Proteolysis Targeting Chimeras in Antiviral Research
2022; Future Science Ltd; Volume: 14; Issue: 7 Linguagem: Inglês
10.4155/fmc-2022-0005
ISSN1756-8927
AutoresJenny Desantis, Laura Goracci,
Tópico(s)Ubiquitin and proteasome pathways
ResumoFuture Medicinal ChemistryVol. 14, No. 7 EditorialOpen AccessProteolysis targeting chimeras in antiviral researchJenny Desantis & Laura GoracciJenny Desantis https://orcid.org/0000-0002-2334-934XDepartment of Chemistry, Biology & Biotechnology, University of Perugia, via Elce di Sotto 8, Perugia, 06123, ItalySearch for more papers by this author & Laura Goracci *Author for correspondence: Tel.: +39 075 585 5632; E-mail Address: laura.goracci@unipg.ithttps://orcid.org/0000-0002-9282-9013Department of Chemistry, Biology & Biotechnology, University of Perugia, via Elce di Sotto 8, Perugia, 06123, ItalySearch for more papers by this authorPublished Online:8 Feb 2022https://doi.org/10.4155/fmc-2022-0005AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInRedditEmail Keywords: antiviral drugscytomegalovirushepatitis C virusinfluenzaPROTACSARS-CoV-2targeted protein degradationTargeted protein degradation (TPD) technology clearly represents a hot topic in drug design that is emerging as a new, exciting approach to the removal of disease-related protein targets from cells [1,2]. Indeed, proteolysis targeting chimeras (PROTACs) are hetero-bifunctional molecules with one end binding to a protein of interest (POI) and the other end, joined by a linker, hijacking an E3 ligase, thus leading to the formation of POI–PROTAC–E3 ternary complexes. This forced interaction can induce POI ubiquitination and its subsequent degradation through the cellular ubiquitin-proteasome system [3]. Since PROTACs are not degraded during the process, this means that a single PROTAC molecule can promote the ubiquitination and degradation of many POI equivalents. This catalytic and event-driven mechanism enables PROTACs to have many advantages over traditional protein inhibitors, such as removing all the POI functions at once, achieving a more prolonged biologic effect, reducing off-target side effects and toxicity and, above all, overcoming drug resistance evolving by either the mutation of a target protein or changes in its abundance [3–5].Although the application of PROTAC technology has been widely confirmed to be successful in cancer-related target proteins (with more than a dozen drug candidates entering clinical investigation [1,2]), their exploration remains marginal in the field of antivirals. Nevertheless, recent studies have envisioned or proven that PROTACs may represent a new weapon to fight pathogenic viruses by inducing the degradation of either viral or host-related protein targets [4,6].One of the first investigations on the applicability of PROTAC technology to a virus-related protein was reported in 2014 by Montrose et al. [7]. They developed peptide-based PROTACs that can induce degradation of the hepatitis B virus (HBV)-encoded X-protein in liver cells, a target protein that is essential for HBV replication and is involved in the development of HBV-induced liver disease, including hepatocellular carcinoma. However, the lack of examination for their ability to inhibit HBV replication or liver disease development confines this early work to a preliminary attempt.Thus, the first application of PROTAC technology against a viral target protein was reported by de Wispelaere et al. in 2019 [8]. Starting from telaprevir, which is a peptidomimetic hepatitis C virus (HCV) protease inhibitor that was approved in 2011 but then withdrawn from the market because of the emergence of resistance mutants, a series of cereblon-addressing bifunctional molecules was designed with the aim of inducing the degradation of HCV NS3/4A protease. Among them, compound DGY-08-097 retained the ability to inhibit HCV protease (IC50: 247 nM) while inducing the enzyme to the ubiquitin-proteasome pathway for degradation (DC50: 50 nM). Quantitative mass spectrometric proteomic analysis of transiently transfected cells confirmed that NS3 protease was the only significantly depleted protein among a total of ∼8700 proteins characterized. Most interesting, it retained antiviral activity against telaprevir-resistant mutant HCV (IC50: 508 and 1561 nM), as demonstrated with HCV replicons containing the amino acid substitution V55A or A156S in the NS3/4A protease.In 2020, with the alarming propagation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the exploitation of this technique to counteract coronaviruses (CoV) infection was also envisioned. Indeed, in a review paper by Liu et al. focused on CoV 3C-like protease (3CLpro) inhibitors, PROTAC degraders were hypothesized to be next-generation anti-CoV drugs [9]. At the end of the cited paper, the authors mentioned reversible covalent PROTACs for 3CLpro that were designed and synthesized in their laboratory, but structures and activities were not disclosed.Recently, a computational study was published aiming at furnishing insights into the design of suitable PROTACs for the main protease (Mpro) of SARS-CoV-2 [10]. Protein–protein docking was used to predict the optimal linker length based on the model of the interaction between SARS-CoV-2 Mpro and a cereblon E3 ligase; thus, molecular dynamics simulation and analysis on generated ternary complexes were used to explore the potential of the designed PROTACs to cause degradation [10]. Although this computational study has still not been experimentally validated and computational strategies for PROTAC design are still in their infancy, it proves the active research in the field of PROTAC technology targeting SARS-CoV-2 proteins. Concerns were raised about the deubiquitinase action of papain-like protease (PLpro), which, in principle, could affect the action of PROTACs, but experimental evidence of this countereffect is not available, and deubiquitinase enzymes in human cells do not seem to prevent PROTAC usage in other pathologies [10]. Nevertheless, the study of viral deubiquitinase enzymes could contribute to better understand PROTAC activity in the antivirals field.In addition to Mpro, in an editorial titled ‘Could PROTACs protect us from COVID-19?’, Zhou proposes the SARS-CoV-2 structural envelope protein E as a suitable target to design PROTACs. The following are the major reasons for this target selection: it was successfully used as a target in SARS infections; it is the only protein in the viral envelope that is not glycosylated, and therefore engagement with small molecules is facilitated; and the degradation of this protein is supposed to result in the inhibition of several viral functions (e.g., viral entry, replication and assembly) [11].Focusing on further SARS-CoV-2 targets, while Chatterjee et al. engineered angiotensin converting enzyme-2 (ACE-2)-derived peptide-based PROTACs able to induce SARS-CoV-2 spike protein degradation, thus achieving antiviral activity [12], Haniff et al. investigated the targeted degradation of the SARS-CoV-2 RNA through a ribonuclease targeting chimera (RIBOTAC) designed by connecting an RNA binder with an RNase L-recruiting small molecule [13].Besides targeting viral proteins, SARS-CoV-2 replication can also be inhibited through a host-directed approach. Indeed, host-directed antivirals are believed to be promising tools for overcoming the resistance related to mutations in the viral genome [14,15].In this context, we recently published the first PROTAC application in which a human host protein rather than a viral one was exploited as a target to inhibit SARS-CoV-2 replication [16]. In particular, we were inspired by the hypothesis that the weak anti-SARS-CoV-2 activity of indomethacin (INM) (EC50: ∼100 μm), a non-steroidal anti-inflammatory drug, could be linked to its ability to inhibit prostaglandin E synthase type 2 (PGES-2), which is a host protein that has been found to interact with SARS-CoV-2 NSP7 protein [17,18]. Thus, taking advantage of one of the principles in PROTAC modality, such as that a high affinity or high inhibition potency of POI ligands is not strictly required for ternary complex formation and proteasomal-dependent POI degradation, we synthesized four first-in-class INM-based PROTACs that were tested for their anti-SARS-CoV-2 activity. Among them, compounds 3 and 5, differing in the nature of linker only, displayed an almost fivefold improved ability to inhibit SARS-CoV-2 viral replication (EC50: 18.1 and 21.5 μm, respectively) [16]. When tested on the β-coronavirus HCoV-OC43 and the α-coronavirus HCoV-229E, these compounds were even more potent (EC50: 4.7–2.5 and 36.5–3.2 μm, respectively), thus exhibiting broad-spectrum antiviral activity against pandemic and epidemic CoVs belonging to different genera of the Coronaviridae family.A few weeks after the publication of our IMN-based PROTACs paper, a second paper about host-directed approaches to finding novel antiviral PROTACs was described, this time against human cytomegalovirus (HCMV) [19]. HCMV represents a major opportunistic human pathogenic herpesvirus worldwide. HCMV infection is typically associated with asymptomatic or mild-symptomatic forms, but it can be a major cause of morbidity and mortality in immunosuppressed individuals and one of the main infection-based risks during pregnancy [19]. Since HCMV replication strongly depends on cyclin-dependent-kinase (CDK) cells, in that study, the selected target host protein was CDK9, with the advantage that selective pharmaceutical kinase inhibitors are well known. In addition, previous studies from the same research group demonstrated that inhibitors of several CDKs (1,2,7 and 9) and pan-CDK inhibitors can have strong anti-CMV activity. Therefore, a commercially available CDK9-directed PROTAC named THAL-SNS032 was tested and revealed concentration-dependent anti-HCMV activity in the mod-nanomolar concentration range (EC50: 0.025 μm). Again, THAL-SNS032 showed a broad antiviral effect when tested on murine CMV and inhibited SARS-CoV-2 replication in a human cell line (EC50: 0.22 and 0.11 μm, respectively), although it was inactive against other viruses (e.g., Zika virus) at the experimental condition used.Finally, in 2021, TPD was also explored as a potential anti-influenza virus treatment. Indeed, oseltamivir-based PROTAC derivatives endowed with anti-influenza activity (low μm range) and neuraminidase degradation ability (DC50 from 0.016 to 2.27 μm) were patented by Wuhan University [20].Overall, the work done so far clearly demonstrates that TPD potential deserves further attention to counteract pathogenic viruses, since PROTACs may expand the repertoire of pathogenic proteins to target beyond those of traditional antivirals and, above all can be more effective against resistance mechanisms acquired by the rapidly adapting viruses. We are confident that in the next future the PROTAC technology within the antiviral research field will grow, and further efforts will be devoted to this promising approach to develop next-generation antivirals.Author contributionsJ Desantis and L Goracci both contributed to the conception of this editorial, to the collection and discussion of the data, to the writing of the editorial and to its final approval in the version to be published. Both authors agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.No writing assistance was utilized in the production of this manuscript.Open accessThis work is licensed under the Attribution-NonCommercial-NoDerivatives 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/References1. Garber K. The PROTAC gold rush. Nat. Biotechnol. 40(1), 12–16 (2021).Crossref, Google Scholar2. Mullard A. Targeted protein degraders crowd into the clinic. Nat. Rev. Drug Discov. 20(4), 247–250 (2021).Crossref, Medline, CAS, Google Scholar3. Hu Z, Crews CM. Recent developments in PROTAC-mediated protein degradation: from bench to clinic. ChemBoiChem 23(2), e202100270 (2021).Medline, Google Scholar4. Grohmann C, Marapana DS, Ebert G. Targeted protein degradation at the host-pathogen interface. Mol. 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Science 370(6521), eabe9403 (2020).Crossref, Medline, CAS, Google Scholar19. Hahn F, Hamilton ST, Wangen C et al. Development of a PROTAC-based targeting strategy provides a mechanistically unique mode of anti-cytomegalovirus activity. Int. J. Mol. Sci. 22(23), 12858 (2021).Crossref, Medline, CAS, Google Scholar20. Zhou H, Wu S, Xu Z. CN112592331 (2021).Google ScholarFiguresReferencesRelatedDetails Vol. 14, No. 7 Follow us on social media for the latest updates Metrics History Received 8 January 2022 Accepted 20 January 2022 Published online 8 February 2022 Published in print April 2022 Information© 2022 Laura Goracci & Jenny DesantisKeywordsantiviral drugscytomegalovirushepatitis C virusinfluenzaPROTACSARS-CoV-2targeted protein degradationAuthor contributionsJ Desantis and L Goracci both contributed to the conception of this editorial, to the collection and discussion of the data, to the writing of the editorial and to its final approval in the version to be published. Both authors agree to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending or royalties.No writing assistance was utilized in the production of this manuscript.Open accessThis work is licensed under the Attribution-NonCommercial-NoDerivatives 4.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/PDF download
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