Development and characterization of DNAzyme candidates demonstrating significant efficiency against human rhinoviruses

Daniel P Potaczek; Sebastian D Unger; Nan Zhang; Styliani Taka; Sven Michel; Nesibe Akdağ; Feng Lan; Markus Helfer; Christoph Hudemann; Markus Eickmann; Chrysanthi Skevaki; Spyridon Megremis; Anne Sadewasser; Bilal Alashkar Alhamwe; Fahd Alhamdan; Mübeccel Akdis; Michael R Edwards; Sebastian L Johnston; Cezmi A Akdis; Stephan Becker; Claus Bachert; Nikolaos G Papadopoulos; Holger Garn; Harald Renz

doi:10.1016/j.jaci.2018.07.026

Development and characterization of DNAzyme candidates demonstrating significant efficiency against human rhinoviruses

J Allergy Clin Immunol. 2019 Apr;143(4):1403-1415. doi: 10.1016/j.jaci.2018.07.026. Epub 2018 Aug 14.

Authors

Daniel P Potaczek¹, Sebastian D Unger², Nan Zhang³, Styliani Taka⁴, Sven Michel⁵, Nesibe Akdağ², Feng Lan³, Markus Helfer⁵, Christoph Hudemann², Markus Eickmann⁶, Chrysanthi Skevaki², Spyridon Megremis⁷, Anne Sadewasser⁵, Bilal Alashkar Alhamwe², Fahd Alhamdan², Mübeccel Akdis⁸, Michael R Edwards⁹, Sebastian L Johnston⁹, Cezmi A Akdis⁸, Stephan Becker⁶, Claus Bachert³, Nikolaos G Papadopoulos¹⁰, Holger Garn², Harald Renz¹¹

Affiliations

¹ Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium; John Paul II Hospital, Krakow, Poland.
² Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium.
³ PreDicta Consortium; Upper Airway Research Laboratory, Department of Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium.
⁴ PreDicta Consortium; Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece.
⁵ Secarna Pharmaceuticals GmbH, Planegg, Germany.
⁶ Institute of Virology, Philipps-University Marburg, Marburg, Germany.
⁷ PreDicta Consortium; Division of Infection, Inflammation and Respiratory Medicine, University of Manchester, London, United Kingdom.
⁸ PreDicta Consortium; Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.
⁹ PreDicta Consortium; Airway Disease Infection Section, National Heart and Lung Institute (NHLI), Imperial College London, London, United Kingdom; Medical Research Council (MRC) and Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom.
¹⁰ PreDicta Consortium; Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; Division of Infection, Inflammation and Respiratory Medicine, University of Manchester, London, United Kingdom.
¹¹ Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), and the inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), Marburg, Germany; PreDicta Consortium. Electronic address: renzh@med.uni-marburg.de.

PMID: 30114391
DOI: 10.1016/j.jaci.2018.07.026

Abstract

Background: Infections with human rhinoviruses (RVs) are responsible for millions of common cold episodes and the majority of asthma exacerbations, especially in childhood. No drugs specifically targeting RVs are available.

Objective: We sought to identify specific anti-RV molecules based on DNAzyme technology as candidates to a clinical study.

Methods: A total of 226 candidate DNAzymes were designed against 2 regions of RV RNA genome identified to be sufficiently highly conserved between virus strains (ie, the 5'-untranslated region and cis-acting replication element) by using 3 test strains: RVA1, RVA16, and RVA29. All DNAzymes were screened for their cleavage efficiency against in vitro-expressed viral RNA. Those showing any catalytic activity were subjected to bioinformatic analysis of their reverse complementarity to 322 published RV genomic sequences. Further molecular optimization was conducted for the most promising candidates. Cytotoxic and off-target effects were excluded in HEK293 cell-based systems. Antiviral efficiency was analyzed in infected human bronchial BEAS-2B cells and ex vivo-cultured human sinonasal tissue.

Results: Screening phase-generated DNAzymes characterized by either good catalytic activity or by high RV strain coverage but no single molecule represented a satisfactory combination of those 2 features. Modifications in length of the binding domains of 2 lead candidates, Dua-01(-L12R9) and Dua-02(-L10R11), improved their cleavage efficiency to an excellent level, with no loss in eminent strain coverage (about 98%). Both DNAzymes showed highly favorable cytotoxic/off-target profiles. Subsequent testing of Dua-01-L12R9 in BEAS-2B cells and sinonasal tissue demonstrated its significant antiviral efficiency.

Conclusions: Effective and specific management of RV infections with Dua-01-L12R9 might be useful in preventing asthma exacerbations, which should be verified by clinical trials.

Keywords: Allergy; DNAzyme; RNA; antisense; antiviral; asthma; atopy; exacerbation; human rhinovirus; therapy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Antiviral Agents / pharmacology*
Common Cold / prevention & control
DNA, Catalytic / pharmacology*
Drug Discovery
Humans
RNA, Viral / drug effects*
Rhinovirus*
Virus Replication / drug effects*

Substances

Antiviral Agents
DNA, Catalytic
RNA, Viral

Grants and funding

G1000758/MRC_/Medical Research Council/United Kingdom