1
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Peng B, Zhang L, He S, Oerlemans R, Quax WJ, Groves MR, Haslinger K. Engineering a Plant Polyketide Synthase for the Biosynthesis of Methylated Flavonoids. J Agric Food Chem 2024; 72:529-539. [PMID: 38109879 PMCID: PMC10786038 DOI: 10.1021/acs.jafc.3c06785] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Homoeriodictyol and hesperetin are naturally occurring O-methylated flavonoids with many health-promoting properties. They are produced in plants in low abundance and as complex mixtures of similar compounds that are difficult to separate. Synthetic biology offers the opportunity to produce various flavonoids in a targeted, bottom-up approach in engineered microbes with high product titers. However, the production of O-methylated flavonoids is currently still highly inefficient. In this study, we investigated and engineered a combination of enzymes that had previously been shown to support homoeriodictyol and hesperetin production in Escherichia coli from fed O-methylated hydroxycinnamic acids. We determined the crystal structures of the enzyme catalyzing the first committed step of the pathway, chalcone synthase from Hordeum vulgare, in three ligand-bound states. Based on these structures and a multiple sequence alignment with other chalcone synthases, we constructed mutant variants and assessed their performance in E. coli toward producing methylated flavonoids. With our best mutant variant, HvCHS (Q232P, D234 V), we were able to produce homoeriodictyol and hesperetin at 2 times and 10 times higher titers than reported previously. Our findings will facilitate further engineering of this enzyme toward higher production of methylated flavonoids.
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Affiliation(s)
- Bo Peng
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Lili Zhang
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Siqi He
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Rick Oerlemans
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Wim J. Quax
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Matthew R. Groves
- XB20
Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
| | - Kristina Haslinger
- Chemical
and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9713AV, The Netherlands
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2
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Sokolova N, Zhang L, Deravi S, Oerlemans R, Groves MR, Haslinger K. Structural characterization and extended substrate scope analysis of two Mg2+-dependent O-methyltransferases from bacteria. Chembiochem 2023; 24:e202300076. [PMID: 36942619 DOI: 10.1002/cbic.202300076] [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: 01/31/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/23/2023]
Abstract
Oxygen-directed methylation is a ubiquitous tailoring reaction in natural product pathways catalysed by O-methyltransferases (OMTs). Promiscuous OMT biocatalysts are thus a valuable asset in the toolkit for sustainable synthesis and optimization of known bioactive scaffolds for drug development. Here, we characterized the enzymatic properties and substrate scope of two bacterial OMTs from Desulforomonas acetoxidans and Streptomyces avermitilis and determined their crystal structures. Both OMTs methylated a wide range of catechol-like substrates, including flavonoids, coumarins, hydroxybenzoic acids and their respective aldehydes, an anthraquinone and an indole. One enzyme also accepted a steroid. The product range included pharmaceutically relevant compounds such as (iso)fraxidin, iso(scopoletin), chrysoeriol, alizarin 1-methyl ether and 2-methoxyestradiol. Interestingly, certain non-catechol flavonoids and hydroxybenzoic acids were also methylated. This study expands the knowledge on substrate preference and structural diversity of bacterial catechol OMTs and paves the way for their use in (combinatorial) pathway engineering.
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Affiliation(s)
- Nika Sokolova
- University of Groningen: Rijksuniversiteit Groningen, Chemical and Pharmaceutical Biology, NETHERLANDS
| | - Lili Zhang
- University of Groningen: Rijksuniversiteit Groningen, XB20 Department of Drug Design, NETHERLANDS
| | - Sadaf Deravi
- University of Groningen: Rijksuniversiteit Groningen, Chemical and Pharmaceutical Biology, NETHERLANDS
| | - Rick Oerlemans
- University of Groningen: Rijksuniversiteit Groningen, XB20 Department of Drug Design, NETHERLANDS
| | - Matthew R Groves
- University of Groningen: Rijksuniversiteit Groningen, XB20 Department of Drug Design, NETHERLANDS
| | - Kristina Haslinger
- University of Groningen: Rijksuniversiteit Groningen, Chemical And Pharmaceutical Biology, Antonius Deusinglaan 1, 9713AV, Groningen, NETHERLANDS
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3
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Gierse RM, Oerlemans R, Reddem ER, Gawriljuk VO, Alhayek A, Baitinger D, Jakobi H, Laber B, Lange G, Hirsch AKH, Groves MR. First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Sci Rep 2022; 12:7221. [PMID: 35508530 PMCID: PMC9068908 DOI: 10.1038/s41598-022-11205-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/15/2022] [Indexed: 11/18/2022] Open
Abstract
The development of drug resistance by Mycobacterium tuberculosis and other pathogenic bacteria emphasizes the need for new antibiotics. Unlike animals, most bacteria synthesize isoprenoid precursors through the MEP pathway. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the first reaction of the MEP pathway and is an attractive target for the development of new antibiotics. We report here the successful use of a loop truncation to crystallize and solve the first DXPS structures of a pathogen, namely M. tuberculosis (MtDXPS). The main difference found to other DXPS structures is in the active site where a highly coordinated water was found, showing a new mechanism for the enamine-intermediate stabilization. Unlike other DXPS structures, a “fork-like” motif could be identified in the enamine structure, using a different residue for the interaction with the cofactor, potentially leading to a decrease in the stability of the intermediate. In addition, electron density suggesting a phosphate group could be found close to the active site, provides new evidence for the D-GAP binding site. These results provide the opportunity to improve or develop new inhibitors specific for MtDXPS through structure-based drug design.
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Affiliation(s)
- Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Rick Oerlemans
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Eswar R Reddem
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands
| | - Victor O Gawriljuk
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.,São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100-Santa Angelina, São Carlos, SP, 13563-120, Brazil
| | - Alaa Alhayek
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Dominik Baitinger
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany
| | - Harald Jakobi
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Bernd Laber
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Gudrun Lange
- Research & Development Crop Science, Bayer AG, Industriepark Höchst, 65926, Frankfurt, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, 66123, Saarbrücken, Germany. .,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany. .,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Matthew R Groves
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9700 AV, Groningen, The Netherlands.
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4
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Zhang Y, Chen H, Zou M, Oerlemans R, Shao C, Ren Y, Zhang R, Huang X, Li G, Cong Y. Hypericin Inhibit Alpha-Coronavirus Replication by Targeting 3CL Protease. Viruses 2021; 13:v13091825. [PMID: 34578406 PMCID: PMC8473218 DOI: 10.3390/v13091825] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3CLpro using different software and found hypericin bound to 3CLpro through two pockets. These binding pockets were further verified by another docking between hypericin and PEDV 3CLpro pocket mutants, and the fluorescence resonance energy transfer (FRET) assay confirmed that hypericin inhibits the PEDV 3CLpro activity. Moreover, the alignments of α-CoV 3CLpro sequences or crystal structure revealed that the pockets mediating hypericin and PEDV 3CLpro binding were highly conserved, especially in transmissible gastroenteritis virus (TGEV). We then validated the anti-TGEV effect of hypericin through viral replication and egression. Overall, our results push forward that hypericin was for the first time shown to have an inhibitory effect on PEDV and TGEV by targeting 3CLpro, and it deserves further attention as not only a pan-anti-α-CoV compound but potentially also as a compound of other coronaviral infections.
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Affiliation(s)
- Yue Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Huijie Chen
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- College of Pharmaceutical Engineering, Jilin Agriculture Science and Technology University, Jilin 132101, China
| | - Mengmeng Zou
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Rick Oerlemans
- Department of Drug Design, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Changhao Shao
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Yudong Ren
- Department of Computer Science and Technology, College of Electrical and Information Technology, Northeast Agricultural University, Harbin 150030, China;
| | - Ruili Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Xiaodan Huang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Guangxing Li
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Correspondence: (G.L.); (Y.C.)
| | - Yingying Cong
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Correspondence: (G.L.); (Y.C.)
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5
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021; 60:18231-18239. [PMID: 34097796 PMCID: PMC8456925 DOI: 10.1002/anie.202105584] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 04/24/2021] [Revised: 05/31/2021] [Indexed: 12/24/2022]
Abstract
Protein crystallography (PX) is widely used to drive advanced stages of drug optimization or to discover medicinal chemistry starting points by fragment soaking. However, recent progress in PX could allow for a more integrated role into early drug discovery. Here, we demonstrate for the first time the interplay of high throughput synthesis and high throughput PX. We describe a practical multicomponent reaction approach to acrylamides and -esters from diverse building blocks suitable for mmol scale synthesis on 96-well format and on a high-throughput nanoscale format in a highly automated fashion. High-throughput PX of our libraries efficiently yielded potent covalent inhibitors of the main protease of the COVID-19 causing agent, SARS-CoV-2. Our results demonstrate, that the marriage of in situ HT synthesis of (covalent) libraires and HT PX has the potential to accelerate hit finding and to provide meaningful strategies for medicinal chemistry projects.
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Affiliation(s)
- Fandi Sutanto
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Shabnam Shaabani
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Rick Oerlemans
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Deniz Eris
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | - Pravin Patil
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Mojgan Hadian
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Meitian Wang
- Photon Science DivisionPaul Scherrer InstituteSwitzerland
| | | | - Matthew R. Groves
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
| | - Alexander Dömling
- University of GroningenDepartment of Drug DesignA. Deusinglaan 19713AVGroningenThe Netherlands
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6
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Sutanto F, Shaabani S, Oerlemans R, Eris D, Patil P, Hadian M, Wang M, Sharpe ME, Groves MR, Dömling A. Combining High‐Throughput Synthesis and High‐Throughput Protein Crystallography for Accelerated Hit Identification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Fandi Sutanto
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Shabnam Shaabani
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rick Oerlemans
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Deniz Eris
- Photon Science Division Paul Scherrer Institute Switzerland
| | - Pravin Patil
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Mojgan Hadian
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Meitian Wang
- Photon Science Division Paul Scherrer Institute Switzerland
| | | | - Matthew R. Groves
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Alexander Dömling
- University of Groningen Department of Drug Design A. Deusinglaan 1 9713 AV Groningen The Netherlands
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7
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Oerlemans R, Ruiz-Moreno AJ, Cong Y, Dinesh Kumar N, Velasco-Velazquez MA, Neochoritis CG, Smith J, Reggiori F, Groves MR, Dömling A. Repurposing the HCV NS3-4A protease drug boceprevir as COVID-19 therapeutics. RSC Med Chem 2020; 12:370-379. [PMID: 34041486 PMCID: PMC8130630 DOI: 10.1039/d0md00367k] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The rapid growth of COVID-19 cases is causing an increasing death toll and also paralyzing the world economy. De novo drug discovery takes years to move from idea and/or pre-clinic to market, and it is not a short-term solution for the current SARS-CoV-2 pandemic. Drug repurposing is perhaps the only short-term solution, while vaccination is a middle-term solution. Here, we describe the discovery path of the HCV NS3-4A protease inhibitors boceprevir and telaprevir as SARS-CoV-2 main protease (3CLpro) inhibitors. Based on our hypothesis that α-ketoamide drugs can covalently bind to the active site cysteine of the SARS-CoV-2 3CLpro, we performed docking studies, enzyme inhibition and co-crystal structure analyses and finally established that boceprevir, but not telaprevir, inhibits replication of SARS-CoV-2 and mouse hepatitis virus (MHV), another coronavirus, in cell culture. Based on our studies, the HCV drug boceprevir deserves further attention as a repurposed drug for COVID-19 and potentially other coronaviral infections as well.
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Affiliation(s)
- Rick Oerlemans
- Department of Drug Design, University of Groningen The Netherlands
| | - Angel Jonathan Ruiz-Moreno
- Department of Drug Design, University of Groningen The Netherlands .,Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Traslacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM) Ciudad de México Mexico.,Programa de Doctorado en Ciencias Biomédicas, UNAM Ciudad de México Mexico
| | - Yingying Cong
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen The Netherlands
| | - Nilima Dinesh Kumar
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen The Netherlands.,Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen Groningen 9700 RB The Netherlands
| | - Marco A Velasco-Velazquez
- Departamento de Farmacología y Unidad Periférica de Investigación en Biomedicina Traslacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM) Ciudad de México Mexico.,Programa de Doctorado en Ciencias Biomédicas, UNAM Ciudad de México Mexico
| | | | - Jolanda Smith
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen Groningen 9700 RB The Netherlands
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen The Netherlands
| | - Matthew R Groves
- Department of Drug Design, University of Groningen The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen The Netherlands .,Telesis Pharma Groningen The Netherlands
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8
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Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev 2020; 12:85-104. [PMID: 32006251 PMCID: PMC7040159 DOI: 10.1007/s12551-020-00619-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [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: 12/04/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is an accessible, rapid, and economical biophysical technique that has seen many applications over the years, ranging from protein folding state detection to the identification of ligands that bind to the target protein. In this review, we discuss the theory, applications, and limitations of DSF, including the latest applications of DSF by ourselves and other researchers. We show that DSF is a powerful high-throughput tool in early drug discovery efforts. We place DSF in the context of other biophysical methods frequently used in drug discovery and highlight their benefits and downsides. We illustrate the uses of DSF in protein buffer optimization for stability, refolding, and crystallization purposes and provide several examples of each. We also show the use of DSF in a more downstream application, where it is used as an in vivo validation tool of ligand-target interaction in cell assays. Although DSF is a potent tool in buffer optimization and large chemical library screens when it comes to ligand-binding validation and optimization, orthogonal techniques are recommended as DSF is prone to false positives and negatives.
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Affiliation(s)
- Kai Gao
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rick Oerlemans
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Matthew R Groves
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands.
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9
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van der Heijden JW, Assaraf YG, Gerards AH, Oerlemans R, Lems WF, Scheper RJ, Dijkmans BAC, Jansen G. Methotrexate analogues display enhanced inhibition of TNF-α production in whole blood from RA patients. Scand J Rheumatol 2013; 43:9-16. [PMID: 23987246 DOI: 10.3109/03009742.2013.797490] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
OBJECTIVES Although methotrexate (MTX) is the anchor drug in the treatment of rheumatoid arthritis (RA), patients experience clinical resistance to MTX upon prolonged treatment. We explored whether new-generation antifolates elicit superior anti-inflammatory properties when compared to MTX, based on their capacity to inhibit tumour necrosis factor (TNF)-α production. METHOD T cells in whole blood from 18 RA patients (including MTX-naïve, MTX- responsive, and MTX non-responsive patients) and seven healthy volunteers were stimulated with αCD3/αCD28 antibodies and incubated ex vivo for 72 h with MTX and eight novel antifolate drugs with potentially favourable biochemical and pharmacological properties. Drug concentrations exerting 50% inhibition (IC-50) of TNF-α production (by enzyme-linked immunosorbent assay, ELISA) were determined as an estimate for their anti-inflammatory capacity. In addition, induction of T-cell apoptosis was evaluated by flow cytometry. RESULTS The new-generation antifolates PT523, PT644, raltitrexed, and GW1843 proved to be potent inhibitors of TNF-α production in activated T cells from all three groups of RA patients and from healthy volunteers. Based on IC-50 values, these antifolates were up to 10.3 times more potent than MTX. The anti-inflammatory effects were observed at drug concentrations that provoked suppression of T-cell activation and induction of apoptosis in 20-40% of activated T cells. CONCLUSION In an ex-vivo setting, novel antifolates elicited marked inhibition of TNF-α production in activated T cells from RA patients. Further clinical evaluation is warranted to investigate whether a low dosage of these antifolates can elicit immunosuppressive effects equivalent to MTX, and whether they are superior to MTX in patients who fail to respond to MTX.
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Affiliation(s)
- J W van der Heijden
- Department of Rheumatology, VU University Medical Center , Amsterdam , The Netherlands
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10
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van Dijk A, Naaijkens BA, Jurgens WJFM, Oerlemans R, Scheffer GL, Kassies J, Aznou J, Brouwer M, van Rossum AC, Schuurhuis GJ, van Milligen FJ, Niessen HWM. The multidrug resistance protein breast cancer resistance protein (BCRP) protects adipose-derived stem cells against ischemic damage. Cell Biol Toxicol 2012; 28:303-15. [PMID: 22801743 DOI: 10.1007/s10565-012-9225-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 07/02/2012] [Indexed: 12/29/2022]
Abstract
Adipose tissue-derived stem cells (ASCs) are promising candidates for regenerative therapy, like after myocardial infarction. However, when transplanted into the infarcted heart, ASCs are jeopardized by the ischemic environment. Interestingly, it has been shown that multidrug resistance (MDR) proteins like the breast cancer resistance protein (BCRP) and P-glycoprotein (P-gp) have a protective effect in haematopoietic stem cells. In ASC, however, only expression of BCRP was shown until now. In this study, we therefore analysed the expression and functional activity of BCRP and P-gp and their putative function in ischemia in ASC. BCRP and P-gp protein expression was studied over time (passages 2-6) using western blot analysis and immunohistochemical staining. MDR activity was analysed using protein-specific substrate extrusion assays. Ischemia was induced using metabolic inhibition. All analyses demonstrated protein expression and activity of BCRP in ASCs. In contrast, only minor expression of P-gp was found, without functional activity. BCRP expression was most prominent in early passage ASCs (p2) and decreased during culture. Finally, ischemia induced expression of BCRP. In addition, when BCRP was blocked, a significant increase in dead ASCs was found already after 1 h of ischemia. In conclusion, ASCs expressed BCRP, especially in early passages. In addition, we now show for the first time that BCRP protects ASCs against ischemia-induced cell death. These data therefore indicate that for transplantation of ASCs in an ischemic environment, like myocardial infarction, the optimal stem cell protective effect of BCRP theoretically will be achieved with early culture passages ASCs.
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Affiliation(s)
- A van Dijk
- Department of Pathology, VU University Medical Centre, Amsterdam, the Netherlands.
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van der Heijden JW, Oerlemans R, Lems WF, Scheper RJ, Dijkmans BAC, Jansen G. The proteasome inhibitor bortezomib inhibits the release of NFkappaB-inducible cytokines and induces apoptosis of activated T cells from rheumatoid arthritis patients. Clin Exp Rheumatol 2009; 27:92-98. [PMID: 19327235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
OBJECTIVE The proteasome is a multicatalytic proteinase complex regulating the intracellular breakdown of many proteins, including those mediating the activation of pro-inflammatory signaling pathways (e.g. NFkappaB), cell proliferation and survival. Conceptually, proteasome inhibitors may therefore elicit potential anti-inflammatory properties by inhibiting these processes and thereby impair the cellular release of pro-inflammatory cytokines such as Tumor Necrosis Factor-alpha (TNF-alpha) in RA patients. METHODS Whole-blood from 19 RA patients (including methotrexate-responsive and non-responsive patients) and 7 healthy volunteers was incubated ex-vivo with the proteasome inhibitor bortezomib after T-cell stimulation with alphaCD3/CD28. Inhibition of cytokine production by bortezomib was measured after 24 and 72 hours by ELISA. Effects of bortezomib on apoptosis and T-cell activation (CD25 expression) were measured by FACS-analysis. RESULTS Bortezomib proved to be a rapid (<24 hour) and potent inhibitor of the release of several NFkappaB-inducible cytokines (including TNF-alpha, IL-1Beta, IL-6 and IL-10) by activated T-cells from healthy volunteers and RA patients, regardless of their clinical responsiveness to methotrexate. Median concentrations of bortezomib required to inhibit TNF-alpha production by 50% (mIC-50) were 12 nM (range: 8-50 nM) for healthy volunteers and 46 nM (range: 18-60 nM) for RA patients. A reduction of T cell activation and a marked induction of T-cell apoptosis were revealed as late effects after bortezomib incubations beyond 24 hours. CONCLUSION Proteasome inhibitors represented by bortezomib may elicit potential anti-inflammatory properties that deserve further exploration in experimental therapies for RA.
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Affiliation(s)
- J W van der Heijden
- Departments of Rheumatology, VU University Medical Center, Amsterdam, The Netherlands
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van der Heijden J, de Jong MC, Dijkmans BAC, Lems WF, Oerlemans R, Kathmann I, Scheffer GL, Scheper RJ, Assaraf YG, Jansen G. Acquired resistance of human T cells to sulfasalazine: stability of the resistant phenotype and sensitivity to non-related DMARDs. Ann Rheum Dis 2004; 63:131-7. [PMID: 14722200 PMCID: PMC1754886 DOI: 10.1136/ard.2003.006494] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND A recent study from our laboratory showed that induction of the multidrug resistance related drug efflux pump ABCG2 contributed to acquired resistance of human T cells to the disease modifying antirheumatic drug (DMARD) sulfasalazine (SSZ). OBJECTIVES To investigate the duration of SSZ resistance and ABCG2 expression after withdrawal of SSZ and rechallenging with SSZ, and to assess the impact of SSZ resistance on responsiveness to other DMARDs. METHODS Human CEM cells (T cell origin) with acquired resistance to SSZ (CEM/SSZ) were characterised for (a) SSZ sensitivity and ABCG2 expression during withdrawal and rechallenge of SSZ, and (b) antiproliferative efficacy of other DMARDs. RESULTS ABCG2 protein expression was stable for at least 4 weeks when CEM/SSZ cells were grown in the absence of SSZ, but gradually declined, along with SSZ resistance levels, to non-detectable levels after withdrawal of SSZ for 6 months. Rechallenging with SSZ led to a rapid (<2.5 weeks) resumption of SSZ resistance and ABCG2 expression as in the original CEM/SSZ cells. CEM/SSZ cells displayed diminished sensitivity to the DMARDs leflunomide (5.1-fold) and methotrexate (1.8-fold), were moderately more sensitive (1.6-2.0 fold) to cyclosporin A and chloroquine, and markedly more sensitive (13-fold) to the glucocorticoid dexamethasone as compared with parental CEM cells. CONCLUSION The drug efflux pump ABCG2 has a major role in conferring resistance to SSZ. The collateral sensitivity of SSZ resistant cells for some other (non-related) DMARDs may provide a further rationale for sequential mono- or combination therapies with distinct DMARDs upon decreased efficacy of SSZ.
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Affiliation(s)
- J van der Heijden
- Department of Rheumatology, Vrije Universiteit Medical Centre, Amsterdam, The Netherlands
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van der Heijden J, de Jong MC, Dijkmans BAC, Lems WF, Oerlemans R, Kathmann I, Schalkwijk CG, Scheffer GL, Scheper RJ, Jansen G. Development of sulfasalazine resistance in human T cells induces expression of the multidrug resistance transporter ABCG2 (BCRP) and augmented production of TNFalpha. Ann Rheum Dis 2004; 63:138-43. [PMID: 14722201 PMCID: PMC1754889 DOI: 10.1136/ard.2002.005249] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To determine whether overexpression of cell membrane associated drug efflux pumps belonging to the family of ATP binding cassette (ABC) proteins contributes to a diminished efficacy of sulfasalazine (SSZ) after prolonged cellular exposure to this disease modifying antirheumatic drug (DMARD). METHODS A model system of human T cells (CEM) was used to expose cells in vitro to increasing concentrations of SSZ for a period of six months. Cells were then characterised for the expression of drug efflux pumps: P-glycoprotein (Pgp, ABCB1), multidrug resistance protein 1 (MRP1, ABCC1), and breast cancer resistance protein (BCRP, ABCG2). RESULTS Prolonged exposure of CEM cells to SSZ provoked resistance to SSZ as manifested by a 6.4-fold diminished antiproliferative effect of SSZ compared with parental CEM cells. CEM cells resistant to SSZ (CEM/SSZ) showed a marked induction of ABCG2/BCRP, Pgp expression was not detectable, while MRP1 expression was even down regulated. A functional role of ABCG2 in SSZ resistance was demonstrated by 60% reversal of SSZ resistance by the ABCG2 blocker Ko143. Release of the proinflammatory cytokine tumour necrosis factor alpha (TNFalpha) was threefold higher in CEM/SSZ cells than in CEM cells. Moreover, twofold higher concentrations of SSZ were required to inhibit TNFalpha release from CEM/SSZ cells compared with CEM cells. CONCLUSION Collectively, ABCG2 induction, augmented TNFalpha release, and less efficient inhibition of TNFalpha production by SSZ may contribute to diminished efficacy after prolonged exposure to SSZ. These results warrant further clinical studies to verify whether drug efflux pumps, originally identified for their roles in cytostatic drug resistance, can also be induced by SSZ or other DMARDs.
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Affiliation(s)
- J van der Heijden
- Department of Rheumatology, Vrije Universiteit Medical Centre, Amsterdam, The Netherlands
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