People's Republic of China
| | - Wenyuan Liu
- Department of Analytical Chemistry , China Pharmaceutical University , Nanjing 210009 , People's Republic of China
| | - Wei Qu
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Haopeng Sun
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
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8
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Abstract
‘Drug promiscuity’ refers to a drug that can act on multiple molecular targets, exhibiting similar or different pharmacological effects. Drugs may interact with unwanted targets, leading to off-target effects (one of the main reasons for side effects). Thus, intervention to prevent off-target effects in the early stages of drug discovery could reduce the risk of failure. The conversion between target and off-target effects is important for drug repurposing. Drug repurposing strategies could reduce research and development costs. This review details the research progress in the rational application of drug promiscuity for the discovery of multi-target drugs, drug repurposing and improving druggability in medicinal chemistry over the last 5 years.
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9
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Rinaldi F, Motti D, Ferraiuolo L, Kaspar BK. High content analysis in amyotrophic lateral sclerosis. Mol Cell Neurosci 2017; 80:180-191. [PMID: 27965018 PMCID: PMC5393940 DOI: 10.1016/j.mcn.2016.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 12/05/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating disease characterized by the progressive loss of motor neurons. Neurons, astrocytes, oligodendrocytes and microglial cells all undergo pathological modifications in the onset and progression of ALS. A number of genes involved in the etiopathology of the disease have been identified, but a complete understanding of the molecular mechanisms of ALS has yet to be determined. Currently, people affected by ALS have a life expectancy of only two to five years from diagnosis. The search for a treatment has been slow and mostly unsuccessful, leaving patients in desperate need of better therapies. Until recently, most pre-clinical studies utilized the available ALS animal models. In the past years, the development of new protocols for isolation of patient cells and differentiation into relevant cell types has provided new tools to model ALS, potentially more relevant to the disease itself as they directly come from patients. The use of stem cells is showing promise to facilitate ALS research by expanding our understanding of the disease and help to identify potential new therapeutic targets and therapies to help patients. Advancements in high content analysis (HCA) have the power to contribute to move ALS research forward by combining automated image acquisition along with digital image analysis. With modern HCA machines it is possible, in a period of just a few hours, to observe changes in morphology and survival of cells, under the stimulation of hundreds, if not thousands of drugs and compounds. In this article, we will summarize the major molecular and cellular hallmarks of ALS, describe the advancements provided by the in vitro models developed in the last few years, and review the studies that have applied HCA to the ALS field to date.
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Affiliation(s)
- Federica Rinaldi
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Dario Motti
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA
| | - Laura Ferraiuolo
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neuroscience, Sheffield Institute of Translational Neuroscience, University of Sheffield, UK
| | - Brian K Kaspar
- Center for Gene Therapy, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neuroscience, The Ohio State University, Columbus, OH, USA; Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA.
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10
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Molokanova E, Mercola M, Savchenko A. Bringing new dimensions to drug discovery screening: impact of cellular stimulation technologies. Drug Discov Today 2017; 22:1045-1055. [PMID: 28179145 DOI: 10.1016/j.drudis.2017.01.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/09/2016] [Accepted: 01/27/2017] [Indexed: 01/08/2023]
Abstract
The current mandate for the drug discovery industry is to develop more efficient drugs faster while reducing the costs associated with their development. Incorporation of cell stimulation technologies during screening assays is expected to revolutionize the discovery of novel drugs as well as safety pharmacology. In this review, we highlight 'classical' and emerging cell stimulation technologies that provide the ability to evaluate the effects of drug candidates on cells in different functional states to assess clinically relevant phenotypes.
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Affiliation(s)
- Elena Molokanova
- Nanotools Bioscience, Encinitas, CA 92024, USA; Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mark Mercola
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Alex Savchenko
- Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, CA 94304, USA; Department of Pediatrics, University of California-San Diego, La Jolla, CA 92093, USA.
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11
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Andrade EL, Bento AF, Cavalli J, Oliveira SK, Freitas CS, Marcon R, Schwanke RC, Siqueira JM, Calixto JB. Non-clinical studies required for new drug development - Part I: early in silico and in vitro studies, new target discovery and validation, proof of principles and robustness of animal studies. Braz J Med Biol Res 2016; 49:e5644. [PMID: 27783811 PMCID: PMC5089235 DOI: 10.1590/1414-431x20165644] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/20/2016] [Indexed: 01/23/2023] Open
Abstract
This review presents a historical overview of drug discovery and the non-clinical stages of the drug development process, from initial target identification and validation, through in silico assays and high throughput screening (HTS), identification of leader molecules and their optimization, the selection of a candidate substance for clinical development, and the use of animal models during the early studies of proof-of-concept (or principle). This report also discusses the relevance of validated and predictive animal models selection, as well as the correct use of animal tests concerning the experimental design, execution and interpretation, which affect the reproducibility, quality and reliability of non-clinical studies necessary to translate to and support clinical studies. Collectively, improving these aspects will certainly contribute to the robustness of both scientific publications and the translation of new substances to clinical development.
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Affiliation(s)
- E L Andrade
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - A F Bento
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J Cavalli
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - S K Oliveira
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - C S Freitas
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - R Marcon
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - R C Schwanke
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J M Siqueira
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
| | - J B Calixto
- Centro de Inovação e Ensaios Pré-clínicos, Florianópolis, SC, Brasil
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12
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Maryanoff BE. Phenotypic Assessment and the Discovery of Topiramate. ACS Med Chem Lett 2016; 7:662-5. [PMID: 27437073 PMCID: PMC4948003 DOI: 10.1021/acsmedchemlett.6b00176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/13/2016] [Indexed: 12/25/2022] Open
Abstract
![]()
The
role of phenotypic assessment in drug discovery is discussed,
along with the discovery and development of TOPAMAX (topiramate),
a billion-dollar molecule for the treatment of epilepsy and migraine.
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Affiliation(s)
- Bruce E. Maryanoff
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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13
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Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibás B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E. Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns. MEDCHEMCOMM 2016; 7:1237-1244. [PMID: 27774140 PMCID: PMC5063042 DOI: 10.1039/c6md00065g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/10/2016] [Indexed: 01/09/2023]
Abstract
Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of in silico and in vitro follow-up work is on the exploration of possible molecular mechanisms and efficacy targets underlying the biological processes interrogated by the phenotypic screening experiments. Herein, we present six exemplar computational protocols for the interpretation of cellular phenotypic screens based on the integration of compound, target, pathway, and disease data established by the IMI Open PHACTS project. The protocols annotate phenotypic hit lists and allow follow-up experiments and mechanistic conclusions. The annotations included are from ChEMBL, ChEBI, GO, WikiPathways and DisGeNET. Also provided are protocols which select from the IUPHAR/BPS Guide to PHARMACOLOGY interaction file selective compounds to probe potential targets and a correlation robot which systematically aims to identify an overlap of active compounds in both the phenotypic as well as any kinase assay. The protocols are applied to a phenotypic pre-lamin A/C splicing assay selected from the ChEMBL database to illustrate the process. The computational protocols make use of the Open PHACTS API and data and are built within the Pipeline Pilot and KNIME workflow tools.
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Affiliation(s)
- D Digles
- Department of Pharmaceutical Chemistry , University of Vienna , Pharmacoinformatics Research Group , Althanstraße 14 , 1090 Wien , Austria .
| | - B Zdrazil
- Department of Pharmaceutical Chemistry , University of Vienna , Pharmacoinformatics Research Group , Althanstraße 14 , 1090 Wien , Austria .
| | - J-M Neefs
- Janssen Research & Development , Turnhoutseweg 30 , B-2340 Beerse , Belgium .
| | - H Van Vlijmen
- Janssen Research & Development , Turnhoutseweg 30 , B-2340 Beerse , Belgium .
| | - C Herhaus
- Merck KGaA, Merck Serono R&D , Computational Chemistry , Frankfurter Straße 250 , 64293 Darmstadt , Germany
| | - A Caracoti
- BIOVIA , a Dassault Systèmes brand , 334 Cambridge Science Park , Cambridge CB4 0WN , UK
| | - J Brea
- Grupo BioFarma-USEF , Departamento de Farmacología , Facultad de Farmacia , Campus Universitario Sur s/n , 15782 Santiago de Compostela , Spain
| | - B Roibás
- Grupo BioFarma-USEF , Departamento de Farmacología , Facultad de Farmacia , Campus Universitario Sur s/n , 15782 Santiago de Compostela , Spain
| | - M I Loza
- Grupo BioFarma-USEF , Departamento de Farmacología , Facultad de Farmacia , Campus Universitario Sur s/n , 15782 Santiago de Compostela , Spain
| | - N Queralt-Rosinach
- Research Programme on Biomedical Informatics (GRIB) , Hospital del Mar Medical Research Institute (IMIM) , Department of Experimental and Health Sciences , Universitat Pompeu Fabra , C/Dr Aiguader 88 , E-08003 Barcelona , Spain
| | - L I Furlong
- Research Programme on Biomedical Informatics (GRIB) , Hospital del Mar Medical Research Institute (IMIM) , Department of Experimental and Health Sciences , Universitat Pompeu Fabra , C/Dr Aiguader 88 , E-08003 Barcelona , Spain
| | - A Gaulton
- European Molecular Biology Laboratory , European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus , Hinxton , Cambridge CB10 1SD , UK
| | - L Bartek
- GlaxoSmithKline , Medicines Research Centre , Stevenage SG1 2NY , UK
| | - S Senger
- GlaxoSmithKline , Medicines Research Centre , Stevenage SG1 2NY , UK
| | - C Chichester
- Swiss Institute of Bioinformatics , CALIPHO Group , CMU Rue Michel-Servet 1 , 1211 Geneva 4 , Switzerland ; Nestlé Institute of Health Sciences SA , EPFL Innovation Park, Bâtiment H , 1015 Lausanne , Switzerland
| | - O Engkvist
- Chemistry Innovation Centre , Discovery Sciences , AstraZeneca R&D Gothenburg , SE-431 83 Mölndal , Sweden
| | - C T Evelo
- Department of Bioinformatics - BiGCaT , P.O. Box 616 , UNS50 Box19 , NL-6200MD Maastricht , The Netherlands
| | - N I Franklin
- Open Innovation Drug Discovery , Discovery Chemistry Eli Lilly and Company , Lilly Corporate Center , DC 1920 , Indianapolis , IN 46285 , USA
| | - D Marren
- Eli Lilly and Company Ltd. , Lilly Research Centre , Erl Wood Manor, Sunninghill Road , Windlesham , Surrey GU20 6PH , England , UK
| | - G F Ecker
- Department of Pharmaceutical Chemistry , University of Vienna , Pharmacoinformatics Research Group , Althanstraße 14 , 1090 Wien , Austria .
| | - E Jacoby
- Janssen Research & Development , Turnhoutseweg 30 , B-2340 Beerse , Belgium .
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14
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One size does not fit all: Challenging some dogmas and taboos in drug discovery. Future Med Chem 2016; 8:29-38. [DOI: 10.4155/fmc.15.167] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Advances in genetics, biology, chemical synthesis and computational methods have contributed to the understanding of diseases and drugs and with all of the above, there is an expectation that we are in a better position than ever before to create effective medicines for our needs. The reality is, however, disconnected from the expectation – US FDA drug approval statistics show that the number of approved drugs, especially the first-in-class drugs, is not commensurate with our improved knowledge. In this perspective, we offer our views on the possible reasons for this, focusing on small-molecule drugs and suggest some ideas for further considerations.
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15
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Fà M, Zhang H, Staniszewski A, Saeed F, Shen LW, Schiefer IT, Siklos MI, Tapadar S, Litosh VA, Libien J, Petukhov PA, Teich AF, Thatcher GR, Arancio O. Novel Selective Calpain 1 Inhibitors as Potential Therapeutics in Alzheimer’s Disease. J Alzheimers Dis 2015; 49:707-21. [DOI: 10.3233/jad-150618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mauro Fà
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Hong Zhang
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Agnieszka Staniszewski
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Faisal Saeed
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Li W. Shen
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Isaac T. Schiefer
- Department of Medicinal and Biological Chemistry, University of Ohio at Toledo, Frederic and Mary Wolfe Center, Toledo, OH, USA
| | - Marton I. Siklos
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Subhasish Tapadar
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Vladislav A. Litosh
- Department of Chemistry, McMicken College of Arts & Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Jenny Libien
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Pavel A. Petukhov
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrew F. Teich
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Gregory R.J. Thatcher
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Ottavio Arancio
- Department of Pathology and Cell Biology, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, USA
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16
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Zhang N, Bailus BJ, Ring KL, Ellerby LM. iPSC-based drug screening for Huntington's disease. Brain Res 2015; 1638:42-56. [PMID: 26428226 DOI: 10.1016/j.brainres.2015.09.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 01/29/2023]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder, caused by an expansion of the CAG repeat in exon 1 of the huntingtin gene. The disease generally manifests in middle age with both physical and mental symptoms. There are no effective treatments or cures and death usually occurs 10-20 years after initial symptoms. Since the original identification of the Huntington disease associated gene, in 1993, a variety of models have been created and used to advance our understanding of HD. The most recent advances have utilized stem cell models derived from HD-patient induced pluripotent stem cells (iPSCs) offering a variety of screening and model options that were not previously available. The discovery and advancement of technology to make human iPSCs has allowed for a more thorough characterization of human HD on a cellular and developmental level. The interaction between the genome editing and the stem cell fields promises to further expand the variety of HD cellular models available for researchers. In this review, we will discuss the history of Huntington's disease models, common screening assays, currently available models and future directions for modeling HD using iPSCs-derived from HD patients. This article is part of a Special Issue entitled SI: PSC and the brain.
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Affiliation(s)
- Ningzhe Zhang
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, United States
| | - Barbara J Bailus
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, United States
| | - Karen L Ring
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, United States
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, CA 94945, United States.
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