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Bauer L, Manganaro R, Zonsics B, Hurdiss DL, Zwaagstra M, Donselaar T, Welter NGE, van Kleef RGDM, Lopez ML, Bevilacqua F, Raman T, Ferla S, Bassetto M, Neyts J, Strating JRPM, Westerink RHS, Brancale A, van Kuppeveld FJM. Rational design of highly potent broad-spectrum enterovirus inhibitors targeting the nonstructural protein 2C. PLoS Biol 2020; 18:e3000904. [PMID: 33156822 PMCID: PMC7673538 DOI: 10.1371/journal.pbio.3000904] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/18/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
There is a great need for antiviral drugs to treat enterovirus (EV) and rhinovirus (RV) infections, which can be severe and occasionally life-threatening. The conserved nonstructural protein 2C, which is an AAA+ ATPase, is a promising target for drug development. Here, we present a structure-activity relationship study of a previously identified compound that targets the 2C protein of EV-A71 and several EV-B species members, but not poliovirus (PV) (EV-C species). This compound is structurally related to the Food and Drug Administration (FDA)-approved drug fluoxetine—which also targets 2C—but has favorable chemical properties. We identified several compounds with increased antiviral potency and broadened activity. Four compounds showed broad-spectrum EV and RV activity and inhibited contemporary strains of emerging EVs of public health concern, including EV-A71, coxsackievirus (CV)-A24v, and EV-D68. Importantly, unlike (S)-fluoxetine, these compounds are no longer neuroactive. By raising resistant EV-A71, CV-B3, and EV-D68 variants against one of these inhibitors, we identified novel 2C resistance mutations. Reverse engineering of these mutations revealed a conserved mechanism of resistance development. Resistant viruses first acquired a mutation in, or adjacent to, the α2 helix of 2C. This mutation disrupted compound binding and provided drug resistance, but this was at the cost of viral fitness. Additional mutations at distantly localized 2C residues were then acquired to increase resistance and/or to compensate for the loss of fitness. Using computational methods to identify solvent accessible tunnels near the α2 helix in the EV-A71 and PV 2C crystal structures, a conserved binding pocket of the inhibitors is proposed. There is a great need for antiviral drugs to treat enterovirus and rhinovirus infections, which can be severe and occasionally life-threatening. This study describes novel small molecule inhibitors that target a broad spectrum of clinically relevant enterovirus species; a common mechanism of resistance development revealed the target to be a highly conserved binding pocket in the viral helicase 2C.
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Affiliation(s)
- Lisa Bauer
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Roberto Manganaro
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Birgit Zonsics
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Daniel L. Hurdiss
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Tim Donselaar
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Naemi G. E. Welter
- Neurotoxicology Research Group, Toxicology Division, Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Regina G. D. M. van Kleef
- Neurotoxicology Research Group, Toxicology Division, Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Moira Lorenzo Lopez
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Federica Bevilacqua
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Thamidur Raman
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Salvatore Ferla
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Marcella Bassetto
- Department of Chemistry, Swansea University, Swansea, United Kingdom
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Jeroen R. P. M. Strating
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Remco H. S. Westerink
- Neurotoxicology Research Group, Toxicology Division, Institute for Risk Assessment Sciences (IRAS), Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Andrea Brancale
- Medicinal Chemistry, School of Pharmacy & Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Frank J. M. van Kuppeveld
- Virology Section, Infectious Disease and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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