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Doijen J, Heo I, Temmerman K, Vermeulen P, Diels A, Jaensch S, Burcin M, Van den Broeck N, Raeymaekers V, Peremans J, Konings K, Clement M, Peeters D, Van Loock M, Koul A, Buyck C, Van Gool M, Van Damme E. A flexible, image-based, high-throughput platform encompassing in-depth cell profiling to identify broad-spectrum coronavirus antivirals with limited off-target effects. Antiviral Res 2024; 222:105789. [PMID: 38158129 DOI: 10.1016/j.antiviral.2023.105789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a major threat to global health. Although the World Health Organization ended the public health emergency status, antiviral drugs are needed to address new variants of SARS-CoV-2 and future pandemics. To identify novel broad-spectrum coronavirus drugs, we developed a high-content imaging platform compatible with high-throughput screening. The platform is broadly applicable as it can be adapted to include various cell types, viruses, antibodies, and dyes. We demonstrated that the antiviral activity of compounds against SARS-CoV-2 variants (Omicron BA.5 and Omicron XBB.1.5), SARS-CoV, and human coronavirus 229E could easily be assessed. The inclusion of cellular dyes and immunostaining in combination with in-depth image analysis enabled us to identify compounds that induced undesirable phenotypes in host cells, such as changes in cell morphology or in lysosomal activity. With the platform, we screened ∼900K compounds and triaged hits, thereby identifying potential candidate compounds carrying broad-spectrum activity with limited off-target effects. The flexibility and early-stage identification of compounds with limited host cell effects provided by this high-content imaging platform can facilitate coronavirus drug discovery. We anticipate that its rapid deployability and fast turnaround can also be applied to combat future pandemics.
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Affiliation(s)
- Jordi Doijen
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Inha Heo
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Koen Temmerman
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Peter Vermeulen
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Annick Diels
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Steffen Jaensch
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Mark Burcin
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | | | | | - Joren Peremans
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Katrien Konings
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Maxime Clement
- Charles River Laboratories, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Danielle Peeters
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Marnix Van Loock
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Anil Koul
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Christophe Buyck
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Michiel Van Gool
- Therapeutics Discovery R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Ellen Van Damme
- Global Public Health R&D, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
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Zaremba A, Zaremba P, Zahorodnia S. De novo designed inhibitor has high affinity to four variants of the RBD of S-glycoprotein of SARS-CoV-2 - an in silico study. J Biomol Struct Dyn 2023; 41:9389-9397. [PMID: 36318624 DOI: 10.1080/07391102.2022.2141886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022]
Abstract
In the years since the rapid invasion of SARS-CoV-2, the world community has fully understood the extent of the danger of this new pathogen. And also the speed with which he is able to adapt both to humans as a species and to the means of combat that are introduced. However, this has already resulted in millions of lost lives and this situation may worsen in the future, due to the further inevitable evolution of the virus. Accordingly, the need for effective drugs is urgent. In this work, using an iterative approach, we de novo designed a molecule that revealed significant affinity to four variants of SARS-CoV-2 - Wuhan, Omicron, Delta and Cluster 5. More precisely, to their receptor-binding domain of S-glycoprotein, in particular, to the site that is directly involved in the recognition of human ACE2.What is confirmed in particular by the ΔGbind of the complexes of RBD of all four SARS-CoV-2 variants with a potential inhibitor: it is in significantly negative values. Along with this, the calculated ADMET parameters can generally be considered acceptable. Accordingly, we believe that the molecule we have designed has a high potential for further development as an effective drug against SARS-CoV-2. However, it currently requires further in vitro and in vivo studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Andrii Zaremba
- Deparment of Reproduction of Viruses, Zabolotny Institute of Microbiology and Virology of NASU, Kyiv, Ukraine
| | - Polina Zaremba
- Deparment of Reproduction of Viruses, Zabolotny Institute of Microbiology and Virology of NASU, Kyiv, Ukraine
| | - Svіtlana Zahorodnia
- Deparment of Reproduction of Viruses, Zabolotny Institute of Microbiology and Virology of NASU, Kyiv, Ukraine
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Chiu W, Schepers J, Francken T, Vangeel L, Abbasi K, Jochmans D, De Jonghe S, Thibaut HJ, Thiel V, Neyts J, Laporte M, Leyssen P. Development of a robust and convenient dual-reporter high-throughput screening assay for SARS-CoV-2 antiviral drug discovery. Antiviral Res 2023; 210:105506. [PMID: 36565756 PMCID: PMC9767876 DOI: 10.1016/j.antiviral.2022.105506] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
Massive efforts on both vaccine development and antiviral research were launched to combat the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We contributed, amongst others, by the development of a high-throughput screening (HTS) antiviral assay against SARS-CoV-2 using a fully automated, high-containment robot system. Here, we describe the development of this novel, convenient and phenotypic dual-reporter virus-cell-based high-content imaging assay using the A549+hACE2+TMPRSS2_mCherry reporter lung carcinoma cell line and an ancestral SARS-CoV-2_Wuhan_mNeonGreen reporter virus. Briefly, by means of clonal selection, a host cell subclone was selected that (i) efficiently supports replication of the reporter virus with high expression, upon infection, of the NeonGreen fluorescent reporter protein, (ii) that is not affected by virus-induced cytopathogenic effects and, (iii) that expresses a strong fluorescent mCherry signal in the nucleus. The selected clone matched these criteria with an infection rate on average of 75% with limited cell death. The average (R)Z'-factors of the assay plates were all >0.8, which indicates a robust assay suitable for HTS purposes. A selection of reference compounds that inhibits SARS-CoV-2 replication in vitro were used to validate this novel dual-reporter assay and confirms the data reported in the literature. This assay is a convenient and powerful tool for HTS of large compound libraries against SARS-CoV-2.
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Affiliation(s)
- Winston Chiu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Joost Schepers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Thibault Francken
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Laura Vangeel
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Kayvan Abbasi
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Translational Platform Virology and Chemotherapy, Gaston Geenslaan 2, 3001, Leuven, Belgium
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern, Switzerland,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Manon Laporte
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 – box 1043, 3000, Leuven, Belgium
| | - Pieter Leyssen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Herestraat 49 - box 1043, 3000, Leuven, Belgium.
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Rational design of novel nucleoside analogues reveals potent antiviral agents for EV71. Eur J Med Chem 2023; 246:114942. [PMID: 36455356 DOI: 10.1016/j.ejmech.2022.114942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/23/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022]
Abstract
Different viruses belonging to distinct viral families, such as enterovirus 71, rely on the host methyltransferase METTL3 for the completion of fundamental cytoplasmic stages of their life cycle. Modulation of the activity of this enzyme could therefore provide a broad-spectrum approach to interfere with viral infections caused by viruses that depend on its activity for the completion of their viral cycle. With the aim to identify antiviral therapeutics with this effect, a series of new nucleoside analogues was rationally designed to act as inhibitors of human METTL3, as a novel approach to interfere with a range of viral infections. Guided by molecular docking studies on the SAM binding pocket of the enzyme, 24 compounds were prepared following multiple-step synthetic protocols, and evaluated for their ability to interfere with the replication of different viruses in cell-based systems, and to directly inhibit the activity of METTL3. While different molecules displayed moderate inhibition of the human methyltransferase in vitro, multiple novel, potent and selective inhibitors of enterovirus 71 were identified.
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