1
|
Tseligka ED, Conzelmann S, Cambet Y, Schaer T, Negro F, Clément S. Identification of selective hepatitis delta virus ribozyme inhibitors by high-throughput screening of small molecule libraries. JHEP Rep 2022; 5:100652. [PMID: 36704052 PMCID: PMC9871325 DOI: 10.1016/j.jhepr.2022.100652] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Background & Aims Chronic hepatitis delta is the most severe form of chronic viral hepatitis and is associated with faster progression towards cirrhosis, liver decompensation, and hepatocellular carcinoma. Hepatitis delta virus (HDV)'s tight dependency on hepatitis B virus and the host cell machinery for its life cycle limits the development of direct-acting antivirals. Thus, we aimed to identify compounds that could block HDV replication by targeting its antigenomic ribozyme. Methods We generated stable Huh7 human hepatoma cells expressing a reporter gene (Gaussia luciferase) either downstream (Gluc-2xRz) or upstream (2xRz-Gluc) of two HDV antigenomic ribozyme sequences. We performed high-throughput screening of three small molecule libraries. The secreted luciferase was measured as a readout of ribozyme inhibition upon addition of the molecules. Each plate was considered valid when the Z factor was >0.4. Specificity and toxicity evaluations were performed for the hits with a Z-score >5 and half-maximal inhibitory concentration was calculated by performing a dose-response experiment. Results A dose-dependent induction of luciferase expression was detected in Gluc-2xRz-transfected cells incubated with the antisense morpholino, suggesting that the catalytic activity of the ribozyme cloned downstream of the reporter gene was efficiently inhibited. Among the 6,644 compounds screened, we identified four compounds that showed a specific inhibitory effect on the HDV antigenomic ribozyme in Gluc-2xRz cells, i.e. three histone deacetylase inhibitors and the purine analogue 8-azaguanine. The latter also significantly decreased HDV replication (by 40%) in differentiated HepaRG cells six days post infection. Conclusion Using a novel cell culture model, we identified four small molecules active against the antigenomic HDV ribozyme. These results may provide insights into the structural requirements of molecules designed for the potent and specific inhibition of HDV replication. Impact and implications Chronic hepatitis delta is the most severe form of chronic viral hepatitis and is associated with faster progression towards cirrhosis, liver decompensation, and the development of hepatocellular carcinoma. Despite the current development of several new compounds, there is still a need for efficient antiviral treatments specifically targeting hepatitis delta virus (HDV). This work describes a novel cell culture model that allows for the high-throughput screening of compounds able to inhibit HDV ribozymes. We identified four small molecules active against the antigenomic HDV ribozyme (the ribozyme involved in the early step of HDV replication), with the strongest activity shown by 8-azaguanine, a purine analogue. Our data may provide insights into the structural requirements of molecules designed to inhibit HDV.
Collapse
Affiliation(s)
- Eirini D. Tseligka
- Department of Pathology and Immunology, University of Geneva, Switzerland
| | | | - Yves Cambet
- Department of Pathology and Immunology, University of Geneva, Switzerland,READS Unit, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tifany Schaer
- Department of Pathology and Immunology, University of Geneva, Switzerland
| | - Francesco Negro
- Clinical Pathology, Geneva University Hospital, Geneva, Switzerland,Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland,Corresponding author. Address: Clinical Pathology, and Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland.
| | - Sophie Clément
- Department of Pathology and Immunology, University of Geneva, Switzerland
| |
Collapse
|
2
|
Namasivayam V, Stefan K, Pahnke J, Stefan SM. Binding mode analysis of ABCA7 for the prediction of novel Alzheimer's disease therapeutics. Comput Struct Biotechnol J 2021; 19:6490-6504. [PMID: 34976306 PMCID: PMC8666613 DOI: 10.1016/j.csbj.2021.11.035] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022] Open
Abstract
The adenosine-triphosphate-(ATP)-binding cassette (ABC) transporter ABCA7 is a genetic risk factor for Alzheimer's disease (AD). Defective ABCA7 promotes AD development and/or progression. Unfortunately, ABCA7 belongs to the group of 'under-studied' ABC transporters that cannot be addressed by small-molecules. However, such small-molecules would allow for the exploration of ABCA7 as pharmacological target for the development of new AD diagnostics and therapeutics. Pan-ABC transporter modulators inherit the potential to explore under-studied ABC transporters as novel pharmacological targets by potentially binding to the proposed 'multitarget binding site'. Using the recently reported cryogenic-electron microscopy (cryo-EM) structures of ABCA1 and ABCA4, a homology model of ABCA7 has been generated. A set of novel, diverse, and potent pan-ABC transporter inhibitors has been docked to this ABCA7 homology model for the discovery of the multitarget binding site. Subsequently, application of pharmacophore modelling identified the essential pharmacophore features of these compounds that may support the rational drug design of innovative diagnostics and therapeutics against AD.
Collapse
Key Words
- ABC transporter (ABCA1, ABCA4, ABCA7)
- ABC, ATP-binding cassette
- AD, Alzheimer’s disease
- APP, amyloid precursor protein
- ATP, Adenosine-triphosphate
- Alzheimer’s disease (AD)
- BBB, blood-brain barrier
- BODIPY-cholesterol, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene-cholesterol
- ECD, extracellular domain
- EH, extracellular helix
- GSH, reduced glutathione
- HTS, high-throughput screening
- IC, intracellular helix
- MOE, Molecular Operating Environment
- MSD, membrane spanning domain
- Multitarget modulation (PANABC)
- NBD, nucleotide binding domain
- NBD-cholesterol, 7-nitro-2-1,3-benzoxadiazol-4-yl-cholesterol
- PDB, protein data bank
- PET tracer (PETABC)
- PET, positron emission tomography
- PLIF, protein ligand interaction
- PSO, particle swarm optimization
- Polypharmacology
- R-domain/region, regulatory domain/region
- RMSD, root mean square distance
- Rational drug design and development
- SNP, single-nucleotide polymorphism
- TM, transmembrane helix
- cryo-EM, cryogenic-electron microscopy
Collapse
Affiliation(s)
- Vigneshwaran Namasivayam
- Department of Pharmaceutical and Cellbiological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Katja Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
| | - Jens Pahnke
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
- LIED, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Department of Pharmacology, Faculty of Medicine, University of Latvia, Jelgavas iela 1, 1004 Rīga, Latvia
| | - Sven Marcel Stefan
- Department of Pathology, Section of Neuropathology, Translational Neurodegeneration Research and Neuropathology Lab (www.pahnkelab.eu), University of Oslo and Oslo University Hospital, Sognsvannsveien 20, 0372 Oslo, Norway
| |
Collapse
|
3
|
Sun J, Zhong H, Wang K, Li N, Chen L. Gains from no real PAINS: Where 'Fair Trial Strategy' stands in the development of multi-target ligands. Acta Pharm Sin B 2021; 11:3417-3432. [PMID: 34900527 PMCID: PMC8642439 DOI: 10.1016/j.apsb.2021.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/24/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
Compounds that selectively modulate multiple targets can provide clinical benefits and are an alternative to traditional highly selective agents for unique targets. High-throughput screening (HTS) for multitarget-directed ligands (MTDLs) using approved drugs, and fragment-based drug design has become a regular strategy to achieve an ideal multitarget combination. However, the unexpected presence of pan-assay interference compounds (PAINS) suspects in the development of MTDLs frequently results in nonspecific interactions or other undesirable effects leading to artefacts or false-positive data of biological assays. Publicly available filters can help to identify PAINS suspects; however, these filters cannot comprehensively conclude whether these suspects are "bad" or innocent. Additionally, these in silico approaches may inappropriately label a ligand as PAINS. More than 80% of the initial hits can be identified as PAINS by the filters if appropriate biochemical tests are not used resulting in false positive data that are unacceptable for medicinal chemists in manuscript peer review and future studies. Therefore, extensive offline experiments should be used after online filtering to discriminate "bad" PAINS and avoid incorrect evaluation of good scaffolds. We suggest that the use of "Fair Trial Strategy" to identify interesting molecules in PAINS suspects to provide certain structure‒function insight in MTDL development.
Collapse
Key Words
- AD, Alzheimer disease
- ALARM NMR, a La assay to detect reactive molecules by nuclear magnetic resonance
- Biochemical experiment
- CADD, computer-aided drug design technology
- CoA, coenzyme A
- EGFR, epidermal growth factor receptor
- Fair trial strategy
- GSH, glutathione
- HER2, human epidermal growth factor receptor 2
- HTS, high-throughput screening
- In silico filtering
- LC−MS, liquid chromatography−mass spectrometry
- MTDLs, multitarget-directed ligands
- Multitarget-directed ligands
- PAINS suspects
- PAINS, pan-assay interference compounds
- QSAR, quantitative structure–activity relationship
- ROS, radicals and oxygen reactive species
Collapse
Affiliation(s)
- Jianbo Sun
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Zhong
- Department of Pharmacology of Traditional Chinese Medicine, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kun Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Na Li
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li Chen
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| |
Collapse
|
4
|
Liu Y, Liu Z, Wang K. The Ca 2+-activated chloride channel ANO1/TMEM16A: An emerging therapeutic target for epithelium-originated diseases? Acta Pharm Sin B 2021; 11:1412-1433. [PMID: 34221860 PMCID: PMC8245819 DOI: 10.1016/j.apsb.2020.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/30/2020] [Revised: 08/19/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Anoctamin 1 (ANO1) or TMEM16A gene encodes a member of Ca2+ activated Cl– channels (CaCCs) that are critical for physiological functions, such as epithelial secretion, smooth muscle contraction and sensory signal transduction. The attraction and interest in ANO1/TMEM16A arise from a decade long investigations that abnormal expression or dysfunction of ANO1 is involved in many pathological phenotypes and diseases, including asthma, neuropathic pain, hypertension and cancer. However, the lack of specific modulators of ANO1 has impeded the efforts to validate ANO1 as a therapeutic target. This review focuses on the recent progress made in understanding of the pathophysiological functions of CaCC ANO1 and the current modulators used as pharmacological tools, hopefully illustrating a broad spectrum of ANO1 channelopathy and a path forward for this target validation.
Collapse
Key Words
- ANO1
- ANO1, anoctamin-1
- ASM, airway smooth muscle
- Ang II, angiotensin II
- BBB, blood–brain barrier
- CAMK, Ca2+/calmodulin-dependent protein kinase
- CF, cystic fibrosis
- CFTR, cystic fibrosis transmembrane conductance regulator
- Ca2+-activated Cl– channels (CaCCs)
- CaCCinh-A01
- CaCCs, Ca2+ activated chloride channels
- Cancer
- Cystic fibrosis
- DRG, dorsal root ganglion
- Drug target
- EGFR, epidermal growth factor receptor
- ENaC, epithelial sodium channels
- ER, endoplasmic reticulum
- ESCC, esophageal squamous cell carcinoma
- FRT, fisher rat thyroid
- GI, gastrointestinal
- GIST, gastrointestinal stromal tumor
- GPCR, G-protein coupled receptor
- HNSCC, head and neck squamous cell carcinoma
- HTS, high-throughput screening
- ICC, interstitial cells of Cajal
- IPAH, idiopathic pulmonary arterial hypertension
- MAPK, mitogen-activated protein kinase
- NF-κB, nuclear factor κB
- PAH, pulmonary arterial hypertension
- PAR2, protease activated receptor 2
- PASMC, pulmonary artery smooth muscle cells
- PIP2, phosphatidylinositol 4,5-bisphosphate
- PKD, polycystic kidney disease
- T16Ainh-A01
- TGF-β, transforming growth factor-β
- TMEM16A
- VGCC, voltage gated calcium channel
- VRAC, volume regulated anion channel
- VSMC, vascular smooth muscle cells
- YFP, yellow fluorescent protein
Collapse
Affiliation(s)
- Yani Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drugs, Qingdao University, Qingdao 266021, China
| | - Zongtao Liu
- Department of Clinical Laboratory, Qingdao Third People's Hospital, Qingdao 266041, China
| | - KeWei Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University Medical College, Qingdao 266073, China
- Institute of Innovative Drugs, Qingdao University, Qingdao 266021, China
- Corresponding authors.
| |
Collapse
|
5
|
Yang J, König A, Park S, Jo E, Sung PS, Yoon SK, Zusinaite E, Kainov D, Shum D, Windisch MP. A new high-content screening assay of the entire hepatitis B virus life cycle identifies novel antivirals. JHEP Rep 2021; 3:100296. [PMID: 34222850 PMCID: PMC8243515 DOI: 10.1016/j.jhepr.2021.100296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Background & Aims Chronic hepatitis B is an incurable disease. Addressing the unmet medical need for therapies has been hampered by a lack of suitable cell culture models to investigate the HBV life cycle in a single experimental setup. We sought to develop a platform suitable to investigate all aspects of the entire HBV life cycle. Methods HepG2-NTCPsec+ cells were inoculated with HBV. Supernatants of infected cells were transferred to naïve cells. Inhibition of infection was determined in primary and secondary infected cells by high-content imaging of viral and cellular factors. Novel antivirals were triaged in cells infected with cell culture- or patient-derived HBV and in stably virus replicating cells. HBV internalisation and target-based receptor binding assays were conducted. Results We developed an HBV platform, screened 2,102 drugs and bioactives, and identified 3 early and 38 late novel HBV life cycle inhibitors using infectious HBV genotype D. Two early inhibitors, pranlukast (EC50 4.3 μM; 50% cytotoxic concentration [CC50] >50 μM) and cytochalasin D (EC50 0.07 μM; CC50 >50 μM), and 2 late inhibitors, fludarabine (EC50 0.1 μM; CC50 13.4 μM) and dexmedetomidine (EC50 6.2 μM; CC50 >50 μM), were further investigated. Pranlukast inhibited HBV preS1 binding, whereas cytochalasin D prevented the internalisation of HBV. Fludarabine inhibited the secretion of HBV progeny DNA, whereas dexmedetomidine interfered with the infectivity of HBV progeny. Patient-derived HBV genotype C was efficiently inhibited by fludarabine (EC50 0.08 μM) and dexmedetomidine (EC50 8.7 μM). Conclusions The newly developed high-content assay is suitable to screen large-scale drug libraries, enables monitoring of the entire HBV life cycle, and discriminates between inhibition of early and late viral life cycle events. Lay summary HBV infection is an incurable, chronic disease with few available treatments. Addressing this unmet medical need has been hampered by a lack of suitable cell culture models to study the entire viral life cycle in a single experimental setup. We developed an image-based approach suitable to screen large numbers of drugs, using a cell line that can be infected by HBV and produces large amounts of virus particles. By transferring viral supernatants from these infected cells to uninfected target cells, we could monitor the entire viral life cycle. We used this system to screen drug libraries and identified novel anti-HBV inhibitors that potently inhibit HBV in various phases of its life cycle. This assay will be an important new tool to study the HBV life cycle and accelerate the development of novel therapeutic strategies. We developed a high-content screening assay suitable to monitor the entire HBV life cycle and eligible to discriminate between early and late viral life cycle inhibition. We screened FDA-approved drugs and bioactives. We confirmed antiviral activity in primary and secondary assays, using stably virus replicating cells and cell culture- and patient-derived HBV. Novel HBV inhibitors prevent receptor binding, virus internalisation, replication, or egress of viral progeny.
Collapse
Key Words
- %CV, percent coefficient of variation
- %Imax, percent maximum inhibition
- CC50, 50% cytotoxic concentration
- CHB, chronic hepatitis B
- CpAM, core protein allosteric modifiers
- DRC, dose–response curve
- Entry
- FDA, Food and Drug Administration
- FDA-approved drugs
- GEq, genome equivalents
- HBV
- HBVpt, patient-derived HBV
- HCC, hepatocellular carcinoma
- HCS, high content screening
- HID, N-hydroxyisoquinolinedione
- HLCs, hepatocyte-like cells
- HTS, high-throughput screening
- HepG2-NTCP
- High-throughput screening
- IFA, immunofluorescence analysis
- IFNα, interferon alpha
- IFNλ, interferon lambda
- LHB, HBV large surface protein
- LMV, lamivudine
- MoA, mechanism of action
- MyrB, myrcludex B
- NTCP, sodium taurocholate cotransporting polypeptide
- PEG, polyethylene glycol
- PF-rcDNA, protein-free relaxed circular DNA
- Patient-derived HBV
- Replication
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SOP, standard operation procedure
- Small-molecule inhibitors
- Supernatant transfer
- TDF, tenofovir disoproxil fumarate
- TI, therapeutic index
- Virion secretion
- cccDNA, covalently closed circular DNA
- dpi, days post-infection
- iPSCs, induced pluripotent stem cells
- p1, passage 1
- p2, passage 2
- pgRNA, pregenomic RNA
Collapse
Affiliation(s)
- Jaewon Yang
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Alexander König
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Soonju Park
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Eunji Jo
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Pil Soo Sung
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Catholic University Liver Research Center, The Catholic University of Korea, Seoul, South Korea
| | - Seung Kew Yoon
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Catholic University Liver Research Center, The Catholic University of Korea, Seoul, South Korea
| | - Eva Zusinaite
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Denis Kainov
- Institute of Technology, University of Tartu, Tartu, Estonia.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - David Shum
- Screening Discovery Platform, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Marc Peter Windisch
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea.,Division of Bio-Medical Science and Technology, University of Science and Technology, Daejeon, South Korea
| |
Collapse
|
6
|
Song Y, Zhao M, Wu Y, Yu B, Liu HM. A multifunctional cross-validation high-throughput screening protocol enabling the discovery of new SHP2 inhibitors. Acta Pharm Sin B 2021; 11:750-762. [PMID: 33777680 PMCID: PMC7982506 DOI: 10.1016/j.apsb.2020.10.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 05/26/2020] [Revised: 08/01/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
The protein tyrosine phosphatase Src homology phosphotyrosyl phosphatase 2 (SHP2) is implicated in various cancers, and targeting SHP2 has become a promising therapeutic approach. We herein described a robust cross-validation high-throughput screening protocol that combined the fluorescence-based enzyme assay and the conformation-dependent thermal shift assay for the discovery of SHP2 inhibitors. The established method can effectively exclude the false positive SHP2 inhibitors with fluorescence interference and was also successfully employed to identify new protein tyrosine phosphatase domain of SHP2 (SHP2-PTP) and allosteric inhibitors. Of note, this protocol showed potential for identifying SHP2 inhibitors against cancer-associated SHP2 mutation SHP2-E76A. After initial screening of our in-house compound library (∼2300 compounds), we identified 4 new SHP2-PTP inhibitors (0.17% hit rate) and 28 novel allosteric SHP2 inhibitors (1.22% hit rate), of which SYK-85 and WS-635 effectively inhibited SHP2-PTP (SYK-85: IC50 = 0.32 μmol/L; WS-635: IC50 = 4.13 μmol/L) and thus represent novel scaffolds for designing new SHP2-PTP inhibitors. TK-147, an allosteric inhibitor, inhibited SHP2 potently (IC50 = 0.25 μmol/L). In structure, TK-147 could be regarded as a bioisostere of the well characterized SHP2 inhibitor SHP-099, highlighting the essential structural elements for allosteric inhibition of SHP2. The principle underlying the cross-validation protocol is potentially feasible to identify allosteric inhibitors or those inactivating mutants of other proteins.
Collapse
Key Words
- AKT, protein kinase B
- ALK, anaplastic lymphoma kinase
- AML, acute myelogenous leukemia
- Allosteric inhibitors
- BTLA, B and T lymphocyte attenuator
- Bis-tris, bis-(2-hydroxyethyl)amino-tris(hydroxymethyl)methane
- DTT, dithiothreitol
- DiFMU, 6,8-difluoro-4-methylumbelliferyl hydroxid
- DiFMUP, 6,8-difluoro-4-methylumbelliferyl phosphate
- Enzyme assay
- FI, fluorescence intensity
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HTS, high-throughput screening
- High-throughput screening
- IC50, half maximal inhibitory concentration
- JAK, janus kinase
- JMML, juvenile myelomonocytic leukaemia
- LB, lysogeny broth
- LOC, ligand only control
- LS, LEOPARD syndrome
- MAPK, mitogen-activated protein kinase
- MEK, extracellular regulated protein kinase kinases
- NPC, no protein control
- NS, Noonan syndrome
- OD, optical density
- PD-1, programmed death 1
- PI3K, phosphatidylinositol 3 kinase
- PMSF, phenylmethanesulfonyl fluoride
- PTP, protein tyrosine phosphatase
- R2, coefficient of determination
- RAS, rat sarcoma
- S/B, signal over background
- SD, standard deviation
- SDS-PAGE, sodium dodecyl sulphate polyacyrlamide gel electrophoresis
- SH2, Src homology 2
- SHP2
- SHP2, Src homology phosphotyrosyl phosphatase 2
- SHP2-PTP, protein tyrosine phosphatase domain of Src homology phosphotyrosyl phosphatase 2
- SHP2-WT, wild type Src homology phosphotyrosyl phosphatase 2
- STAT, signal transducer and activator of transcription
- Thermal shift assay
- Tm, melting temperature
- p-IRS1, phosphorylated insulin receptor substrate 1
- ΔTm, melting temperature change
Collapse
Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Min Zhao
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
7
|
Jiang T, Wang G, Liu Y, Feng L, Wang M, Liu J, Chen Y, Ouyang L. Development of small-molecule tropomyosin receptor kinase (TRK) inhibitors for NTRK fusion cancers. Acta Pharm Sin B 2021; 11:355-372. [PMID: 33643817 PMCID: PMC7893124 DOI: 10.1016/j.apsb.2020.05.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 03/04/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Tropomyosin receptor kinase A, B and C (TRKA, TRKB and TRKC), which are well-known members of the cell surface receptor tyrosine kinase (RTK) family, are encoded by the neurotrophic receptor tyrosine kinase 1, 2 and 3 (NTRK1, NTRK2 and NTRK3) genes, respectively. TRKs can regulate cell proliferation, differentiation and even apoptosis through the RAS/MAPKs, PI3K/AKT and PLCγ pathways. Gene fusions involving NTRK act as oncogenic drivers of a broad diversity of adult and pediatric tumors, and TRKs have become promising antitumor targets. Therefore, achieving a comprehensive understanding of TRKs and relevant TRK inhibitors should be urgently pursued for the further development of novel TRK inhibitors for potential clinical applications. This review focuses on summarizing the biological functions of TRKs and NTRK fusion proteins, the development of small-molecule TRK inhibitors with different chemotypes and their activity and selectivity, and the potential therapeutic applications of these inhibitors for future cancer drug discovery efforts.
Collapse
Key Words
- AFAP1, actin filament-associated protein 1
- AML, acute myeloid leukemia
- ARHGEF2, Rho/Rac guanine nucleotide exchange factor 2
- BCAN, brevican
- BDNF, brain-derived neurotrophic factor
- BTBD1, BTB (POZ) domain containing 1
- CDK-2, cyclin-dependent kinase 2
- CR, complete response
- CRC, colorectal cancer
- CTCs, sequencing of circulating tumor cells
- DFG, Asp-Phe-Gly
- DOR, durable objective responses
- ETV6, ETS translocation variant 6
- EWG, electron-withdrawing group
- FDA, U.S. Food and Drug Administration
- FISH, fluorescence in situ hybridization
- GBM, glioblastoma multiforme
- HNSCC, head and neck squamous cell carcinoma
- HTS, high-throughput screening
- ICC, intrahepatic cholangiocarcinoma
- IG-C2, Ig-like C2 type I
- LMNA, lamin A/C
- MASC, mammary analogue secretory carcinoma
- MPRIP, myosin phosphatase Rho interacting protein
- NACC2, NACC family member 2
- NCCN, National Comprehensive Cancer Network
- NFASC, neurofascin
- NGF, nerve growth factor
- NGS, next-generation sequencing of tumor tissue
- NSCLC, non-small cell lung cancer
- NT3, neurotrophin-3
- NTRK fusion cancer
- NTRK, neurotrophic receptor tyrosine kinase
- Neurotrophic receptor tyrosine kinase fusions
- OAK, osteoarthritis of the knee
- ORR, overall response rate
- PAN3, poly(A) nuclease 3
- PPL, periplakin
- PROTAC proteolysis targeting chimera, QKI
- RABGTPase activating protein 1-like, RFWD2
- RTK, receptor tyrosine kinase
- SAR, structure–activity relationship
- SBC, secretory breast carcinoma
- SCYL3, SCY1 like pseudokinase 3
- SQSTM1, sequestosome 1
- Small-molecule inhibitor
- TFG, TRK-fused gene
- TP53, tumor protein P53
- TPM3, tropomyosin 3
- TPR, translocated promoter region
- TRIM24, tripartite motif containing 24
- TRK, tropomyosin receptor kinase
- Tropomyosin receptor kinase
- VCL, vinculin
- VEGFR2, vascular endothelial growth factor receptor 2
- quaking I protein, RABGAP1L
- ring finger and WD repeat domain 2, E3 ubiquitin protein ligase
Collapse
Affiliation(s)
- Tingting Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Meng Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| |
Collapse
|
8
|
Contreras F, Nutschel C, Beust L, Davari MD, Gohlke H, Schwaneberg U. Can constraint network analysis guide the identification phase of KnowVolution? A case study on improved thermostability of an endo-β-glucanase. Comput Struct Biotechnol J 2020; 19:743-751. [PMID: 33552446 PMCID: PMC7822948 DOI: 10.1016/j.csbj.2020.12.034] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulases are industrially important enzymes, e.g., in the production of bioethanol, in pulp and paper industry, feedstock, and textile. Thermostability is often a prerequisite for high process stability and improving thermostability without affecting specific activities at lower temperatures is challenging and often time-consuming. Protein engineering strategies that combine experimental and computational are emerging in order to reduce experimental screening efforts and speed up enzyme engineering campaigns. Constraint Network Analysis (CNA) is a promising computational method that identifies beneficial positions in enzymes to improve thermostability. In this study, we compare CNA and directed evolution in the identification of beneficial positions in order to evaluate the potential of CNA in protein engineering campaigns (e.g., in the identification phase of KnowVolution). We engineered the industrially relevant endoglucanase EGLII from Penicillium verruculosum towards increased thermostability. From the CNA approach, six variants were obtained with an up to 2-fold improvement in thermostability. The overall experimental burden was reduced to 40% utilizing the CNA method in comparison to directed evolution. On a variant level, the success rate was similar for both strategies, with 0.27% and 0.18% improved variants in the epPCR and CNA-guided library, respectively. In essence, CNA is an effective method for identification of positions that improve thermostability.
Collapse
Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Christina Nutschel
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Laura Beust
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| |
Collapse
|
9
|
Xie C, Slagboom J, Albulescu LO, Somsen GW, Vonk FJ, Casewell NR, Kool J. Neutralising effects of small molecule toxin inhibitors on nanofractionated coagulopathic Crotalinae snake venoms. Acta Pharm Sin B 2020; 10:1835-1845. [PMID: 33163338 PMCID: PMC7606088 DOI: 10.1016/j.apsb.2020.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/29/2022] Open
Abstract
Repurposing small molecule drugs and drug candidates is considered as a promising approach to revolutionise the treatment of snakebite envenoming. In this study, we investigated the inhibiting effects of the small molecules varespladib (nonspecific phospholipase A2 inhibitor), marimastat (broad spectrum matrix metalloprotease inhibitor) and dimercaprol (metal ion chelator) against coagulopathic toxins found in Crotalinae (pit vipers) snake venoms. Venoms from Bothrops asper, Bothrops jararaca, Calloselasma rhodostoma and Deinagkistrodon acutus were separated by liquid chromatography, followed by nanofractionation and mass spectrometry identification undertaken in parallel. Nanofractions of the venom toxins were then subjected to a high-throughput coagulation assay in the presence of different concentrations of the small molecules under study. Anticoagulant venom toxins were mostly identified as phospholipases A2, while procoagulant venom activities were mainly associated with snake venom metalloproteinases and snake venom serine proteases. Varespladib was found to effectively inhibit most anticoagulant venom effects, and also showed some inhibition against procoagulant toxins. Contrastingly, marimastat and dimercaprol were both effective inhibitors of procoagulant venom activities but showed little inhibitory capability against anticoagulant toxins. The information obtained from this study aids our understanding of the mechanisms of action of toxin inhibitor drug candidates, and highlights their potential as future snakebite treatments.
Collapse
Key Words
- ACN, acetonitrile
- Antivenom
- CTL, C-type lectins
- Chelators
- DMSO, dimethyl sulfoxide
- Dimercaprol
- FA, formic acid
- HTS, high-throughput screening
- LC, liquid chromatography
- MS, mass spectrometry
- Marimastat
- NOI, no observed inhibition
- Nanofractionation
- PBS, phosphate buffered saline
- PLA2, phospholipase A2
- PN, partly neutralised at 20 μmol/L inhibitor concentrations
- SVMP, snake venom metalloproteinase
- SVSP, snake venom serine protease
- Snakebite
- TIC, total ion current
- Varespladib
- WHO, World Health Organization
- XIC, extracted ion current
Collapse
Affiliation(s)
- Chunfang Xie
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam 1098 XH, The Netherlands
| | - Julien Slagboom
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam 1098 XH, The Netherlands
| | - Laura-Oana Albulescu
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Govert W. Somsen
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam 1098 XH, The Netherlands
| | - Freek J. Vonk
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam 1098 XH, The Netherlands
- Naturalis Biodiversity Center, Leiden 2333 CR, The Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam 1098 XH, The Netherlands
| |
Collapse
|
10
|
Zhu Y, Yang L, Xu J, Yang X, Luan P, Cui Q, Zhang P, Wang F, Li R, Ding X, Jiang L, Lin G, Zhang J. Discovery of the anti-angiogenesis effect of eltrombopag in breast cancer through targeting of HuR protein. Acta Pharm Sin B 2020; 10:1414-25. [PMID: 32963940 DOI: 10.1016/j.apsb.2020.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 12/24/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 01/26/2023] Open
Abstract
HuR (human antigen R), an mRNA-binding protein responsible for poor prognosis in nearly all kinds of malignancies, is a potential anti-tumor target for drug development. While screening HuR inhibitors with a fluorescence polarization (FP) based high-throughput screening (HTS) system, the clinically used drug eltrombopag was identified. Activity of eltrombopag on molecular level was verified with FP, electrophoretic mobility shift assay (EMSA), simulation docking and surface plasmon resonance (SPR). Further, we showed that eltrombopag inhibited in vitro cell proliferation of multiple cancer cell lines and macrophages, and the in vivo anti-tumor activity was also demonstrated in a 4T1 tumor-bearing mouse model. The in vivo data showed that eltrombopag was efficient in reducing microvessels in tumor tissues. We then confirmed the HuR-dependent anti-angiogenesis effect of eltrombopag in 4T1 cells and RAW264.7 macrophages with qRT-PCR, HuR-overexpression and HuR-silencing assays, RNA stability assays, RNA immunoprecipitation and luciferase assays. Finally, we analyzed the in vitro anti-angiogenesis effect of eltrombopag on human umbilical vein endothelial cells (HUVECs) mediated by macrophages with cell scratch assay and in vitro Matrigel angiogenesis assay. With these data, we revealed the HuR-dependent anti-angiogenesis effect of eltrombopag in breast tumor, suggesting that the existing drug eltrombopag may be used as an anti-cancer drug.
Collapse
Key Words
- ARE, AU-rich element
- Angiogenesis
- Anti-tumor
- ELB, eltrombopag
- ELISA, enzyme linked immune sorbent assay
- EMSA, electrophoretic mobility shift assay
- Eltrombopag
- FP, fluorescence polarization
- HTS, high-throughput screening
- HUVEC, human umbilical vein endothelial cell
- HuR
- HuR, human antigen R
- IHC, immunohistochemistry
- RIP, RNA immunoprecipitation
- SPR, surface plasmon resonance
- mRNAs stability
- qRT-PCR, quantitative real-time PCR
Collapse
|
11
|
Trevarton A, Zhou Y, Yang D, Rewcastle GW, Flanagan JU, Braithwaite A, Shepherd PR, Print CG, Wang MW, Lasham A. Orthogonal assays for the identification of inhibitors of the single-stranded nucleic acid binding protein YB-1. Acta Pharm Sin B 2019; 9:997-1007. [PMID: 31649849 DOI: 10.1016/j.apsb.2018.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/03/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 02/01/2023] Open
Abstract
We have previously shown that high expression of the nucleic acid binding factor YB-1 is strongly associated with poor prognosis in a variety of cancer types. The 3-dimensional protein structure of YB-1 has yet to be determined and its role in transcriptional regulation remains elusive. Drug targeting of transcription factors is often thought to be difficult and there are very few published high-throughput screening approaches. YB-1 predominantly binds to single-stranded nucleic acids, adding further difficulty to drug discovery. Therefore, we have developed two novel screening assays to detect compounds that interfere with the transcriptional activation properties of YB-1, both of which may be generalizable to screen for inhibitors of other nucleic acid binding molecules. The first approach is a cell-based luciferase reporter gene assay that measures the level of activation of a fragment of the E2F1 promoter by YB-1. The second approach is a novel application of the AlphaScreen system, to detect interference of YB-1 interaction with a single-stranded DNA binding site. These complementary assays examine YB-1 binding to two discrete nucleic acid sequences using two different luminescent signal outputs and were employed sequentially to screen 7360 small molecule compounds leading to the identification of three putative YB-1 inhibitors.
Collapse
Key Words
- AlphaScreen
- CSD, cold shock domain
- CTD, C-terminal domain
- Cancer
- DMSO, dimethylsulfoxide
- E2F1, E2F transcription factor 1
- EGR1, early growth response 1
- HTS, high-throughput screening
- Luciferase
- NTD, N-terminal domain
- Single-stranded DNA
- Transcription factor
- YB-1
- YB-1, Y-box binding protein-1
- YBX1, Y-box binding protein gene 1
- cDNA, complementary DNA
- dsDNA, double-stranded DNA
- shRNA, short-hairpin RNA
- siRNA, small-interfering RNA
- ssDNA, single-stranded DNA
Collapse
|
12
|
Scheepstra M, Hekking KFW, van Hijfte L, Folmer RHA. Bivalent Ligands for Protein Degradation in Drug Discovery. Comput Struct Biotechnol J 2019; 17:160-176. [PMID: 30788082 PMCID: PMC6369262 DOI: 10.1016/j.csbj.2019.01.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [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: 11/14/2018] [Revised: 01/16/2019] [Accepted: 01/19/2019] [Indexed: 01/19/2023] Open
Abstract
Targeting the "undruggable" proteome remains one of the big challenges in drug discovery. Recent innovations in the field of targeted protein degradation and manipulation of the ubiquitin-proteasome system open up new therapeutic approaches for disorders that cannot be targeted with conventional inhibitor paradigms. Proteolysis targeting chimeras (PROTACs) are bivalent ligands in which a compound that binds to the protein target of interest is connected to a second molecule that binds an E3 ligase via a linker. The E3 protein is usually either Cereblon or Von Hippel-Lindau. Several examples of selective PROTAC molecules with potent effect in cells and in vivo models have been reported. The degradation of specific proteins via these bivalent molecules is already allowing for the study of biochemical pathways and cell biology with more specificity than was possible with inhibitor compounds. In this review, we provide a comprehensive overview of recent developments in the field of small molecule mediated protein degradation, including transcription factors, kinases and nuclear receptors. We discuss the potential benefits of protein degradation over inhibition as well as the challenges that need to be overcome.
Collapse
Key Words
- ABCB1, ATP-binding cassette sub-family B member 1
- AD, Alzheimer's disease
- AHR, aryl hydrogen receptor
- ALK, anaplastic lymphoma kinase
- Aβ, amyloid-β
- BET, bromodomain and extra-terminal
- BTK, Bruton's tyrosine kinase
- Bcl6, B-cell lymphoma 6
- Bivalent ligand
- Brd4, bromodomain 4
- CDK9, cyclin dependent kinase 9
- CK2, Casein kinase 2
- CLIPTAC, click-formed proteolysis targeting chimera
- CRBN, Cereblon
- Chimera
- DC50, the compound concentration that results in 50% target protein degradation
- DHODH, Dihydroorotate dehydrogenase
- Degrader
- ERK1, extracellular signal-regulated kinase 1
- ERRα, estrogen-related receptor alpha
- ERα, estrogen receptor alpha
- EZH2, enhancer of zeste homolog 2
- FLT3, FMS-like tyrosine kinase-3
- FRS2, fibroblast growth factor receptor substrate 2
- GCN5, general control nonderepressible 5
- GPCR, G-protein coupled receptor
- GST, glutathione S-transferase
- HDAC, histone deacetylase
- HTS, high-throughput screening
- MDM2, mouse double-minute 2 homolog
- MetAP-2, methionine aminopeptidase-2
- PCAF, P300/CBP-associated factor
- PEG, polyethylene glycol
- PI3K, phosphatidylinositol-3-kinase
- PLK-1, polo-like kinase 1
- POI, protein of interest
- PROTAC
- PROTAC, proteolysis targeting chimeras
- Proteasome
- Protein degradation
- RAR, retinoic acid receptor
- RIPK2, receptor-interacting serine/threonine-protein kinase 2
- RTK, receptor tyrosine kinase
- SARM, selective androgen receptor modulator
- SNIPER, specific and non-genetic IAP-dependent protein eraser
- TBK1, TANK-Binding kinase 1
- TRIM24, tripartite motif-containing 24 (also known as TIF1α)
- VHL, Von Hippel-Lindau
- cIAP1, cellular inhibitor of apoptosis protein
Collapse
Affiliation(s)
| | - Koen F W Hekking
- Mercachem BV, Kerkenbos 1013, 6546 BB, Nijmegen, the Netherlands
| | - Luc van Hijfte
- Mercachem BV, Kerkenbos 1013, 6546 BB, Nijmegen, the Netherlands
| | | |
Collapse
|
13
|
Yuliantie E, Dai X, Yang D, Crack PJ, Wang MW. High-throughput screening for small molecule inhibitors of the type-I interferon signaling pathway. Acta Pharm Sin B 2018; 8:889-899. [PMID: 30505658 PMCID: PMC6251811 DOI: 10.1016/j.apsb.2018.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 03/28/2018] [Revised: 05/26/2018] [Accepted: 06/21/2018] [Indexed: 01/05/2023] Open
Abstract
Interferons (IFNs) are cytokines with fundamental roles in resistance to infections, cancer and other diseases. Type-I IFNs, interferon α (IFN-α) and interferon β (IFN-β), act through a shared receptor complex (IFNAR) comprised of IFNAR1 and IFNAR2 subunits. Binding of type-I IFN to IFNAR1 will robustly activate Janus activated kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway. Aberrant activation of the type-I IFN response results in a spectrum of disorders called interferonopathies. The purpose of this research is to develop an assay for high-throughput screening (HTS) of small molecule inhibitors of the type-I IFN signaling pathway. Inhibition of type-I IFN signaling can be beneficial in terms of therapeutic use and understanding the underlying mechanism of action. We report here a HTS campaign with the secreted embryonic alkaline phosphatase (SEAP) reporter gene assay against 32,000 compounds which yielded 25 confirmed hits. These compounds were subsequently characterized for their cytotoxicity, effects on STAT phosphorylation and activities in IFN regulatory factor (IRF) transcription.
Collapse
Key Words
- CV, coefficient of variation
- DMEM, Dulbecco׳s modified Eagle׳s medium
- DMSO, dimethyl sulfoxide
- FRET, fluorescence resonance energy transfer
- HEK, human embryonic kidney
- HTS, high-throughput screening
- High-throughput screening
- IFN regulatory factor
- IFN, interferon
- IFNAR, IFN alpha receptor
- IRF, IFN regulatory factor
- ISGF3, IFN-stimulated gene factor 3
- ISRE, IFN-stimulated response element
- Inhibitor
- Interferon α receptor
- JAK, Janus activated kinase
- JAK-STAT
- S/B, signal to background ratio
- SEAP, secreted embryonic alkaline phosphatase
- STAT, signal transducer and activator of transcription
- Secreted embryonic alkaline phosphatase
- TYK, tyrosine kinase
- cDNA, complementary DNA
- pSTAT, phosphorylated STAT
Collapse
|
14
|
Watanabe Y, Kawaguchi K, Saito S, Okabe T, Yonesu K, Egashira S, Kameya M, Morita M, Kashiwayama Y, Imanaka T. An HTRF based high-throughput screening for discovering chemical compounds that inhibit the interaction between Trypanosoma brucei Pex5p and Pex14p. Biochem Biophys Rep 2016; 6:260-265. [PMID: 28955883 PMCID: PMC5600434 DOI: 10.1016/j.bbrep.2016.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/14/2016] [Revised: 04/12/2016] [Accepted: 05/06/2016] [Indexed: 11/16/2022] Open
Abstract
The glycosome, a peroxisome-related organelle, is essential for the growth and survival of trypanosomatid protozoa. In glycosome biogenesis, Pex5p recognizes newly synthesized glycosomal matrix proteins via peroxisome-targeting signal type-1 (PTS-1) and transports them into glycosomes through an interaction with Pex14p, a component of the matrix protein import machinery on the glycosomal membrane. Knockdown of the PEX5 or PEX14 with RNAi has been shown to inhibit the growth of Trypanosoma brucei. Thus, compounds that inhibit the interaction of TbPex5p–TbPex14p are expected to become lead compounds in the development of anti-trypanosomal drugs. Here, we report a homogenous time-resolved fluorescence (HTRF) assay for the screening of compounds that inhibit the TbPex5p–TbPex14p interaction. The binding of GST-TbPex14p and TbPex5p-His with or without additional compounds was evaluated by measuring the energy transfer of the HTRF pair, using a terbium-labeled anti GST antibody as the donor and an FITC-labeled anti His antibody as the acceptor. The assay was performed in a 384-well plate platform and exhibits a Z’-factor of 0.85–0.91, while the coefficiency of variation is 1.1–7.7%, suggesting it can be readily adapted to a high-throughput format for the automated screening of chemical libraries. We screened 20,800 compounds and found 11 compounds that inhibited energy transfer. Among them, in a pull-down assay one compound exhibited selective inhibition of TbPex5p–TbPex14p without any HsPex5p–HsPex14p interaction. An HTRF-based TbPex5p–TbPex14p interaction assay system was established. A compound was found that selectively inhibits the TbPex5p–TbPex14p interaction. This system is applicable for drug discovery against other glycosomal proteins.
Collapse
Affiliation(s)
- Yuichi Watanabe
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Kosuke Kawaguchi
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Syuken Saito
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyoaki Yonesu
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinichiro Egashira
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masafumi Kameya
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Masashi Morita
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshinori Kashiwayama
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tsuneo Imanaka
- Department of Biological Chemistry, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| |
Collapse
|
15
|
Abed DA, Goldstein M, Albanyan H, Jin H, Hu L. Discovery of direct inhibitors of Keap1-Nrf2 protein-protein interaction as potential therapeutic and preventive agents. Acta Pharm Sin B 2015; 5:285-99. [PMID: 26579458 PMCID: PMC4629420 DOI: 10.1016/j.apsb.2015.05.008] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [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: 05/05/2015] [Accepted: 05/11/2015] [Indexed: 02/07/2023] Open
Abstract
The Keap1–Nrf2–ARE pathway is an important antioxidant defense mechanism that protects cells from oxidative stress and the Keap1–Nrf2 protein–protein interaction (PPI) has become an important drug target to upregulate the expression of ARE-controlled cytoprotective oxidative stress response enzymes in the development of therapeutic and preventive agents for a number of diseases and conditions. However, most known Nrf2 activators/ARE inducers are indirect inhibitors of Keap1–Nrf2 PPI and they are electrophilic species that act by modifying the sulfhydryl groups of Keap1׳s cysteine residues. The electrophilicity of these indirect inhibitors may cause "off-target" side effects by reacting with cysteine residues of other important cellular proteins. Efforts have recently been focused on the development of direct inhibitors of Keap1–Nrf2 PPI. This article reviews these recent research efforts including the development of high throughput screening assays, the discovery of peptide and small molecule direct inhibitors, and the biophysical characterization of the binding of these inhibitors to the target Keap1 Kelch domain protein. These non-covalent direct inhibitors of Keap1–Nrf2 PPI could potentially be developed into effective therapeutic or preventive agents for a variety of diseases and conditions.
Collapse
Key Words
- 1O2, singlet oxygen
- AD, Alzheimer׳s disease
- ARE, antioxidant response element
- BTB, broad complex, tramtrack and bric-a-brac
- Bach1, BTB and CNC homology 1
- CBP, cAMP response element binding (CREB) protein
- CDDO-Me, bardoxolone methyl
- COPD, chronic obstructive pulmonary disease
- CTR, C-terminal region
- CVD, cardiovascular disease
- DGR, double glycine repeats
- Direct inhibitors of protein–protein interaction
- FITC, flurescein isothiocyanate
- FP, fluorescence polarization
- GCL, glutamate-cysteine ligase
- GPx, glutathione peroxidase
- GST, glutathione S-transferase
- H2O2, hydrogen peroxide
- HO-1, heme-oxygenase-1
- HTS, high-throughput screening
- High throughput screening assays
- IBS, inflammatory bowel disease
- IVR, intervening region
- Keap1
- Keap1, Kelch-like ECH-associated protein 1
- MD, molecular dynamics
- NMR, .
- NO, nitric oxide
- NQO1, NAD(P)H quinone oxidoreductase I
- NTR, N-terminal region
- Nrf2
- Nrf2, nuclear factor erythroid 2–related factor 2
- Oxidative stress
- PD, Parkinson׳s disease
- PPI, protein–protein interaction
- RNS, reactive nitrogen species
- ROS, reactive oxygen species
- SOD, superoxide dismutase
- SPR, surface plasmon resonance
- STZ, streptozotocin
- Structure–activity relationships
- THIQ, tetrahydroisoquinoline
- TRX, thioredoxin
- X-ray crystallography
- [Formula: see text], peroxynitrate
- [Formula: see text], superoxide, OH·, hydroxyl radical
- vitamin C, ascorbate
- vitamin E, tocopherols
Collapse
|
16
|
Kang Z, Zhang J, Jin P, Yang S. Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes. Bioengineered 2015; 6:136-40. [PMID: 25621864 DOI: 10.1080/21655979.2015.1011029] [Citation(s) in RCA: 12] [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] [Indexed: 10/23/2022] Open
Abstract
Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.
Collapse
Affiliation(s)
- Zhen Kang
- a Key Laboratory of Industrial Biotechnology; Ministry of Education ; Jiangnan University ; Wuxi , Jiangsu China
| | | | | | | |
Collapse
|
17
|
Memic A, Khademhosseini A. Finding the winning combination. Combinatorial screening of three dimensional niches to guide stem cell osteogenesis. Organogenesis 2014; 10:299-302. [PMID: 25482315 DOI: 10.4161/org.29646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 02/04/2023] Open
Abstract
The ability to predict and guide stem cell differentiation remains a major challenge in regenerative medicine. Numerous dynamic microenvironmental cues often provide synergistic or combinatorial signals that influence the fate of stem cells, and ultimately drive functional tissue formation. This interplay between microenvironmental cues within tissues is under intense investigation. Our goal was to better understand this interplay within the framework of a systematic 3D platform that would enable high-throughput screening (HTS) of factors that contribute to stem cell fate decisions. It is important that such platforms provide valid biomimetic microenvironments, which can be translated to macroscale constructs. Specifically, we reported on a technique for screening of combinatorial 3D niches to guide the osteogenic differentiation of human mesenchymal stem cells (hMSCs). This platform offers a rapid, cost-effective and multiplexed approach for a variety of tissue engineering applications.
Collapse
Key Words
- 2D, two dimensional
- 3D, three dimensional
- ALP, alkaline phosphatase
- BMP, bone morphogenic proteins
- ECM, extracellular matrix
- FN, fibronectin
- GE, methacrylated gelatin
- HTS, high-throughput screening
- LN, laminin
- OCN, osteocalcin
- biomaterials
- biomimetics
- hMSCs, human mesenchymal stem cells
- high-throughput screening
- stem cell differentiation
- tissue engineering
Collapse
Affiliation(s)
- Adnan Memic
- a Center of Nanotechnology ; King Abdulaziz University ; Jeddah , Saudi Arabia
| | | |
Collapse
|