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Ferreira IC, Torrejón E, Abecasis B, Alexandre BM, Gomes RA, Verslype C, van Pelt J, Barbas A, Simão D, Bandeiras TM, Bortoluzzi A, Rebelo SP. Aldehyde Dehydrogenase 2 (ALDH2): A novel sorafenib target in hepatocellular carcinoma unraveled by the proteome-wide cellular thermal shift assay. SLAS Discov 2024; 29:100154. [PMID: 38521503 DOI: 10.1016/j.slasd.2024.100154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
Sorafenib is a multikinase inhibitor indicated for first-line treatment of unresectable hepatocellular carcinoma. Despite its widespread use in the clinic, the existing knowledge of sorafenib mode-of-action remains incomplete. To build upon the current understanding, we used the Cellular Thermal Shift Assay (CETSA) coupled to Mass Spectrometry (CETSA-MS) to monitor compound binding to its target proteins in the cellular context on a proteome-wide scale. Among the potential sorafenib targets, we identified aldehyde dehydrogenase 2 (ALDH2), an enzyme that plays a major role in alcohol metabolism. We validated the interaction of sorafenib with ALDH2 by orthogonal methods using pure recombinant protein, proving that this interaction is not mediated by other cellular components. Moreover, we showed that sorafenib inhibits ALDH2 activity, supporting a functional role for this interaction. Finally, we were able to demonstrate that both ALDH2 protein expression and activity were reduced in sorafenib-resistant cells compared to the parental cell line. Overall, our study allowed the identification of ALDH2 as a novel sorafenib target and sheds light on its potential role in both hepatocellular carcinoma and sorafenib resistance condition.
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Affiliation(s)
- Inês C Ferreira
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Estefania Torrejón
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; ITQB, ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bernardo Abecasis
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Bruno M Alexandre
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; ITQB, ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Ricardo A Gomes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; ITQB, ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Chris Verslype
- Department of Gastroenterology and Hepatology, KU Leuven, Leuven, Belgium
| | - Jos van Pelt
- Department of Oncology, Laboratory of Clinical Digestive Oncology, KU, Leuven, Belgium
| | - Ana Barbas
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Bayer Portugal, Carnaxide, Portugal
| | - Daniel Simão
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal
| | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; ITQB, ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Alessio Bortoluzzi
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; ITQB, ITQB-NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Sofia P Rebelo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal.
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Wu XY, Zhao ZY, Osman EEA, Wang XJ, Choo YM, Benjamin MM, Xiong J, Hamann MT, Luo C, Hu JF. Platanosides from Platanus × acerifolia: New molecules, SAR, and target validation of a strong lead for drug-resistant bacterial infections and the associated sepsis. Bioorg Chem 2024; 143:107103. [PMID: 38211549 DOI: 10.1016/j.bioorg.2024.107103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
Three undescribed (1-3) and nine known (4-12) platanosides were isolated and characterized from a bioactive extract of the May leaves of Platanus × acerifolia that initially showed inhibition against Staphylococcus aureus. Targeted compound mining was guided by an LC-MS/MS-based molecular ion networking (MoIN) strategy combined with conventional isolation procedures from a unique geographic location. The novel structures were mainly determined by 2D NMR and computational (NMR/ECD calculations) methods. Compound 1 is a rare acylated kaempferol rhamnoside possessing a truxinate unit. 6 (Z,E-platanoside) and 7 (E,E-platanoside) were confirmed to have remarkable inhibitory effects against both methicillin-resistant S. aureus (MIC: ≤ 16 μg/mL) and glycopeptide-resistant Enterococcus faecium (MIC: ≤ 1 μg/mL). These platanosides were subjected to docking analyses against FabI (enoyl-ACP reductase) and PBP1/2 (penicillin binding protein), both of which are pivotal enzymes governing bacterial growth but not found in the human host. The results showed that 6 and 7 displayed superior binding affinities towards FabI and PBP2. Moreover, surface plasmon resonance studies on the interaction of 1/7 and FabI revealed that 7 has a higher affinity (KD = 1.72 μM), which further supports the above in vitro data and is thus expected to be a novel anti-antibacterial drug lead.
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Affiliation(s)
- Xi-Ying Wu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, PR China
| | - Ze-Yu Zhao
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ezzat E A Osman
- Department of Medicinal Chemistry, Theodor Bilharz Research Institute, Kornaish El-Nile St., Giza 12411, Egypt
| | - Xiao-Juan Wang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, Gansu, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Yeun-Mun Choo
- Chemistry Department, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Menny M Benjamin
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA
| | - Juan Xiong
- School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Mark T Hamann
- Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, PR China
| | - Jin-Feng Hu
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Zhejiang 318000, PR China; School of Pharmacy, Fudan University, Shanghai 201203, PR China; Colleges of Pharmacy and Medicine, Medical University of South Carolina, Charleston 29425-5700, USA.
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3
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Yao Z, Chen L, Hu M, Meng F, Chen M, Wang G. The discovery of a new potent FXR agonist based on natural product screening. Bioorg Chem 2024; 143:106979. [PMID: 37995646 DOI: 10.1016/j.bioorg.2023.106979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
FXR agonistic activity screening was conducted based on natural product resources containing 38 structurally diverse sesquiterpenoids isolated from Xylopia vielana. Among them, 34 undescribed sesquiterpenoids with 5 different skeleton types were first characterized by HRESIMS, NMR data, ECD calculations and X-ray crystallographic analysis. High-content screening for FXR agonistic activity of these compounds demonstrated that 13 compounds could activate FXR. Then molecular docking results suggested that hydrogen bonding and hydrophobic interactions might contribute to the main interaction of active compounds with FXR. The preliminary structure-activity relationships (SARs) of those isolates were also discussed. The most potent compound 27 significantly elevated the transcriptional activity of the FXR target gene BSEP promoter (EC50 = 14.26 μM) by a dual-luciferase reporter assay. Western blotting indicated that compound 27 activated the FXR-associated pathway, thereby upregulating SHP and BSEP expression, and downregulating CYP7A1 and NTCP expression. We further revealed that FXR was the target protein of compound 27 through diverse target validation methods, including CETSA, SIP, and DARTS under the intervention of temperature, organic reagents and protease. Pharmacological in vivo experiments showed that compound 27 effectively ameliorated α-naphthyl isothiocyanate (ANIT)-induced cholestasis in mice, as evidenced by the ameliorative histopathology of the liver and the decrease in biochemical markers: alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), total bilirubin (TBIL), direct bilirubin (DBIL), and total bile acid (TBA). This work showed a practical strategy for the discovery of new FXR agonists from natural products and provided potential insights for sesquiterpenoids as FXR agonist lead compounds.
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Affiliation(s)
- Zongwen Yao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Lin Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Min Hu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Fancheng Meng
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
| | - Guowei Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
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Carvalho GA, Chiareli RA, Pedrazzi JFC, Silva-Amaral D, da Rocha ALB, Oliveira-Lima OC, Lião LM, de Souza-Fagundes EM, Schildknecht S, Leist M, Del-Bel EA, Gomez RS, Birbrair A, Menegatti R, Pinto MCX. Novel Proline Transporter Inhibitor (LQFM215) Presents Antipsychotic Effect in Ketamine Model of Schizophrenia. Neurochem Res 2024; 49:170-183. [PMID: 37684384 DOI: 10.1007/s11064-023-04018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
The glutamatergic hypothesis of schizophrenia suggests a correlation between NMDA receptor hypofunction and negative psychotic symptoms. It has been observed that the expression of the proline transporter (PROT) in the central nervous system (CNS) is associated with glutamatergic neurotransmission, as L-proline has the capacity to activate and modulate AMPA and NMDA receptors. In this study, we aimed to investigate whether inhibition of proline transporters could enhance glutamatergic neurotransmission and potentially exhibit antipsychotic effects in an experimental schizophrenia model. Using molecular dynamics analysis in silico, we validated an innovative PROT inhibitor, LQFM215. We quantified the cytotoxicity of LQFM215 in the Lund human mesencephalic cell line (LUHMES). Subsequently, we employed the ketamine-induced psychosis model to evaluate the antipsychotic potential of the inhibitor, employing behavioral tests including open-field, three-chamber interaction, and prepulse inhibition (PPI). Our results demonstrate that LQFM215, at pharmacologically active concentrations, exhibited negligible neurotoxicity when astrocytes were co-cultured with neurons. In the ketamine-induced psychosis model, LQFM215 effectively reduced hyperlocomotion and enhanced social interaction in a three-chamber social approach task across all administered doses. Moreover, the compound successfully prevented the ketamine-induced disruption of sensorimotor gating in the PPI test at all tested doses. Overall, these findings suggest that PROT inhibition could serve as a potential therapeutic target for managing symptoms of schizophrenia model.
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Affiliation(s)
- Gustavo Almeida Carvalho
- Laboratório de Neuroquímica e Neurofarmacologia, Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Av. Esperança, S/N, UFG, Prédio ICB II, Sala 114, Goiânia, GO, 74690-900, Brazil
| | - Raphaela Almeida Chiareli
- Laboratório de Neuroquímica e Neurofarmacologia, Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Av. Esperança, S/N, UFG, Prédio ICB II, Sala 114, Goiânia, GO, 74690-900, Brazil
| | - João Francisco Cordeiro Pedrazzi
- Departamento de Neurociências e Ciências do Comportamento, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Danyelle Silva-Amaral
- Departamento de Neurociências e Ciências do Comportamento, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), São Paulo, Brazil
| | | | - Onésia Cristina Oliveira-Lima
- Laboratório de Neuroquímica e Neurofarmacologia, Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Av. Esperança, S/N, UFG, Prédio ICB II, Sala 114, Goiânia, GO, 74690-900, Brazil
| | | | | | - Stefan Schildknecht
- Faculty of Life Sciences, Albstadt-Sigmaringen University, 72488, Sigmaringen, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Doerenkamp-Zbinden Foundation, University of Konstanz, Konstanz, Germany
| | - Elaine Aparecida Del-Bel
- Departamento de Neurociências e Ciências do Comportamento, Faculdade de Medicina de Ribeirão Preto (FMRP), Universidade de São Paulo (USP), São Paulo, Brazil
| | - Renato Santiago Gomez
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexander Birbrair
- Department of Dermatology, Medical Sciences Center, University of Wisconsin-Madison, Rm 4385, 1300 University Avenue, Madison, WI, 53706, USA
| | - Ricardo Menegatti
- Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Mauro Cunha Xavier Pinto
- Laboratório de Neuroquímica e Neurofarmacologia, Departamento de Farmacologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Av. Esperança, S/N, UFG, Prédio ICB II, Sala 114, Goiânia, GO, 74690-900, Brazil.
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Talevi A. Computer-Aided Drug Discovery and Design: Recent Advances and Future Prospects. Methods Mol Biol 2024; 2714:1-20. [PMID: 37676590 DOI: 10.1007/978-1-0716-3441-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Computer-aided drug discovery and design involve the use of information technologies to identify and develop, on a rational ground, chemical compounds that align a set of desired physicochemical and biological properties. In its most common form, it involves the identification and/or modification of an active scaffold (or the combination of known active scaffolds), although de novo drug design from scratch is also possible. Traditionally, the drug discovery and design processes have focused on the molecular determinants of the interactions between drug candidates and their known or intended pharmacological target(s). Nevertheless, in modern times, drug discovery and design are conceived as a particularly complex multiparameter optimization task, due to the complicated, often conflicting, property requirements.This chapter provides an updated overview of in silico approaches for identifying active scaffolds and guiding the subsequent optimization process. Recent groundbreaking advances in the field have also analyzed the integration of state-of-the-art machine learning approaches in every step of the drug discovery process (from prediction of target structure to customized molecular docking scoring functions), integration of multilevel omics data, and the use of a diversity of computational approaches to assist target validation and assess plausible binding pockets.
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Affiliation(s)
- Alan Talevi
- Laboratory of Bioactive Compound Research and Development (LIDeB), Faculty of Exact Sciences, National University of La Plata (UNLP), La Plata, Argentina.
- Argentinean National Council of Scientific and Technical Research (CONICET), La Plata, Argentina.
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Ma L, Li M, Gou S, Wang W, Liu K, Zhang Y. Native-compound-Coupled Affinity Matrix (NCAM) in target identification and validation of bioactive compounds: Application, mechanism and outlooks. Bioorg Chem 2023; 140:106828. [PMID: 37690368 DOI: 10.1016/j.bioorg.2023.106828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023]
Abstract
In drug discovery and development, the direct target identification of bioactive small molecules plays a significant role for understanding the mechanism of action, predicting the side effects, and rationally designing more potent compounds. However, due to the complicated regulatory processes in a cell together with thousands of biomacromolecules, target identification is always the major obstacle. New methods and technologies are continuously invented to tackle this problem. Nevertheless, the mainly used tools possess several disadvantages. High synthetic skills are typically required to laboriously synthesize a probe for protein enrichment. To detect the ligand-protein interaction by analyzing proteins' responses to proteolytic or thermal treatment, costly and precise instruments are always necessary. Therefore, convenient and practical techniques are urgently needed. Over the past decades, a strategy using native compounds without the requirement of chemical modification, also termed Native-compound-Coupled Affinity Matrix (NCAM), is developing continuously. Two practical tactics based on "label-free" compounds have been invented and used, that is Photo-cross-linked Small-molecule Affinity Matrix (PSAM) and Native-compound-Coupled CNBr-activated Beads (NCCB). Presently, we will elucidate the characteristics, coupling mechanism, advantages and disadvantages, and future prospect of NCAM in specific target identification and validation.
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Affiliation(s)
- Lu Ma
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Menglong Li
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Shanshan Gou
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wei Wang
- Departments of Pharmacology & Toxicology and Chemistry & Biochemistry, and BIO5 Institute, University of Arizona, Tucson, AZ 85721, United States
| | - Kangdong Liu
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yueteng Zhang
- Basic Medical Research Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China.
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Kjær C, Palasca O, Barzaghi G, Bak LK, Durhuus RKJ, Jakobsen E, Pedersen L, Bartels ED, Woldbye DPD, Pinborg LH, Jensen LJ. Differential Expression of the β3 Subunit of Voltage-Gated Ca 2+ Channel in Mesial Temporal Lobe Epilepsy. Mol Neurobiol 2023; 60:5755-5769. [PMID: 37341859 PMCID: PMC10471638 DOI: 10.1007/s12035-023-03426-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
The purpose of this study was to identify and validate new putative lead drug targets in drug-resistant mesial temporal lobe epilepsy (mTLE) starting from differentially expressed genes (DEGs) previously identified in mTLE in humans by transcriptome analysis. We identified consensus DEGs among two independent mTLE transcriptome datasets and assigned them status as "lead target" if they (1) were involved in neuronal excitability, (2) were new in mTLE, and (3) were druggable. For this, we created a consensus DEG network in STRING and annotated it with information from the DISEASES database and the Target Central Resource Database (TCRD). Next, we attempted to validate lead targets using qPCR, immunohistochemistry, and Western blot on hippocampal and temporal lobe neocortical tissue from mTLE patients and non-epilepsy controls, respectively. Here we created a robust, unbiased list of 113 consensus DEGs starting from two lists of 3040 and 5523 mTLE significant DEGs, respectively, and identified five lead targets. Next, we showed that CACNB3, a voltage-gated Ca2+ channel subunit, was significantly regulated in mTLE at both mRNA and protein level. Considering the key role of Ca2+ currents in regulating neuronal excitability, this suggested a role for CACNB3 in seizure generation. This is the first time changes in CACNB3 expression have been associated with drug-resistant epilepsy in humans, and since efficient therapeutic strategies for the treatment of drug-resistant mTLE are lacking, our finding might represent a step toward designing such new treatment strategies.
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Affiliation(s)
- Christina Kjær
- Biomedical Laboratory Science, Department of Technology, Faculty of Health and Technology, University College Copenhagen, Sigurdsgade 26, 1St, 2200 Copenhagen, Denmark
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Oana Palasca
- Disease Systems Biology Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Guido Barzaghi
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Lasse K. Bak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
| | - Rúna K. J. Durhuus
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Specific Pharma A/S, Borgmester Christiansens Gade 40, 2450 Copenhagen, SV Denmark
| | - Emil Jakobsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Takeda Pharma A/S, Delta Park 45, 2665 Vallensbaek Strand, Denmark
| | - Louise Pedersen
- Biomedical Laboratory Science, Department of Technology, Faculty of Health and Technology, University College Copenhagen, Sigurdsgade 26, 1St, 2200 Copenhagen, Denmark
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
| | - Emil D. Bartels
- Dept. of Clinical Biochemistry, 2600 RigshospitaletCopenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David P. D. Woldbye
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars H. Pinborg
- Epilepsy Clinic & Neurobiology Research Unit, Copenhagen University Hospital, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lars Juhl Jensen
- Disease Systems Biology Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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Tu Y, Tan L, Tao H, Li Y, Liu H. CETSA and thermal proteome profiling strategies for target identification and drug discovery of natural products. Phytomedicine 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Monitoring target engagement at various stages of drug development is essential for natural product (NP)-based drug discovery and development. The cellular thermal shift assay (CETSA) developed in 2013 is a novel, broadly applicable, label-free biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins, which enables direct assessment of drug-target engagement in physiologically relevant contexts, including intact cells, cell lysates and tissues. This review aims to provide an overview of the work principles of CETSA and its derivative strategies and their recent progress in protein target validation, target identification and drug lead discovery of NPs. METHODS A literature-based survey was conducted using the Web of Science and PubMed databases. The required information was reviewed and discussed to highlight the important role of CETSA-derived strategies in NP studies. RESULTS After nearly ten years of upgrading and evolution, CETSA has been mainly developed into three formats: classic Western blotting (WB)-CETSA for target validation, thermal proteome profiling (TPP, also known as MS-CETSA) for unbiased proteome-wide target identification, and high-throughput (HT)-CETSA for drug hit discovery and lead optimization. Importantly, the application possibilities of a variety of TPP approaches for the target discovery of bioactive NPs are highlighted and discussed, including TPP-temperature range (TPP-TR), TPP-compound concentration range (TPP-CCR), two-dimensional TPP (2D-TPP), cell surface-TPP (CS-TPP), simplified TPP (STPP), thermal stability shift-based fluorescence difference in 2D gel electrophoresis (TS-FITGE) and precipitate supported TPP (PSTPP). In addition, the key advantages, limitations and future outlook of CETSA strategies for NP studies are discussed. CONCLUSION The accumulation of CETSA-based data can significantly accelerate the elucidation of the mechanism of action and drug lead discovery of NPs, and provide strong evidence for NP treatment against certain diseases. The CETSA strategy will certainly bring a great return far beyond the initial investment and open up more possibilities for future NP-based drug research and development.
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Affiliation(s)
- Yanbei Tu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hongxun Tao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Dann GP, Liu H, Nowak RP, Jones LH. Cereblon target validation using a covalent inhibitor of neosubstrate recruitment. Methods Enzymol 2023; 681:155-167. [PMID: 36764755 DOI: 10.1016/bs.mie.2022.08.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Small molecule ligands of cereblon (CRBN), a component of an E3 ubiquitin ligase complex, such as immunomodulatory drugs (IMiDs) or proteolysis targeting chimeras (PROTACs), induce new interactions between the E3 and a target protein that is subsequently polyubiquitinated and proteasomally degraded. The development of new degraders requires validation of CRBN-dependence and existing methods include the use of engineered CRBN knockout cell lines, or PROTACs directed to CRBN itself. Technical limitations of these approaches necessitate a simple and rapid pharmacological method of CRBN inhibition. We developed a sulfonyl fluoride covalent CRBN ligand based on the IMiD EM12 called EM12-SO2F that was designed to engage His353 on the surface of the IMiD binding site. EM12-SO2F does not act as a molecular glue degrader like other IMiDs, and instead serves as an inhibitor of such function by blocking the degrader binding site. We demonstrate utility of EM12-SO2F by inhibiting the degradation of the zinc-finger transcription factor and CRBN neosubstrate IKZF1 by the molecular glue degrader lenalidomide. Increasingly, libraries of degrader molecules are being screened phenotypically to identify starting points for hit elaboration, that simultaneously reveals new therapeutic targets amenable to degradation. Indeed, targeted protein degradation has become an exciting new therapeutic modality and EM12-SO2F augments the chemical biology toolbox that will advance this area of drug discovery research.
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Affiliation(s)
- Geoffrey P Dann
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Hu Liu
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Radosław P Nowak
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Lyn H Jones
- Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States.
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10
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Yahiya S, Saunders CN, Hassan S, Straschil U, Fischer OJ, Rueda-Zubiaurre A, Haase S, Vizcay-Barrena G, Famodimu MT, Jordan S, Delves MJ, Tate EW, Barnard A, Fuchter MJ, Baum J. A novel class of sulphonamides potently block malaria transmission by targeting a Plasmodium vacuole membrane protein. Dis Model Mech 2023; 16:286739. [PMID: 36715290 PMCID: PMC9934914 DOI: 10.1242/dmm.049950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/13/2022] [Indexed: 01/31/2023] Open
Abstract
Phenotypic cell-based screens are critical tools for discovering candidate drugs for development, yet identification of the cellular target and mode of action of a candidate drug is often lacking. Using an imaging-based screen, we recently discovered an N-[(4-hydroxychroman-4-yl)methyl]-sulphonamide (N-4HCS) compound, DDD01035881, that blocks male gamete formation in the malaria parasite life cycle and subsequent transmission of the parasite to the mosquito with nanomolar activity. To identify the target(s) of DDD01035881, and of the N-4HCS class of compounds more broadly, we synthesised a photoactivatable derivative, probe 2. Photoaffinity labelling of probe 2 coupled with mass spectrometry identified the 16 kDa Plasmodium falciparum parasitophorous vacuole membrane protein Pfs16 as a potential parasite target. Complementary methods including cellular thermal shift assays confirmed that the parent molecule DDD01035881 stabilised Pfs16 in lysates from activated mature gametocytes. Combined with high-resolution, fluorescence and electron microscopy data, which demonstrated that parasites inhibited with N-4HCS compounds phenocopy the targeted deletion of Pfs16 in gametocytes, these data implicate Pfs16 as a likely target of DDD01035881. This finding establishes N-4HCS compounds as being flexible and effective starting candidates from which transmission-blocking antimalarials can be developed in the future.
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Affiliation(s)
- Sabrina Yahiya
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Charlie N Saunders
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Sarah Hassan
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Ursula Straschil
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Oliver J Fischer
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Ainoa Rueda-Zubiaurre
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Silvia Haase
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Gema Vizcay-Barrena
- Centre for Ultrastructural Imaging, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Mufuliat Toyin Famodimu
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Sarah Jordan
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Michael J Delves
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Anna Barnard
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Matthew J Fuchter
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 OBZ, UK
| | - Jake Baum
- Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, South Kensington, London SW7 2AZ, UK
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11
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Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stępień Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Süssmuth RD, Ghilarov D. Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Nat Catal 2023; 6:52-67. [PMID: 36741192 PMCID: PMC9886550 DOI: 10.1038/s41929-022-00904-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023]
Abstract
The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between Escherichia coli topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and E. coli topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
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Affiliation(s)
| | - Kay Hommernick
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Iraj Behroz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Marcel Kulike
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Zuzanna Pakosz-Stępień
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Lukasz Mazurek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Maria Seidel
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Maria Kunert
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | | | | | - Bernhard Loll
- moloX GmbH, Berlin, Germany.,Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - John B Weston
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,John Innes Centre, Norwich Research Park, Norwich, UK
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12
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Courtney CM, Sharma S, Fallgren C, Weil MM, Chatterjee A, Nagpal P. Reversing radiation-induced immunosuppression using a new therapeutic modality. Life Sci Space Res (Amst) 2022; 35:127-139. [PMID: 36336358 DOI: 10.1016/j.lssr.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/05/2022] [Accepted: 05/09/2022] [Indexed: 06/16/2023]
Abstract
Radiation-induced immune suppression poses significant health challenges for millions of patients undergoing cancer chemotherapy and radiotherapy treatment, and astronauts and space tourists travelling to outer space. While a limited number of recombinant protein therapies, such a Sargramostim, are approved for accelerating hematologic recovery, the pronounced role of granulocyte-macrophage colony-stimulating factor (GM-CSF or CSF2) as a proinflammatory cytokine poses additional challenges in creating immune dysfunction towards pathogenic autoimmune diseases. Here we present an approach to high-throughput drug-discovery, target validation, and lead molecule identification using nucleic acid-based molecules. These Nanoligomer™ molecules are rationally designed using a bioinformatics and an artificial intelligence (AI)-based ranking method and synthesized as a single-modality combining 6-different design elements to up- or downregulate gene expression of target gene, resulting in elevated or diminished protein expression of intended target. This method additionally alters related gene network targets ultimately resulting in pathway modulation. This approach was used to perturb and identify the most effective upstream regulators and canonical pathways for therapeutic intervention to reverse radiation-induced immunosuppression. The lead Nanoligomer™ identified in a screen of human donor derived peripheral blood mononuclear cells (PBMCs) upregulated Erythropoietin (EPO) and showed the greatest reversal of radiation induced cytokine changes. It was further tested in vivo in a mouse radiation-model with low-dose (3 mg/kg) intraperitoneal administration and was shown to regulate gene expression of epo in lung tissue as well as counter immune suppression. These results point to the broader applicability of our approach towards drug-discovery, and potential for further investigation of our lead molecule as reversible gene therapy to treat adverse health outcomes induced by radiation exposure.
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Affiliation(s)
- Colleen M Courtney
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Sadhana Sharma
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Christina Fallgren
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Michael M Weil
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, United States
| | - Anushree Chatterjee
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States
| | - Prashant Nagpal
- Colorado Technology Center, Sachi Bioworks, 685 S Arthur Avenue, Louisville, CO 80027 United States.
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13
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Abstract
We describe an approach to early stage drug discovery that explicitly engages with the complexities of human biology. The combined computational and experimental approach is formulated on a conceptual framework in which network biology is used to bridge between individual molecular entities and the cellular phenotype that emerges when those entities interact in a network. Multiple aspects of early stage discovery are addressed including the data-driven elucidation of biological processes implicated in disease, target identification and validation, phenotypic discovery of active molecules and their mechanism of action, and extraction of genetic target support from human population genetics data. Validation is described via summary of a number of discovery projects and details from a project aimed at COVID-19 disease.
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Affiliation(s)
- Jonny Wray
- e-therapeutics plc, Long Hanborough, UK.
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14
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Abstract
This review provides the feasible literature on drug discovery through ML tools and techniques that are enforced in every phase of drug development to accelerate the research process and deduce the risk and expenditure in clinical trials. Machine learning techniques improve the decision-making in pharmaceutical data across various applications like QSAR analysis, hit discoveries, de novo drug architectures to retrieve accurate outcomes. Target validation, prognostic biomarkers, digital pathology are considered under problem statements in this review. ML challenges must be applicable for the main cause of inadequacy in interpretability outcomes that may restrict the applications in drug discovery. In clinical trials, absolute and methodological data must be generated to tackle many puzzles in validating ML techniques, improving decision-making, promoting awareness in ML approaches, and deducing risk failures in drug discovery.
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Affiliation(s)
- Suresh Dara
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Swetha Dhamercherla
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Surender Singh Jadav
- Centre for Molecular Cancer Research (CMCR) and Vishnu Institute of Pharmaceutical Education and Research (VIPER), Narsapur, Medak, 502313 Telangana India
| | - CH Madhu Babu
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Jaipur, 302023 Rajasthan India
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15
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Norouzi-Barough L, Bayat A. Validation strategies for identifying drug targets in dermal fibrotic disorders. Drug Discov Today 2021; 26:2474-2485. [PMID: 34229083 DOI: 10.1016/j.drudis.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/19/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022]
Abstract
Fibrotic skin disorders, such as keloid disease (KD), are common clinically challenging disorders with unknown etiopathogenesis and ill-defined treatment strategies that affect millions of people worldwide. Thus, there is an urgent need to discover novel therapeutics. The validation of potential drug targets is an obligatory step in discovering and developing new therapeutic agents for the successful treatment of dermal fibrotic conditions, such as KD. The integration of multi-omics data with traditional and modern technological approaches, such as RNA interference (RNAi) and genome-editing tools, would provide unique opportunities to identify and validate novel targets in KD during early drug development. Thus, in this review, we summarize the current and emerging drug discovery process with a focus on validation strategies of potential drug targets identified in dermal fibrosis.
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Affiliation(s)
- Leyla Norouzi-Barough
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ardeshir Bayat
- Centre for Dermatology Research, NIHR Manchester Biomedical Research Centre, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK; Medical Research Council-Wound Healing Unit, Division of Dermatology, University of Cape Town, Cape Town, South Africa.
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16
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Vitiello M, Cathcart B, Caporali A, Meloni M. Manipulating Pericyte Function with MicroRNAs. Methods Mol Biol 2021; 2235:139-53. [PMID: 33576975 DOI: 10.1007/978-1-0716-1056-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
MicroRNAs (miRNAs) are expressed in all cell types, including pericytes, and play essential roles in vascular development, homeostasis, and disease. Manipulation of pericytes with miRNA mimics and inhibitors represents an essential tool to study the role of pericytes in vascular development and regeneration and to better understand the therapeutic potential of miRNA manipulation in pericytes. Here we describe methods for manipulating pericyte function by using miRNA mimics and inhibitors. We also describe methods to assess pericyte function (proliferation and migration) after manipulation with miRNAs and explain how miRNA gene targets can be identified and validated in pericytes after manipulation with miRNA.
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17
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Hoque M, Wai Wong S, Recasens A, Abbassi R, Nguyen N, Zhang D, Stashko MA, Wang X, Frye S, Day BW, Baell J, Munoz L. MerTK activity is not necessary for the proliferation of glioblastoma stem cells. Biochem Pharmacol 2021; 186:114437. [PMID: 33571503 DOI: 10.1016/j.bcp.2021.114437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022]
Abstract
MerTK has been identified as a promising target for therapeutic intervention in glioblastoma. Genetic studies documented a range of oncogenic processes that MerTK targeting could influence, however robust pharmacological validation has been missing. The aim of this study was to assess therapeutic potential of MerTK inhibitors in glioblastoma therapy. Unlike previous studies, our work provides several lines of evidence that MerTK activity is dispensable for glioblastoma growth. We observed heterogeneous responses to MerTK inhibitors that could not be correlated to MerTK inhibition or MerTK expression in cells. The more selective MerTK inhibitors UNC2250 and UNC2580A lack the anti-proliferative potency of less-selective inhibitors exemplified by UNC2025. Functional assays in MerTK-high and MerTK-deficient cells further demonstrate that the anti-cancer efficacy of UNC2025 is MerTK-independent. However, despite its efficacy in vitro, UNC2025 failed to attenuate glioblastoma growth in vivo. Gene expression analysis from cohorts of glioblastoma patients identified that MerTK expression correlates negatively with proliferation and positively with quiescence genes, suggesting that MerTK regulates dormancy rather than proliferation in glioblastoma. In summary, this study demonstrates the importance of orthogonal inhibitors and disease-relevant models in target validation studies and raises a possibility that MerTK inhibitors could be used to target dormant glioblastoma cells.
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Affiliation(s)
- Monira Hoque
- School of Medical Sciences, Faculty of Medicine and Health and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Siu Wai Wong
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ariadna Recasens
- School of Medical Sciences, Faculty of Medicine and Health and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Ramzi Abbassi
- School of Medical Sciences, Faculty of Medicine and Health and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia
| | - Nghi Nguyen
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Dehui Zhang
- University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Michael A Stashko
- University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Xiaodong Wang
- University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Stephen Frye
- University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Bryan W Day
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia
| | - Jonathan Baell
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Lenka Munoz
- School of Medical Sciences, Faculty of Medicine and Health and Charles Perkins Centre, The University of Sydney, NSW 2006, Australia.
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18
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Abstract
This chapter describes one of the most reliable quantitative assays to test the silencing of a possible target gene by a specific miRNA using a luciferase reporter gene. The experimental procedure first consists in cloning both the wild-type and mutated forms of the 3'UTR of the miRNA-predicted mRNA target downstream of a firefly luciferase reporter. Next, each construct is co-transfected together with the miRNA into HeLa cells, and the reporter expression is monitored. Changes in luciferase levels will indicate whether or not an miRNA can bind to the UTR and regulate its expression.
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19
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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20
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Mossa AH, Galan A, Cammisotto PG, Velasquez Flores M, Shamout S, Barcelona P, Saragovi HU, Campeau L. Antagonism of proNGF or its receptor p75 NTR reverses remodelling and improves bladder function in a mouse model of diabetic voiding dysfunction. Diabetologia 2020; 63:1932-1946. [PMID: 32699962 DOI: 10.1007/s00125-020-05222-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/18/2020] [Indexed: 10/23/2022]
Abstract
AIMS/HYPOTHESIS Although 80% of diabetic patients will suffer from voiding difficulties and urinary symptoms, defined as diabetic voiding dysfunction (DVD), therapeutic targets and treatment options are limited. We hypothesise that the blockade of the pro-nerve growth factor (NGF)/p75 neurotrophin receptor (p75NTR) axis by an anti-proNGF monoclonal antibody or by a small molecule p75NTR antagonist (THX-B) can restore bladder remodelling (represented by bladder weight) in an animal model of DVD. Secondary outcomes of the study include improvements in bladder compliance, contractility and morphology, as well as in voiding behaviour, proNGF/NGF balance and TNF-α expression. METHODS In a streptozotocin-induced mouse model of diabetes, diabetic mice received either a blocking anti-proNGF monoclonal antibody or a p75NTR antagonist small molecule as weekly systemic injections for 4 weeks. Animals were tested at baseline (at 2 weeks of diabetes induction), and after 2 and 4 weeks of treatment. Outcomes measured were voiding function with voiding spot assays and cystometry. Bladders were assessed by histological, contractility and protein expression assays. RESULTS Diabetic mice showed features of DVD as early as 2 weeks after diabetes diagnosis (baseline) presented by hypertrophy, reduced contractility and abnormal cystometric parameters. Following treatment initiation, a twofold increase (p < 0.05) in untreated diabetic mouse bladder weight and thickness compared with non-diabetic controls was observed, and this change was reversed by p75NTR antagonism (37% reduction in bladder weight compared with untreated diabetic mice [95% CI 14%, 60%]) after 4 weeks of treatment. However, blocking proNGF did not help to reverse bladder hypertrophy. While diabetic mice had significantly worse cystometric parameters and contractile responses than non-diabetic controls, proNGF antagonism normalised bladder compliance (0.007 [Q1-Q3; 0.006-0.009] vs 0.015 [Q1-Q3; 0.014-0.029] ml/cmH2O in untreated diabetic mice, representing 62% reduction [95% CI 8%, 110%], p < 0.05) and contractility to KCl, carbachol and electrical field stimulation (p < 0.05 compared with the diabetic group) after 2 weeks of treatment. These effects were not observed after 4 weeks of treatment with proNGF antagonist. p75NTR antagonism did not show important improvements in cystometric parameters after 2 weeks of treatment. Slightly improved bladder compliance (0.01 [Q1-Q3; 0.009-0.012] vs 0.013 [Q1-Q3; 0.011-0.016] ml/cmH2O for untreated diabetic mice) was seen in the p75NTR antagonist-treated group after 4 weeks of treatment with significantly stabilised contractile responses to KCl, carbachol and electric field stimulation (p < 0.05 for each) compared with diabetic mice. Bladder dysfunction observed in diabetic mice was associated with a significant increase in bladder proNGF/NGF ratio (3.1 [±1.2] vs 0.26 [±0.04] ng/pg in control group, p < 0.05 at week 2 of treatment) and TNF-α (p < 0.05). The proNGF/NGF ratio was partially reduced (about 60% reduction) with both treatments (1.03 [±0.6] ng/pg for proNGF antibody-treated group and 1.4 [±0.76] ng/pg for p75NTR blocker-treated group after 2 weeks of treatment), concomitant with a significant decrease in the bladder levels of TNF-α (p < 0.05), despite persistent hyperglycaemia. CONCLUSIONS/INTERPRETATION Our findings indicate that blockade of proNGF and the p75NTR receptor in diabetes can impede the development and progression of DVD. The reported improvements in morphological and functional features in our DVD model validates the proNGF/p75NTR axis as a potential therapeutic target in this pathology. Graphical abstract.
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Affiliation(s)
- Abubakr H Mossa
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Alba Galan
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Philippe G Cammisotto
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Monica Velasquez Flores
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - Samer Shamout
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
- Division of Urology, Department, of Surgery, McGill University, Montreal, QC, Canada
| | - Pablo Barcelona
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
| | - H Uri Saragovi
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
- Center for Experimental Therapeutics, Jewish General Hospital, Montreal, QC, Canada
- Department of Ophthalmology and Vision Sciences, McGill University, Montreal, QC, Canada
| | - Lysanne Campeau
- Lady Davis Research Institute, McGill University, 3755 Chemin de la Cote-Ste-Catherine, Montreal, QC, H3T 1E2, Canada.
- Division of Urology, Department, of Surgery, McGill University, Montreal, QC, Canada.
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21
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Al-Mansoori L, Al-Jaber H, Madani AY, Mazloum NA, Agouni A, Ramanjaneya M, Abou-Samra AB, Elrayess MA. Suppression of GATA-3 increases adipogenesis, reduces inflammation and improves insulin sensitivity in 3T3L-1 preadipocytes. Cell Signal 2020; 75:109735. [PMID: 32795510 DOI: 10.1016/j.cellsig.2020.109735] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/21/2020] [Accepted: 08/08/2020] [Indexed: 02/06/2023]
Abstract
Impaired adipogenesis plays an important role in the development of obesity-associated insulin resistance and type 2 diabetes. Adipose tissue inflammation is a crucial mediator of this process. GATA-3 plays important roles in adipogenesis and inflammation. The aim of this study is to investigate the impact of GATA-3 suppression on improving adipogenesis, lowering inflammation and reversing insulin resistance. GATA-3 levels were measured in subcutaneous (SC) and omental (OM) adipose tissues obtained from insulin sensitive (IS) and insulin resistant (IR) obese individuals during weight reduction surgeries. The effect of GATA-3 suppression on adipogenesis, expression of inflammatory cytokines and insulin resistance biomarkers was performed in 3T3L-1 mouse preadipocytes via transfection with GATA-3-specific DNAzyme. GATA-3 expression was higher in OM compared to SC adipose tissues and in stromal vascular fraction-derived differentiating preadipocytes from IR obese individuals compared to their IS counterparts. Suppression of GATA-3 expression in 3T3L-1 mouse preadipocytes with GATA-3 specific inhibitor reversed 4-hydroxynonenal-induced impaired adipogenesis and triggered changes in the expression of insulin signaling-related genes. GATA-3 inhibition also modulated the expression of IL-6 and IL-10 and lowered the expression of insulin resistance biomarkers (PAI-1 and resistin) and insulin resistance phosphoproteins (p-BAD, p-PTEN and p-GSK3β). Inhibiting GATA-3 improves adipocytes differentiation, modulates the secretion of inflammatory cytokines and improves insulin sensitivity in insulin resistant cells. Suppression of GATA-3 could be a promising tool to improve adipogenesis, restore insulin sensitivity and lower obesity-associated inflammation in insulin resistant individuals.
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22
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Zhao B, Liu N, Chen L, Geng S, Fan Z, Xing J. Direct label-free methods for identification of target proteins in agrochemicals. Int J Biol Macromol 2020; 164:1475-1483. [PMID: 32763403 DOI: 10.1016/j.ijbiomac.2020.07.237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Green agrochemicals are important guarantee for food production and security, and target protein identification is the most important basis for development of novel agrochemicals. Affinity chromatography methods for immobilization of agrochemicals have been widely used to identify and confirm new targets. However, this method often requires modification of the active molecules which can affect or damage its biological activity, and biomacromolecules, particularly most natural products, are hard to be modified either. In order to overcome the shortcomings of molecular modification, label-free technology has been developed based on evaluating responses to thermal or proteolytic treatments. Combined with the chemical biology technology and molecular biology technology, it has been used in the development of drugs and agrochemicals. Herein, common methods of label-free technology for identification of direct target of agrochemicals are reviewed, including the principle, advantages, limitations and applications in the research of agrochemicals in the last decade. And the methods for validation of candidate targets obtained by the label-free methods are also reviewed, which are important to obtain the accurate and reliable targets. Combined application of these methods will greatly reduce the experimental costs and shorten the period for the new target identification and validation by improving its accuracy, which will provide a systematic solution for new ecological agrochemicals research and development.
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Affiliation(s)
- Bin Zhao
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Ning Liu
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071001, PR China
| | - Lai Chen
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Shuo Geng
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China.
| | - Jihong Xing
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071001, PR China.
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23
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Dao VTV, Elbatreek MH, Altenhöfer S, Casas AI, Pachado MP, Neullens CT, Knaus UG, Schmidt HHHW. Isoform-selective NADPH oxidase inhibitor panel for pharmacological target validation. Free Radic Biol Med 2020; 148:60-69. [PMID: 31883469 DOI: 10.1016/j.freeradbiomed.2019.12.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 12/24/2019] [Indexed: 02/07/2023]
Abstract
Dysfunctional reactive oxygen species (ROS) signaling is considered an important disease mechanism. Therapeutically, non-selective scavenging of ROS by antioxidants, however, has failed in multiple clinical trials to provide patient benefit. Instead, pharmacological modulation of disease-relevant, enzymatic sources of ROS appears to be an alternative, more promising and meanwhile successfully validated approach. With respect to targets, the family of NADPH oxidases (NOX) stands out as main and dedicated ROS sources. Validation of the different NOX isoforms has been mainly through genetically modified rodent models and is lagging behind in other species. It is unclear whether the different NOX isoforms are sufficiently distinct to allow selective pharmacological modulation. Here we show for five widely used NOX inhibitors that isoform selectivity can be achieved, although individual compound specificity is as yet insufficient. NOX1 was most potently (IC50) targeted by ML171 (0.1 μM); NOX2, by VAS2870 (0.7 μM); NOX4, by M13 (0.01 μM) and NOX5, by ML090 (0.01 μM). In addition, some non-specific antioxidant and assay artefacts may limit the interpretation of data, which included, surprisingly, the clinically advanced NOX inhibitor, GKT136901. In a human ischemic blood-brain barrier hyperpermeability model where genetic target validation is not an option, we provide proof-of-principle that pharmacological target validation for different NOX isoforms is possible by applying an inhibitor panel at IC50 concentrations. Moreover, our findings encourage further lead optimization and development efforts for isoform-selective NOX inhibitors in different indications.
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Affiliation(s)
- Vu Thao-Vi Dao
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands; Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt, Germany
| | - Mahmoud H Elbatreek
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands; Department for Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Sebastian Altenhöfer
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands
| | - Ana I Casas
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands
| | - Mayra P Pachado
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands
| | - Christopher T Neullens
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands
| | - Ulla G Knaus
- Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Harald H H W Schmidt
- Department for Pharmacology and Personalised Medicine, FHML, Maastricht University, Maastricht, the Netherlands.
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24
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Antony M, Scranton V, Srivastava P, Verma R. Micro RNA 181c-5p: A promising target for post-stroke recovery in socially isolated mice. Neurosci Lett 2020; 715:134610. [PMID: 31722236 PMCID: PMC7054848 DOI: 10.1016/j.neulet.2019.134610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/28/2019] [Accepted: 11/02/2019] [Indexed: 02/06/2023]
Abstract
Dysregulation of microRNAs (miRNAs) has been tied to several neurological disorders, including ischemic stroke. It has also been established that social environments can modulate miRNA profiles. We have previously shown that post-stroke social isolation (SI) is linked to poor stroke outcomes and that miR-181c-5p emerged as one of few lead miRNAs that was downregulated in both stroke and SI. Therefore, in this study we examined the potential role of miR-181c-5p mimic in reversing the detrimental effects of post-stroke SI. Two to three-month-old C57BL/6 male mice were pair-housed (PH) for at least two weeks. After two weeks, mice underwent stroke survival surgery using middle cerebral artery occlusion (MCAO) and were randomly assigned to one of two housing conditions: stroke isolation (ST-ISO) or stroke pair-housing with a healthy partner (ST-PH). ST-ISO mice were randomized to receive either miR-181c-5p mimic or a scrambled RNA (7 mg/kg i.v./day×drug) control at 24 h and 48 h after stroke. The effects of miR-181c-5p mimic treatment were evaluated at 1, 3, and 7 days after stroke at histological, behavioral, and biochemical levels. Target genes of miR-181c-5p were then analyzed by qPCR using an RT2 Profiler qPCR Array of pre-coated miR-181c gene targets. Temporal profile expression data suggested that miR-181c-5p was significantly downregulated (p < 0.05 vs ST-PH) up to 7 days after post-stroke SI. MiR-181c-5p mimic treatment significantly increased miR-181c-5p expression in brain tissue and showed partial swift recovery in sensorimotor deficit. Target gene analysis identified downregulation of several calcium signaling-related genes, e.g., Cpne2 and Gria 1 & 2 after miR-181c-5p mimic treatment. In summary, present data suggests that miR-181c-5p is a potential target for post-stroke SI. Data also suggests that genes related to calcium and glutamate signaling might be involved in the beneficial effect of the miR-181c-5p mimic.
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Affiliation(s)
- Maria Antony
- Department of Neuroscience, UConn Health, Farmington, CT 06032, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06268, USA
| | | | | | - Rajkumar Verma
- Department of Neuroscience, UConn Health, Farmington, CT 06032, USA.
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25
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Hwang BB, Engel L, Goueli SA, Zegzouti H. A homogeneous bioluminescent immunoassay to probe cellular signaling pathway regulation. Commun Biol 2020; 3:8. [PMID: 31909200 PMCID: PMC6941952 DOI: 10.1038/s42003-019-0723-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
Monitoring cellular signaling events can help better understand cell behavior in health and disease. Traditional immunoassays to study proteins involved in signaling can be tedious, require multiple steps, and are not easily adaptable to high throughput screening (HTS). Here, we describe a new immunoassay approach based on bioluminescent enzyme complementation. This immunoassay takes less than two hours to complete in a homogeneous "Add and Read" format and was successfully used to monitor multiple signaling pathways' activation through specific nodes of phosphorylation (e.g pIκBα, pAKT, and pSTAT3). We also tested deactivation of these pathways with small and large molecule inhibitors and obtained the expected pharmacology. This approach does not require cell engineering. Therefore, the phosphorylation of an endogenous substrate is detected in any cell type. Our results demonstrate that this technology can be broadly adapted to streamline the analysis of signaling pathways of interest or the identification of pathway specific inhibitors.
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Affiliation(s)
| | - Laurie Engel
- 1R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711 USA
| | - Said A Goueli
- 1R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711 USA.,2Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Hicham Zegzouti
- 1R&D Department, Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711 USA
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26
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Lim CSQ, Ha KP, Clarke RS, Gavin LA, Cook DT, Hutton JA, Sutherell CL, Edwards AM, Evans LE, Tate EW, Lanyon-Hogg T. Identification of a potent small-molecule inhibitor of bacterial DNA repair that potentiates quinolone antibiotic activity in methicillin-resistant Staphylococcus aureus. Bioorg Med Chem 2019; 27:114962. [PMID: 31307763 PMCID: PMC6892255 DOI: 10.1016/j.bmc.2019.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 11/03/2022]
Abstract
The global emergence of antibiotic resistance is one of the most serious challenges facing modern medicine. There is an urgent need for validation of new drug targets and the development of small molecules with novel mechanisms of action. We therefore sought to inhibit bacterial DNA repair mediated by the AddAB/RecBCD protein complexes as a means to sensitize bacteria to DNA damage caused by the host immune system or quinolone antibiotics. A rational, hypothesis-driven compound optimization identified IMP-1700 as a cell-active, nanomolar potency compound. IMP-1700 sensitized multidrug-resistant Staphylococcus aureus to the fluoroquinolone antibiotic ciprofloxacin, where resistance results from a point mutation in the fluoroquinolone target, DNA gyrase. Cellular reporter assays indicated IMP-1700 inhibited the bacterial SOS-response to DNA damage, and compound-functionalized Sepharose successfully pulled-down the AddAB repair complex. This work provides validation of bacterial DNA repair as a novel therapeutic target and delivers IMP-1700 as a tool molecule and starting point for therapeutic development to address the pressing challenge of antibiotic resistance.
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Affiliation(s)
- Carine S Q Lim
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Kam Pou Ha
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Rebecca S Clarke
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Leigh-Anne Gavin
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Declan T Cook
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Jennie A Hutton
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Charlotte L Sutherell
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Lindsay E Evans
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK.
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
| | - Thomas Lanyon-Hogg
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
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27
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Mauricio R, Benn C, Davis J, Dawson G, Dawson LA, Evans A, Fox N, Gallacher J, Hutton M, Isaac J, Jones DN, Jones L, Lalli G, Libri V, Lovestone S, Moody C, Noble W, Perry H, Pickett J, Reynolds D, Ritchie C, Rohrer JD, Routledge C, Rowe J, Snyder H, Spires-Jones T, Swartz J, Truyen L, Whiting P. Tackling gaps in developing life-changing treatments for dementia. Alzheimers Dement (N Y) 2019; 5:241-253. [PMID: 31297438 PMCID: PMC6597931 DOI: 10.1016/j.trci.2019.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Since the G8 dementia summit in 2013, a number of initiatives have been established with the aim of facilitating the discovery of a disease-modifying treatment for dementia by 2025. This report is a summary of the findings and recommendations of a meeting titled "Tackling gaps in developing life-changing treatments for dementia", hosted by Alzheimer's Research UK in May 2018. The aim of the meeting was to identify, review, and highlight the areas in dementia research that are not currently being addressed by existing initiatives. It reflects the views of leading experts in the field of neurodegeneration research challenged with developing a strategic action plan to address these gaps and make recommendations on how to achieve the G8 dementia summit goals. The plan calls for significant advances in (1) translating newly identified genetic risk factors into a better understanding of the impacted biological processes; (2) enhanced understanding of selective neuronal resilience to inform novel drug targets; (3) facilitating robust and reproducible drug-target validation; (4) appropriate and evidence-based selection of appropriate subjects for proof-of-concept clinical trials; (5) improving approaches to assess drug-target engagement in humans; and (6) innovative approaches in conducting clinical trials if we are able to detect disease 10-15 years earlier than we currently do today.
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Affiliation(s)
| | | | - John Davis
- Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, UK
| | - Gerry Dawson
- P1 Vital, Howbery Business Park, Wallingford, Oxfordshire, UK
| | - Lee A. Dawson
- Cerevance Ltd, Cambridge Science Park, Cambridge, UK
| | | | - Nick Fox
- Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - John Gallacher
- Department of Psychiatry, University of Oxford, Oxford, UK
| | | | - John Isaac
- Neuroscience External Innovation, Neuroscience Therapeutic Area, Johnson & Johnson Innovation, London, UK
| | - Declan N.C. Jones
- Neuroscience External Innovation, Neuroscience Therapeutic Area, Johnson & Johnson Innovation, London, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, Wales, UK
| | | | - Vincenzo Libri
- Institute of Neurology, University College London, London, UK
| | | | | | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Hugh Perry
- Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | | | | | - Craig Ritchie
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Jonathan D. Rohrer
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | | | - James Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Tara Spires-Jones
- UK Dementia Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Jina Swartz
- European Innovation Hub, Merck Sharp and Dohme, London, UK
| | - Luc Truyen
- Janssen Research & Development LLC, Titusville, NJ, USA
| | - Paul Whiting
- Dementia Research Institute, UCL, London, UK
- ARUK Drug Discovery Institute, Institute of Neurology, University College London, London, UK
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28
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Shehata M, Kim H, Vellanki R, Waterhouse PD, Mahendralingam M, Casey AE, Koritzinsky M, Khokha R. Identifying the murine mammary cell target of metformin exposure. Commun Biol 2019; 2:192. [PMID: 31123716 PMCID: PMC6527562 DOI: 10.1038/s42003-019-0439-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 04/23/2019] [Indexed: 02/07/2023] Open
Abstract
The heterogeneity of breast cancer makes current therapies challenging. Metformin, the anti-diabetic drug, has shown promising anti-cancer activities in epidemiological studies and breast cancer models. Yet, how metformin alters the normal adult breast tissue remains elusive. We demonstrate metformin intake at a clinically relevant dose impacts the hormone receptor positive (HR+) luminal cells in the normal murine mammary gland. Metformin decreases total cell number, progenitor capacity and specifically reduces DNA damage in normal HR+ luminal cells, decreases oxygen consumption rate and increases cell cycle length of luminal cells. HR+ luminal cells demonstrate the lowest levels of mitochondrial respiration and capacity to handle oxidative stress compared to the other fractions, suggesting their intrinsic susceptibility to long-term metformin exposure. Uncovering HR+ luminal cells in the normal mammary gland as the major cell target of metformin exposure could identify patients that would most benefit from repurposing this anti-diabetic drug for cancer prevention/therapy purposes.
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Affiliation(s)
- Mona Shehata
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | - Hyeyeon Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | - Ravi Vellanki
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | - Paul D. Waterhouse
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | | | - Alison E. Casey
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | - Marianne Koritzinsky
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
| | - Rama Khokha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7 Canada
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29
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Abstract
High throughput sequencing has revolutionized our ability to identify aberrant RNA expression and mutations that cause or contribute to disease. These data can be used directly to design oligonucleotide-based modalities using Watson-Crick pairing to target unstructured regions in an RNA. A complementary, although more difficult, strategy to deactivate a malfunctioning RNA is to target highly structured regions with small molecules. Indeed, RNA structures are directly causative of disease. Herein, we discuss emerging strategies to design high affinity, selective, bioactive ligands targeting RNA, or small molecules interacting with RNA (SMIRNAs), and target validation and profiling methods. An experimental foundation is required for a lead identification strategy for RNA structures, constructed from a library-vs.-library screen that probes vast libraries of small molecules for binding RNA three dimensional folds. Dubbed 2-dimensional combinatorial screening (2DCS), the resulting data can be mined against transcriptomes or the composite of RNAs that are produced in an organism to define folded RNA structures that can be targeted. By applying SMIRNAs to cells and using target validation tools such as Chemical Cross-Linking and Isolation by Pull-down (Chem-CLIP) and Small Molecule Nucleic Acid Profiling by Cleavage Applied to RNA (RiboSNAP), all targets engaged in cells can be defined, along with rules for molecular recognition to affect RNA biology. This chapter will describe lessons learned in applying these approaches in vitro, in cells, and in pre-clinical animal models of disease, enabling SMIRNAs to capture opportunities in chemical biology.
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Affiliation(s)
- Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States.
| | | | - Yue Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States
| | - Matthew G Costales
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, United States
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30
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Carvalho D, Taylor KR, Olaciregui NG, Molinari V, Clarke M, Mackay A, Ruddle R, Henley A, Valenti M, Hayes A, Brandon ADH, Eccles SA, Raynaud F, Boudhar A, Monje M, Popov S, Moore AS, Mora J, Cruz O, Vinci M, Brennan PE, Bullock AN, Carcaboso AM, Jones C. ALK2 inhibitors display beneficial effects in preclinical models of ACVR1 mutant diffuse intrinsic pontine glioma. Commun Biol 2019; 2:156. [PMID: 31098401 PMCID: PMC6509210 DOI: 10.1038/s42003-019-0420-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is a lethal childhood brainstem tumour, with a quarter of patients harbouring somatic mutations in ACVR1, encoding the serine/threonine kinase ALK2. Despite being an amenable drug target, little has been done to-date to systematically evaluate the role of ACVR1 in DIPG, nor to screen currently available inhibitors in patient-derived tumour models. Here we show the dependence of DIPG cells on the mutant receptor, and the preclinical efficacy of two distinct chemotypes of ALK2 inhibitor in vitro and in vivo. We demonstrate the pyrazolo[1,5-a]pyrimidine LDN-193189 and the pyridine LDN-214117 to be orally bioavailable and well-tolerated, with good brain penetration. Treatment of immunodeprived mice bearing orthotopic xenografts of H3.3K27M, ACVR1R206H mutant HSJD-DIPG-007 cells with 25 mg/kg LDN-193189 or LDN-214117 for 28 days extended survival compared with vehicle controls. Development of ALK2 inhibitors with improved potency, selectivity and advantageous pharmacokinetic properties may play an important role in therapy for DIPG patients.
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Grants
- Wellcome Trust
- C13468/A14078 Cancer Research UK
- 106169/ZZ14/Z Wellcome Trust
- CHILDREN with CANCER UK
- This work was supported by Children with Cancer UK, Abbie’s Army and the DIPG Collaborative, the Lyla Nsouli Foundation and Lucas’ Legacy, the McKenna Claire Foundation and Fondo Alicia Pueyo. The Queensland Children’s Tumour Bank is supported by the Children’s Hospital Foundation. We thank Louise Howell (ICR) for excellent technical assistance. This work was supported by the Xarxa de Bancs de Tumors de Catalunya (XBTC), sponsored by Pla Director d’Oncologia de Catalunya. AMC acknowledges funding from ISCIII-FEDER (CP13/00189). A.B. and A.N.B acknowledge funding from the Amateurs Trust, Roemex Ltd and FOP Friends. The SGC is a registered charity (number 1097737) that receives funds from AbbVie, Bayer Pharma AG, Boehringer Ingelheim, Canada Foundation for Innovation, Eshelman Institute for Innovation, Genome Canada, Innovative Medicines Initiative (EU/EFPIA) [ULTRA-DD grant no. 115766], Janssen, MSD, Merck KGaA, Novartis Pharma AG, Ontario Ministry of Economic Development and Innovation, Pfizer, São Paulo Research Foundation-FAPESP, Takeda and Wellcome [106169/ZZ14/Z]. This study makes use of data generated by Cancer Research UK Genomics Initiative (C13468/A14078). The authors acknowledge NHS funding to the NIHR Biomedical Research Centre at The Royal Marsden and the ICR.
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Affiliation(s)
- Diana Carvalho
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Kathryn R. Taylor
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Stanford University School of Medicine, Stanford, 94305 CA USA
| | | | - Valeria Molinari
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Matthew Clarke
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Alan Mackay
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Ruth Ruddle
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Alan Henley
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Melanie Valenti
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Angela Hayes
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | | | - Suzanne A. Eccles
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Florence Raynaud
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
| | - Aicha Boudhar
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Michelle Monje
- Stanford University School of Medicine, Stanford, 94305 CA USA
| | - Sergey Popov
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Department of Cellular Pathology, University Hospital of Wales, Cardiff, CF14 4XW UK
| | - Andrew S. Moore
- Diamantina Institute and Child Health Research Centre, The University of Queensland, Brisbane, QLD 4101 Australia
- Oncology Service, Queensland Children’s Hospital, Brisbane, QLD 4029 Australia
| | - Jaume Mora
- Institut de Recerca Sant Joan de Deu, Barcelona, 08950 Esplugues de Llobregat Spain
| | - Ofelia Cruz
- Institut de Recerca Sant Joan de Deu, Barcelona, 08950 Esplugues de Llobregat Spain
| | - Mara Vinci
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
- Bambino Gesù Children’s Hospital, Rome, 00165 Roma RM Italy
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Alex N. Bullock
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ UK
| | | | - Chris Jones
- Divisions of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG UK
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG UK
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31
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Affiliation(s)
- Hai Jiang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue-yang Road, Shanghai, 200031 China
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Velagapudi SP, Li Y, Disney MD. A cross-linking approach to map small molecule-RNA binding sites in cells. Bioorg Med Chem Lett 2019; 29:1532-1536. [PMID: 30987892 DOI: 10.1016/j.bmcl.2019.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 10/27/2022]
Abstract
Methods to identify RNAs bound by small molecules in cells are sparse. Herein, an advance to identify the direct RNA targets of small molecules in cells is described. The approach, dubbed Chemical Cross-Linking and Isolation by Pull-down to Map Small Molecule-RNA Binding Sites (Chem-CLIP-Map-Seq), appends a cross-linker and a purification tag onto a small molecule. In cells, the compound binds to RNA and undergoes a proximity-based reaction. The cross-linked RNA is purified and then amplified using a universal reverse transcription (RT) primer and gene-specific PCR primers. At nucleotides proximal to the binding site, RT "stops" are observed. This approach has broad utility in identifying and validating the RNA targets and binding sites of small molecules in the context of a complex cellular system.
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Affiliation(s)
| | - Yue Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
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33
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Rong X, Tian H, Yang L, Li W. Function-first ligandomics for ocular vascular research and drug target discovery. Exp Eye Res 2019; 182:57-64. [PMID: 30904565 DOI: 10.1016/j.exer.2019.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 12/29/2022]
Abstract
Human eyes may develop different vascular diseases with neovascularization and/or leakage, including wet age-related macular degeneration (AMD), diabetic macular edema (DME), proliferative diabetic retinopathy (PDR), retinopathy of prematurity, corneal neovascularization and intraocular tumors. A breakthrough in therapy is the advent and approval of vascular endothelial growth factor (VEGF) inhibitors. However, anti-VEGF drugs not only have limited efficacy to treat AMD, DME and PDR but also are not approved for other ocular indications. The key to addressing these unmet clinical needs is to develop novel therapies against VEGF-independent angiogenic factors or signaling pathways for alternative or combination therapy. We recently developed the first paradigm of ligandomics for global mapping of cell-wide ligands as well as disease-selective ligands. Therapies targeting disease-selective angiogenic or vascular leakage factors likely have high efficacy, minimal side effects, wide therapeutic windows and relatively low drug attrition rates. A critical challenge is how to distinguish between genuine drug targets and spurious hits identified by high-throughput ligandomics. Here we exploited the unique advantages of the eye and extracellular ligands by combining ligandomics with "function-first" and/or "therapy-first" analyses to efficiently characterize functional activity, disease selectivity, pathogenic role and therapeutic potential of identified ligands. The innovative function- or therapy-first ligandomics will systematically and reliably delineate disease-selective angiogenic or vascular leakage factors and markedly facilitate ocular vascular research and ligand-guided targeted anti-angiogenic therapy.
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Affiliation(s)
- Xin Rong
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | | | - Liu Yang
- Department of Ophthalmology, Peking University First Hospital, Beijing, China
| | - Wei Li
- Bascom Palmer Eye Institute, Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL, USA.
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34
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Abstract
Phenotypic screening in disease-relevant models identifies small molecule hits with desirable efficacy but often with unknown modes of action. Target identification and validation are integral to successful biomedical research. Technologies are required to validate the biological target (or targets) through which a pharmacological agent is proposed to exert its effects. This work details the rational structure-based design, synthetic preparation and cell-based application of a clickable sulfonyl fluoride chemical probe to directly report on the mechanism of a series of compounds previously discovered in a reporter gene assay. Quantification of drug-target occupancy in living human primary cells enabled a deeper understanding of the molecular pharmacology of the chemotype. The technology described herein should be of broad interest to those involved in chemical biology research and the drug discovery endeavor.
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Affiliation(s)
- Lyn H Jones
- Jnana Therapeutics, Boston, MA, United States.
| | - Hua Xu
- Pfizer Inc, Medicine Design, Cambridge, MA, United States
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35
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Abstract
Small molecule-induced targeted protein degradation is a powerful approach for drug target validation given its selectivity, high kinetic resolution, dose dependency, and reversibility. Out of the several methods that have been reported so far, the 12 kDa degradation tag (dTAG) system has the advantage of hijacking a degradation machinery that is ubiquitously expressed in all human tissues. Therefore it is independent of expressing additional, exogenous factors and additionally permits target validation in vivo. Here, we describe the protocol for generation and validation of clones harboring knock-in of a selectable dTAG cassette at the endogenous locus of proteins of interest using the near-haploid cell line KBM7.
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Affiliation(s)
- Matthias Brand
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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36
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Cetti E, Di Marco T, Mauro G, Mazzoni M, Lecis D, Minna E, Gioiosa L, Brich S, Pagliardini S, Borrello MG, Pruneri G, Anania MC, Greco A. Mitosis perturbation by MASTL depletion impairs the viability of thyroid tumor cells. Cancer Lett 2019; 442:362-72. [PMID: 30445205 DOI: 10.1016/j.canlet.2018.11.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022]
Abstract
Even if thyroid tumors are generally curable, a fraction will develop resistance to therapy and progress towards undifferentiated forms, whose treatment remains a demanding challenge. To identify potential novel targets for treatment of thyroid cancer, in a previous study using siRNA-mediated functional screening, we identified several genes that are essential for the growth of thyroid tumor, but not normal cells. Among the top-ranking hits, we found microtubule associated serine/threonine kinase-like (MASTL), which is known to play an essential role in mitosis regulation, and is also involved in the DNA damage response. Herein, we examine the effects of MASTL depletion on growth and viability of thyroid tumor cells. MASTL depletion impaired cell proliferation and increased the percentage of cells presenting nuclear anomalies, which are indicative of mitotic catastrophe. Furthermore, MASTL depletion was associated with enhanced DNA damage. All these effects eventually led to cell death, characterized by the presence of apoptotic markers. Moreover, MASTL depletion sensitized thyroid tumor cells to cisplatin. Our results demonstrate that MASTL represents vulnerability for thyroid tumor cells, which could be explored as a therapeutic target for thyroid cancer.
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37
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Müller S, Ackloo S, Arrowsmith CH, Bauser M, Baryza JL, Blagg J, Böttcher J, Bountra C, Brown PJ, Bunnage ME, Carter AJ, Damerell D, Dötsch V, Drewry DH, Edwards AM, Edwards J, Elkins JM, Fischer C, Frye SV, Gollner A, Grimshaw CE, IJzerman A, Hanke T, Hartung IV, Hitchcock S, Howe T, Hughes TV, Laufer S, Li VMJ, Liras S, Marsden BD, Matsui H, Mathias J, O'Hagan RC, Owen DR, Pande V, Rauh D, Rosenberg SH, Roth BL, Schneider NS, Scholten C, Singh Saikatendu K, Simeonov A, Takizawa M, Tse C, Thompson PR, Treiber DK, Viana AYI, Wells CI, Willson TM, Zuercher WJ, Knapp S, Mueller-Fahrnow A. Donated chemical probes for open science. eLife 2018; 7:e34311. [PMID: 29676732 PMCID: PMC5910019 DOI: 10.7554/elife.34311] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/29/2018] [Indexed: 12/12/2022] Open
Abstract
Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project.
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Affiliation(s)
- Susanne Müller
- Structural Genomics ConsortiumBuchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | - Suzanne Ackloo
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | | | | | | | - Julian Blagg
- Cancer Research UK Cancer Therapeutics UnitThe Institute of Cancer ResearchLondonUnited Kingdom
| | | | - Chas Bountra
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Peter J Brown
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | | | - Adrian J Carter
- Discovery ResearchBoehringer IngelheimIngelheim am RheinGermany
| | - David Damerell
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe-UniversityFrankfurt am MainGermany
- Center for Biomolecular Magnetic ResonanceGoethe UniversityFrankfurt am MainGermany
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - Aled M Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - James Edwards
- Janssen Pharmaceutical Research and Development LLCSpring HouseUnited States
| | - Jon M Elkins
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - Andreas Gollner
- Discovery ResearchBoehringer IngelheimBiberach an der RissGermany
| | | | - Adriaan IJzerman
- Division of Medicinal ChemistryLeiden UniversityLeidenNetherlands
| | - Thomas Hanke
- Structural Genomics ConsortiumBuchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | | | | | | | | | - Stefan Laufer
- Department of Pharmaceutical ChemistryEberhard Karls Universität TübingenTübingenGermany
| | | | - Spiros Liras
- Worldwide Medicinal ChemistryPfizerCambridgeUnited States
| | - Brian D Marsden
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
- Kennedy Institute of RheumatologyUniversity of OxfordOxfordUnited Kingdom
| | | | - John Mathias
- Worldwide Medicinal ChemistryPfizerCambridgeUnited States
| | | | - Dafydd R Owen
- Worldwide Medicinal ChemistryPfizerCambridgeUnited States
| | - Vineet Pande
- Discovery SciencesJanssen-Pharmaceutical Companies of Johnson & JohnsonBeerseBelgium
| | - Daniel Rauh
- Fakultät für Chemie und Chemische BiologieTechnische Universität DortmundDortmundGermany
| | | | - Bryan L Roth
- The National Institute of Mental Health Psychoactive Active Drug Screening ProgramUniversity of North Carolina Chapel Hill School of MedicineChapel HillUnited States
| | - Natalie S Schneider
- Structural Genomics ConsortiumBuchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | | | | | - Anton Simeonov
- National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaUnited States
| | | | | | - Paul R Thompson
- Department of Biochemistry and PharmacologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | | | - Amélia YI Viana
- Discovery ResearchBoehringer IngelheimIngelheim am RheinGermany
| | - Carrow I Wells
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - Timothy M Willson
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillUnited States
| | - Stefan Knapp
- Structural Genomics ConsortiumBuchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
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Abstract
Glandular epithelial cells differentiate into three-dimensional (3D) multicellular or acinar structures, particularly when embedded in laminin-rich extracellular matrix (ECM). The spectrum of different multicellular morphologies formed in 3D is a reliable indicator for the differentiation potential of normal, non-transformed cells compared to different stages of malignant progression. Motile cancer cells may actively invade the matrix, utilizing epithelial, mesenchymal, or mixed modes of motility. Dynamic phenotypic changes involved in 3D tumor cell invasion are also very sensitive to small-molecule inhibitors that, e.g., target the actin cytoskeleton. Our strategy is to recapitulate the formation and the histology of complex solid cancer tissues in vitro, based on cell culture technologies that promote the intrinsic differentiation potential of normal and transformed epithelial cells, and also including stromal fibroblasts and other key components of the tumor microenvironment. We have developed a streamlined stand-alone software solution that supports the detailed quantitative phenotypic analysis of organotypic 3D cultures. This approach utilizes the power of automated image analysis as a phenotypic readout in cell-based assays. AMIDA (Automated Morphometric Image Data Analysis) allows quantitative measurements of a large number of multicellular structures, which can form a multitude of different organoid shapes, sizes, and textures according to their capacity to engage in epithelial differentiation programs or not. At the far end of this spectrum of tumor-relevant differentiation properties, there are highly invasive tumor cells or multicellular structures that may rapidly invade the surrounding ECM, but fail to form higher-order epithelial tissue structures. Furthermore, this system allows us to monitor dynamic changes that can result from the extraordinary plasticity of tumor cells, e.g., epithelial-to-mesenchymal transition in live cell settings. Furthermore, AMIDA supports an automated workflow, and can be combined with quality control and statistical tools for data interpretation and visualization. Our approach supports the growing needs for user-friendly, straightforward solutions that facilitate cell-based organotypic 3D assays in basic research, drug discovery, and target validation.
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Affiliation(s)
- Malin Åkerfelt
- High-Content Screening Laboratory (HCSLab), Institute of Biomedicine, University of Turku, Itäinen Pitkäkatu 4B, 20520, Turku, Finland
| | - Mervi Toriseva
- High-Content Screening Laboratory (HCSLab), Institute of Biomedicine, University of Turku, Itäinen Pitkäkatu 4B, 20520, Turku, Finland
| | - Matthias Nees
- High-Content Screening Laboratory (HCSLab), Institute of Biomedicine, University of Turku, Itäinen Pitkäkatu 4B, 20520, Turku, Finland.
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39
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Bakshi M, Kim TK, Mulenga A. Disruption of blood meal-responsive serpins prevents Ixodes scapularis from feeding to repletion. Ticks Tick Borne Dis 2018; 9:506-518. [PMID: 29396196 PMCID: PMC5857477 DOI: 10.1016/j.ttbdis.2018.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 12/29/2022]
Abstract
Serine protease inhibitors (serpins) are thought to mediate the tick's evasion of the host's serine protease-mediated defense pathways such as inflammation and blood clotting. This study describes characterization and target validation of 11 blood meal-responsive serpins that are associated with nymph and adult Ixodes scapularis tick feeding as revealed by quantitative (q)RT-PCR and RNAi silencing analyses. Given the high number of targets, we used combinatorial (co) RNAi silencing to disrupt candidate serpins in two groups (G): seven highly identical and four non-identical serpins based on amino acid identities, here after called GI and GII respectively. We show that injection of both GI and GII co-dsRNA into unfed nymph and adult I. scapularis ticks triggered suppression of cognate serpin mRNA. We show that disruption of GII, but not GI serpins significantly reduced feeding efficiency of both nymph and adult I. scapularis ticks. Knockdown of GII serpin transcripts caused significant respective mortalities of ≤40 and 71% of nymphal and adult ticks that occurred within 24-48 h of attachment. This is significant, as the observed lethality preceded the tick feeding period when transmission of tick borne pathogens is predominant. We suspect that some of the GII serpins (S9, S17, S19 and S32) play roles in the tick detachment process in that upon detachment, mouthparts of GII co-dsRNA injected were covered with a whitish gel-like tissue that could be the tick cement cone. Normally, ticks do not retain tissue on their mouthparts upon detachment. Furthermore, disruption of GII serpins reduced tick blood meal sizes and the adult tick's ability to convert the blood meal to eggs. We discuss our data with reference to tick feeding physiology and conclude that some of the GII serpins are potential targets for anti-tick vaccine development.
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Affiliation(s)
- Mariam Bakshi
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 422 Raymond Stotzer, TAMU 4467, College Station, TX 77843, USA
| | - Tae Kwon Kim
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 422 Raymond Stotzer, TAMU 4467, College Station, TX 77843, USA
| | - Albert Mulenga
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, 422 Raymond Stotzer, TAMU 4467, College Station, TX 77843, USA.
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40
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Menzner AK, Gilbert DF. A Protocol for In Vitro High-Throughput Chemical Susceptibility Screening in Differentiating NT2 Stem Cells. Methods Mol Biol 2018; 1601:61-70. [PMID: 28470517 DOI: 10.1007/978-1-4939-6960-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incidence of neurological diseases including learning and developmental disorders has increased in recent years. Concurrently, the number and volume of worldwide registered and traded chemicals have also increased. There is a broad consensus that the developing brain is particularly sensitive to damage by chemicals and that evaluation of chemicals for developmental toxicity or neurotoxicity is critical to human health. Human pluripotent embryonal carcinoma (NTERA-2 or NT2) cells are increasingly considered as a suitable model for in vitro developmental toxicity and neurotoxicity (DT/DNT) studies as they undergo neuronal differentiation upon stimulation with retinoic acid (RA) and allow toxicity assessment at different stages of maturation. Here we describe a protocol for cell fitness screening in differentiating NT2 cells based on the analysis of intracellular ATP levels allowing for the identification of chemicals which are potentially harmful to the developing brain. The described method is suitable to be adapted to low-, medium-, and high-throughput screening and allows multiplexing with other cell fitness indicators. While the presented protocol focuses on cell fitness screening in human pluripotent stem cells it may also be applied to other in vitro models.
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Affiliation(s)
- Ann-Katrin Menzner
- Department of Internal Medicine 5, University Medical Center Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel F Gilbert
- Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Institute of Medical Biotechnology, Paul-Gordan-Street 3, 91052, Erlangen, Germany.
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41
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Abstract
High-throughput cell viability assays are broadly used in RNAi and small molecule screening experiments to identify compounds that selectively kill cancer cells or as counter screens to exclude the compounds that have a generic effect on cell growth. While there are several assaying techniques available, cellular fitness is often assessed on the basis of one single and often rather indirect physiological indicator. This can lead to inconsistencies and poor correspondence between cell viability screening experiments, conducted under comparable conditions but with different viability indicators. Multiplexing, i.e., the combination of different individual assaying techniques in one experiment and subsequent comparative analysis of multiparametric data can decrease inter-assay variability and increase dataset concordance. Here, we describe a protocol for a multiplexing approach for high-throughput cell viability screening to address the issues encountered in the classical strategy using a single fitness indicator described above. The method combines a biochemical, luminescence-based approach and two fluorescence-based assay types. The biochemical method assesses cellular fitness by quantifying intracellular ATP concentration. Calcein labeling reflects cell fitness through membrane integrity and indirect measurement of ATP-dependent enzymatic esterase activity. Hoechst DNA stain correlates cell fitness with cellular DNA content. The presented multiplexing approach is suitable for low, medium and high-throughput screening and has the potential to decrease inter-assay variability and increase dataset concordance as well as reproducibility of experimental results.
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42
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Rizvi NF, Smith GF. RNA as a small molecule druggable target. Bioorg Med Chem Lett 2017; 27:5083-8. [PMID: 29097169 DOI: 10.1016/j.bmcl.2017.10.052] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/11/2017] [Accepted: 10/22/2017] [Indexed: 12/20/2022]
Abstract
Small molecule drugs have readily been developed against many proteins in the human proteome, but RNA has remained an elusive target for drug discovery. Increasingly, we see that RNA, and to a lesser extent DNA elements, show a persistent tertiary structure responsible for many diverse and complex cellular functions. In this digest, we have summarized recent advances in screening approaches for RNA targets and outlined the discovery of novel, drug-like small molecules against RNA targets from various classes and therapeutic areas. The link of structure, function, and small-molecule Druggability validates now for the first time that RNA can be the targets of therapeutic agents.
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43
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Geerts H, Hofmann-Apitius M, Anastasio TJ. Knowledge-driven computational modeling in Alzheimer's disease research: Current state and future trends. Alzheimers Dement 2017; 13:1292-1302. [PMID: 28917669 DOI: 10.1016/j.jalz.2017.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/05/2017] [Accepted: 08/01/2017] [Indexed: 11/24/2022]
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD) follow a slowly progressing dysfunctional trajectory, with a large presymptomatic component and many comorbidities. Using preclinical models and large-scale omics studies ranging from genetics to imaging, a large number of processes that might be involved in AD pathology at different stages and levels have been identified. The sheer number of putative hypotheses makes it almost impossible to estimate their contribution to the clinical outcome and to develop a comprehensive view on the pathological processes driving the clinical phenotype. Traditionally, bioinformatics approaches have provided correlations and associations between processes and phenotypes. Focusing on causality, a new breed of advanced and more quantitative modeling approaches that use formalized domain expertise offer new opportunities to integrate these different modalities and outline possible paths toward new therapeutic interventions. This article reviews three different computational approaches and their possible complementarities. Process algebras, implemented using declarative programming languages such as Maude, facilitate simulation and analysis of complicated biological processes on a comprehensive but coarse-grained level. A model-driven Integration of Data and Knowledge, based on the OpenBEL platform and using reverse causative reasoning and network jump analysis, can generate mechanistic knowledge and a new, mechanism-based taxonomy of disease. Finally, Quantitative Systems Pharmacology is based on formalized implementation of domain expertise in a more fine-grained, mechanism-driven, quantitative, and predictive humanized computer model. We propose a strategy to combine the strengths of these individual approaches for developing powerful modeling methodologies that can provide actionable knowledge for rational development of preventive and therapeutic interventions. Development of these computational approaches is likely to be required for further progress in understanding and treating AD.
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Affiliation(s)
- Hugo Geerts
- In Silico Biosciences, Berwyn, PA, USA; Perelman School of Medicine, Univ. of Pennsylvania.
| | - Martin Hofmann-Apitius
- Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Thomas J Anastasio
- Department of Molecular and Integrative Physiology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Ashrafi A, Garcia P, Kollmus H, Schughart K, Del Sol A, Buttini M, Glaab E. Absence of regulator of G-protein signaling 4 does not protect against dopamine neuron dysfunction and injury in the mouse 6-hydroxydopamine lesion model of Parkinson's disease. Neurobiol Aging 2017; 58:30-33. [PMID: 28697377 DOI: 10.1016/j.neurobiolaging.2017.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 06/11/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
Abstract
Regulator of G-protein signaling 4 (RGS4), a member of the RGS family of proteins that inactivate G-proteins, has gained interest as a potential drug target for neurological disorders, such as epilepsy and Parkinson's disease (PD). In the case of PD, the main current options for alleviating motor symptoms are dopamine replacement therapies, which have limitations because of side effects and reduced effectiveness over the long term. Research on new nondopaminergic PD drug targets has indicated that inhibition of RGS4 could be an effective adjuvant treatment option. The effectiveness of RGS4 inhibition for an array of PD-linked functional and structural neuroprotection end points has not yet been demonstrated. Here, we use the 6-hydroxydopamine (6-OHDA) lesioning model of the nigrostriatal pathway in mice to address this question. We observe, using a battery of behavioral and pathological measures, that mice deficient for RGS4 are not protected from 6-OHDA-induced injury and show enhanced susceptibility in some measures of motor function. Our results suggest that inhibition of RGS4 as a nondopaminergic target for PD should be approached with caution.
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Affiliation(s)
- Amer Ashrafi
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Heike Kollmus
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Schughart
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Department of Infection Genetics, University of Veterinary Medicine Hannover, Hannover, Germany; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, USA
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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Kafkas Ş, Dunham I, McEntyre J. Literature evidence in open targets - a target validation platform. J Biomed Semantics 2017; 8:20. [PMID: 28587637 DOI: 10.1186/s13326-017-0131-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
Background We present the Europe PMC literature component of Open Targets - a target validation platform that integrates various evidence to aid drug target identification and validation. The component identifies target-disease associations in documents and ranks the documents based on their confidence from the Europe PMC literature database, by using rules utilising expert-provided heuristic information. The confidence score of a given document represents how valuable the document is in the scope of target validation for a given target-disease association by taking into account the credibility of the association based on the properties of the text. The component serves the platform regularly with the up-to-date data since December, 2015. Results Currently, there are a total number of 1168365 distinct target-disease associations text mined from >26 million PubMed abstracts and >1.2 million Open Access full text articles. Our comparative analyses on the current available evidence data in the platform revealed that 850179 of these associations are exclusively identified by literature mining. Conclusions This component helps the platform’s users by providing the most relevant literature hits for a given target and disease. The text mining evidence along with the other types of evidence can be explored visually through https://www.targetvalidation.org and all the evidence data is available for download in json format from https://www.targetvalidation.org/downloads/data.
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Abstract
Type 2 diabetes is a global epidemic with major effects on healthcare expenditure and quality of life. Currently available treatments are inadequate for the prevention of comorbidities, yet progress towards new therapies remains slow. A major barrier is the insufficiency of traditional preclinical models for predicting drug efficacy and safety. Human genetics offers a complementary model to assess causal mechanisms for target validation. Genetic perturbations are 'experiments of nature' that provide a uniquely relevant window into the long-term effects of modulating specific targets. Here, we show that genetic discoveries over the past decades have accurately predicted (now known) therapeutic mechanisms for type 2 diabetes. These findings highlight the potential for use of human genetic variation for prospective target validation, and establish a framework for future applications. Studies into rare, monogenic forms of diabetes have also provided proof-of-principle for precision medicine, and the applicability of this paradigm to complex disease is discussed. Finally, we highlight some of the limitations that are relevant to the use of genome-wide association studies (GWAS) in the search for new therapies for diabetes. A key outstanding challenge is the translation of GWAS signals into disease biology and we outline possible solutions for tackling this experimental bottleneck.
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Affiliation(s)
- Soren K Thomsen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LE, UK
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LE, UK.
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- National Institute of Health Research Oxford Biomedical Research Centre, Churchill Hospital, Oxford, UK.
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Falcão VCA, Villela AD, Rodrigues-Junior VS, Pissinate K, Eichler P, Pinto AFM, Basso LA, Santos DS, Bizarro CV. Validation of Mycobacterium tuberculosis dihydroneopterin aldolase as a molecular target for anti-tuberculosis drug development. Biochem Biophys Res Commun 2017; 485:814-819. [PMID: 28257847 DOI: 10.1016/j.bbrc.2017.02.137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/27/2017] [Indexed: 12/17/2022]
Abstract
An early step of target validation in antimicrobial drug discovery is to prove that a gene coding for a putative target is essential for pathogen's viability. However, little attention has been paid to demonstrate the causal links between gene essentiality and a particular protein function that will be the focus of a drug discovery effort. This should be considered an important step in target validation since a growing number of proteins are found to exhibit multiple and unrelated tasks. Here, we show that the Mycobacterium tuberculosis (Mtb) folB gene is essential and that this essentiality depends on the dihydroneopterin aldolase/epimerase activities of its protein product, the FolB protein from the folate biosynthesis pathway. The wild-type (WT) MtFolB and point mutants K99A and Y54F were cloned, expressed, purified and monitored for the aldolase, epimerase and oxygenase activities using HPLC. In contrast to the WT MtFolB, both mutants have neither aldolase nor epimerase activities in the conditions assayed. We then performed gene knockout experiments and showed that folB gene is essential for Mtb survival under the conditions tested. Moreover, only the WT folB sequence could be used as a rescue copy in gene complementation studies. When the sequences of mutants K99A or Y54F were used for complementation, no viable colonies were obtained, indicating that aldolase and/or epimerase activities are crucial for Mtb survival. These results provide a solid basis for further work aiming to develop new anti-TB agents acting as inhibitors of the aldolase/epimerase activities of MtFolB.
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Affiliation(s)
- V C A Falcão
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - A D Villela
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - V S Rodrigues-Junior
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - K Pissinate
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - P Eichler
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - A F M Pinto
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil
| | - L A Basso
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil; Programa de Pós-Graduação em Medicina e Ciências da Saúde (PUCRS), Porto Alegre, RS, Brazil
| | - D S Santos
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil
| | - C V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular (PUCRS), Brazil.
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Abstract
Multiplex Immunohistochemistry (mIHC) allows for the simultaneous detection of multiple targets of interest in a single tissue section. Using this method it is therefore possible to evaluate several effectors of a signal transduction pathway at one time, co-localization of markers, or distribution of molecules relative to one another within tissues. This method plays an important role in characterizing molecular signaling and the outcome of signal ablation when assessing mechanisms of drug action. Additionally, this approach can be used to characterize: the tumor microenvironment including vascular architecture and hypoxia, cellular proliferation, cell death as well as drug distribution. Medium to high-throughput images can be obtained via automation of slide imaging and analysis. Here we describe the basic principles of designing and implementing an mIHC protocol to create parameter tumor maps of a variety of specifically labeled markers.
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Ogawa S, Awaga Y, Takashima M, Hama A, Matsuda A, Takamatsu H. Antinociceptive effect of clinical analgesics in a nonhuman primate model of knee osteoarthritis. Eur J Pharmacol 2016; 786:179-85. [PMID: 27266666 DOI: 10.1016/j.ejphar.2016.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 05/27/2016] [Accepted: 06/03/2016] [Indexed: 12/19/2022]
Abstract
A number of potential analgesic pharmacotherapies developed in preclinical osteoarthritis animal models have failed clinical trials. A possible basis for the lack of translation of preclinical findings to clinical efficacy is the use of a preclinical species that is distinct from that of humans. The current study tested clinical analgesics in a nonhuman primate model of knee osteoarthritis. Following a medial meniscectomy, the animals developed a robust ipsilateral reduction in knee pressure threshold (hyperalgesia) and an ipsilateral reduction in weight bearing (resting pain). The serotonin-noradrenalin reuptake inhibitor duloxetine and opioid morphine increased ipsilateral pressure threshold and weight bearing. By contrast, the anticonvulsant pregabalin did not affect either pressure hyperalgesia or resting pain. The current findings in the nonhuman primate model of osteoarthritis parallel clinical findings, in that duloxetine and opioids are used in the management of osteoarthritis pain whereas pregabalin is not. The current findings also suggest the possible differentiation of pharmacotherapeutics in a nonhuman primate model, of distinguishing potential clinically useful analgesics for the management of osteoarthritic pain from those that are not.
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Feric NT, Radisic M. Maturing human pluripotent stem cell-derived cardiomyocytes in human engineered cardiac tissues. Adv Drug Deliv Rev 2016; 96:110-34. [PMID: 25956564 DOI: 10.1016/j.addr.2015.04.019] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/24/2015] [Accepted: 04/25/2015] [Indexed: 12/19/2022]
Abstract
Engineering functional human cardiac tissue that mimics the native adult morphological and functional phenotype has been a long held objective. In the last 5 years, the field of cardiac tissue engineering has transitioned from cardiac tissues derived from various animal species to the production of the first generation of human engineered cardiac tissues (hECTs), due to recent advances in human stem cell biology. Despite this progress, the hECTs generated to date remain immature relative to the native adult myocardium. In this review, we focus on the maturation challenge in the context of hECTs, the present state of the art, and future perspectives in terms of regenerative medicine, drug discovery, preclinical safety testing and pathophysiological studies.
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