Next-Generation Phenotypic Screening in Early Drug Discovery for Infectious Diseases

Aulner, Nathalie; Danckært, Anne; Ihm, JongEun; Shum, David; Shorte, Spencer

doi:10.1016/j.pt.2019.05.004

Cited by 71 publications

(57 citation statements)

References 86 publications

(108 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The repurposing of approved pharmaceutical drugs and drug candidates provides an alternative approach that allows for the rapid identification of potential drug leads to manage rapidly emerging viral infections. Cell-based phenotypic screening has proven to be valuable 31 , but the complexity of this approach is not readily compatible with high-throughput pipelines, and it cannot identify the molecular target or mechanism of action 32 . In this study, the convergence of structure-based ab initio drug design, virtual screening and high-throughput screening proved to be an efficient strategy to find antiviral leads against SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 99%

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Jin

et al. 2020

Nature

3,656

121

4,499

View full text Add to dashboard Cite

A new coronavirus (CoV) identified as COVID-19 virus is the etiological agent responsible for the 2019-2020 viral pneumonia outbreak that commenced in Wuhan [1][2][3][4] . Currently there are no targeted therapeutics and effective treatment options remain very limited. In order to rapidly discover lead compounds for clinical use, we initiated a program of combined structure-assisted drug design, virtual drug screening and high-throughput screening to identify new drug leads that target the COVID-19 virus main protease (M pro ). M pro is a key CoV enzyme, which plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for this virus 5,6 . Here, we identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of COVID-19 virus M pro in complex with this compound. Next, through a combination of structure-based virtual and high-throughput screening, we assayed over 10,000 compounds including approved drugs, drug candidates in clinical trials, and other pharmacologically active compounds as inhibitors of M pro . Six of these compounds inhibited M pro with IC 50 values ranging from 0.67 to 21.4 μM. Ebselen also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of this screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases for which no specific drugs or vaccines are available.CoVs infect humans and other animal species, causing a variety of highly prevalent and severe diseases, including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS) 7 . The COVID-19 virus genome is comprised of ~30,000 nucleotides; its replicase gene encodes two overlapping polyproteins, pp1a and pp1ab, required for viral replication and transcription 3,4 . The functional polypeptides are released from the polyproteins by extensive proteolytic processing, predominantly by a 33.8-kDa main protease (M pro ), also referred to as the 3C-like protease. M pro digests the polyprotein at no less than 11 conserved sites, starting with the autolytic cleavage of this enzyme itself from pp1a and pp1ab 8 . The functional importance of M pro in the viral life cycle, together with the absence of closely related homologues in humans, identify the M pro as an attractive target for antiviral drug design 9 .To facilitate the rapid discovery of antiviral compounds with clinical potential, we developed a strategy combining structure-assisted drug design, virtual drug screening and high-throughput screening to repurpose existing drugs to target COVID-19 virus M pro . Establishing a high-throughput activity assayRecombinant COVID-19 virus M pro with native N and C termini was expressed in Escherichia coli and subsequently purified (Extended Data Fig. 1a, b). The molecular weight of COVID-19 virus M pro as determined by mass spectroscopy is 33797.0 Da, consistent with its theoretical molecular weight 337...

show abstract

Section: Discussionmentioning

confidence: 99%

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Jin

et al. 2020

Nature

3,656

121

4,499

View full text Add to dashboard Cite

show abstract

“…The repurposing of approved pharmaceutical drugs and drug candidates provides an alternative approach to rapidly identify potential drug leads to manage rapidly emerging viral infections. Cell-based phenotypic screening has proven to be valuable 30 , but the complexity of this approach is not readily compatible with high-throughput pipelines, and it cannot identify the molecular target or mechanism of action 31 . In this study, the convergence of structure-based ab initio drug design, virtual screening and high-throughput screening proved to be an efficient strategy to find antiviral leads against COVID-19 virus.…”

Section: Discussionmentioning

confidence: 99%

Structure of M^profrom COVID-19 virus and discovery of its inhibitors

Jin

et al. 2020

Preprint

383

625

View full text Add to dashboard Cite

SUMMARYA new coronavirus (CoV) identified as COVID-19 virus is the etiological agent responsible for the 2019-2020 viral pneumonia outbreak that commenced in Wuhan1–4. Currently there is no targeted therapeutics and effective treatment options remain very limited. In order to rapidly discover lead compounds for clinical use, we initiated a program of combined structure-assisted drug design, virtual drug screening and high-throughput screening to identify new drug leads that target the COVID-19 virus main protease (Mpro). Mpro is a key CoV enzyme, which plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for this virus5,6. Here, we identified a mechanism-based inhibitor, N3, by computer-aided drug design and subsequently determined the crystal structure of COVID-19 virus Mpro in complex with this compound. Next, through a combination of structure-based virtual and high-throughput screening, we assayed over 10,000 compounds including approved drugs, drug candidates in clinical trials, and other pharmacologically active compounds as inhibitors of Mpro. Six of these inhibit Mpro with IC50 values ranging from 0.67 to 21.4 μM. Ebselen also exhibited promising antiviral activity in cell-based assays. Our results demonstrate the efficacy of this screening strategy, which can lead to the rapid discovery of drug leads with clinical potential in response to new infectious diseases where no specific drugs or vaccines are available.

show abstract

“…As in other fields of drug development, two basic approaches can be followed to identify novel compounds with efficacy against AE: (i) mechanism-/target-based screening (bottom-up approach), or (ii) phenotypic screening of whole organisms (top-down approach) ( Geary et al, 2015 ; Müller and Hemphill, 2016 ; Aulner et al, 2019 ). For target-based screening, a valid molecular target in the parasite has to be identified and validated, before specific inhibitors are designed and screened.…”

Section: Identification Of Novel Drugs Against Alveolar Echinococcosimentioning

confidence: 99%

“…Phenotypic screening of whole organisms has so far been the approach which led to all anti-parasitic drugs on the market ( Aulner et al, 2019 ). For E. multilocularis and AE, the methods described in 3.1. can be applied for such screenings ( Lundström-Stadelmann et al, 2019 ).…”

Section: Identification Of Novel Drugs Against Alveolar Echinococcosimentioning

confidence: 99%

Drug repurposing applied: Activity of the anti-malarial mefloquine against Echinococcus multilocularis

Lundström‐Stadelmann

Rufener

Hemphill

2020

International Journal for Parasitology: Drugs and Drug Resistan

View full text Add to dashboard Cite

The current chemotherapeutical treatment against alveolar echinococcosis relies exclusively on benzimidazoles, which are not parasiticidal and can induce severe toxicity. There are no alternative treatment options. To identify novel drugs with activity against Echinococcus multilocularis metacestodes, researchers have studied potentially interesting drug targets (e.g. the parasite's energy metabolism), and/or adopted drug repurposing approaches by undertaking whole organism screenings. We here focus on drug screening approaches, which utilize an in vitro screening cascade that includes assessment of the drug-induced physical damage of metacestodes, the impact on metacestode viability and the viability of isolated parasite stem cells, structure-activity relationship (SAR) analysis of compound derivatives, and the mode of action. Finally, once in vitro data are indicative for a therapeutic window, the efficacy of selected compounds is assessed in experimentally infected mice. Using this screening cascade, we found that the anti-malarial mefloquine was active against E. multilocularis metacestodes in vitro and in vivo . To shed more light into the mode of action of mefloquine, SAR analysis on mefloquine analogues was performed. E. multilocularis ferritin was identified as a mefloquine-binding protein, but its precise role as a drug target remains to be elucidated. In mice that were infected either intraperitoneally with metacestodes or orally with eggs, oral treatment with mefloquine led to a significant reduction of parasite growth compared to the standard treatment with albendazole. However, mefloquine was not acting parasiticidally. Assessment of mefloquine plasma concentrations in treated mice showed that levels were reached which are close to serum concentrations that are achieved in humans during long-term malaria prophylaxis. Mefloquine might be applied in human AE patients as a salvage treatment. Future studies should focus on other repurposed anti-infective compounds (MMV665807, niclosamide, atovaquone), which showed stronger in vitro activity against E. multilocularis than mefloquine.

show abstract

Next-Generation Phenotypic Screening in Early Drug Discovery for Infectious Diseases

Cited by 71 publications

References 86 publications

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Structure of M^profrom COVID-19 virus and discovery of its inhibitors

Drug repurposing applied: Activity of the anti-malarial mefloquine against Echinococcus multilocularis

Contact Info

Product

Resources

About

Next-Generation Phenotypic Screening in Early Drug Discovery for Infectious Diseases

Cited by 71 publications

References 86 publications

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Structure of Mprofrom COVID-19 virus and discovery of its inhibitors

Drug repurposing applied: Activity of the anti-malarial mefloquine against Echinococcus multilocularis

Contact Info

Product

Resources

About

Structure of M^profrom COVID-19 virus and discovery of its inhibitors