SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design

Srinivasan, Vasundara; Brognaro, H.; Prabhu, Prince R.; Souza, Edmarci Elisa de; Guenther, S.; Reinke, P.; Lane, Thomas J; Ginn, H.; Han, Huijong; Ewert, Wiebke; Sprenger, J.; Koua, F.; Werner, N.; Andaleeb, Hina; Ullah, Najeeb; Franca, B. Alves; Wang, Mengying; Barra, Angélica Luana C.; Perbandt, Markus; Schwinzer, M.; Schmidt, Christina; Brings, Lea; Lorenzen, Kristina; Schubert, Robin; Machado, Rafael Rahal Guaragna; Candido, Erika Donizette; Oliveira, Danielle Bruna Leal; Durigon, Edison Luiz; Yefanov, Oleksandr; Lieske, J.; Gelisio, Luca; Domaracký, M.; Middendorf, Philipp; Groessler, M.; Trost, F.; Galchenkova, M.; Saouane, S.; Hakanpaeae, J.; Wolf, Markus; Turk, Dušan; Pearson, Arwen R.; Chapman, Henry N.; Hinrichs, Winfried; Wrenger, Carsten; Meents, A.; Betzel, Christian

doi:10.1101/2021.11.17.468943

Cited by 4 publications

(13 citation statements)

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“…Three phenolic compoundsmethyl 3,4-dihydroxybenzoate (HE9, 20 ), 4-(2-hydroxyethyl)phenol (YRL, 21 ), and 4-hydroxybenzaldehyde (HBA, 22 )were identified as allosteric SARS-CoV-2 PL pro inhibitors through a high-throughput X-ray crystallization . The screened library contains 500 compounds from the International Center for Chemical and Biological Sciences (ICCBS) Molecular Bank.…”

Section: Sars-cov-2 Plpro Inhibitorsmentioning

confidence: 99%

“… 52 This site is also the drug-binding site for GRL0617 ( 4 ) and its analogues. 16 The X-ray crystal structures for the apo SARS-CoV-2 PL pro , drug-bound form, 52 − 55 and complex forms with ubiquitin ( Figure 2 A) and ISG15 ( Figure 2 B) have been solved, 56 paving the way for structure-based drug design and understanding the virology of PL pro .…”

Section: Introductionmentioning

confidence: 99%

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Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease

Tan

Jadhav

et al. 2022

J. Med. Chem.

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SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PL pro ) mediates the cleavage of viral polyprotein and modulates the host’s innate immune response upon viral infection, rendering it a promising antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PL pro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PL pro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PL pro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PL pro inhibitors to the clinic.

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Section: Sars-cov-2 Plpro Inhibitorsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease

Tan

Jadhav

et al. 2022

J. Med. Chem.

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“…Others also identified 6-thioguanine and 6-mercaptopurine ( Sivakumar and Stein, 2021 ; Swaim et al, 2021 ), which were later invalidated as either inactive or toxic in follow-up cellular assays ( Ma and Wang, 2022 ). Finally, a number of naturally occurring compounds were also highlighted ( Srinivasan et al, 2021 ) for their activity as allosteric inhibitors of PLpro (preprint at the time of writing this Review). Structures of these ( Figure 1 ) highlighted that they inhibit substrate binding at the S2 site of PLpro, a feature not yet seen for any PLpro inhibitors.…”

Section: Overview Of the Plpro Inhibitor Binding Sitementioning

confidence: 99%

Inhibitors of SARS-CoV-2 PLpro

2022

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The emergence of SARS-CoV-2 causing the COVID-19 pandemic, has highlighted how a combination of urgency, collaboration and building on existing research can enable rapid vaccine development to fight disease outbreaks. However, even countries with high vaccination rates still see surges in case numbers and high numbers of hospitalized patients. The development of antiviral treatments hence remains a top priority in preventing hospitalization and death of COVID-19 patients, and eventually bringing an end to the SARS-CoV-2 pandemic. The SARS-CoV-2 proteome contains several essential enzymatic activities embedded within its non-structural proteins (nsps). We here focus on nsp3, that harbours an essential papain-like protease (PLpro) domain responsible for cleaving the viral polyprotein as part of viral processing. Moreover, nsp3/PLpro also cleaves ubiquitin and ISG15 modifications within the host cell, derailing innate immune responses. Small molecule inhibition of the PLpro protease domain significantly reduces viral loads in SARS-CoV-2 infection models, suggesting that PLpro is an excellent drug target for next generation antivirals. In this review we discuss the conserved structure and function of PLpro and the ongoing efforts to design small molecule PLpro inhibitors that exploit this knowledge. We first discuss the many drug repurposing attempts, concluding that it is unlikely that PLpro-targeting drugs already exist. We next discuss the wealth of structural information on SARS-CoV-2 PLpro inhibition, for which there are now ∼30 distinct crystal structures with small molecule inhibitors bound in a surprising number of distinct crystallographic settings. We focus on optimisation of an existing compound class, based on SARS-CoV PLpro inhibitor GRL-0617, and recapitulate how new GRL-0617 derivatives exploit different features of PLpro, to overcome some compound liabilities.

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“…Here we considered additional PLpro binders from the protein data bank. Among these, three recently described phenolic fragments were further analyzed and included in the compound extensions ( Srinivasan et al, 2021 ), as they were found in adjacent binding positions of the S2 site of SARS-CoV-2 PLpro and show partial overlap with our ligands ( Supplementary Figure S5 ). 4-(2-hydroxyethyl)-phenol (YRL; PDB: 7ofs) and 4-hydroxybenzaldehyde (HBA; PDB: 7oft) bind in a pocket next to the phenol moiety of the thiosemicarbazones T1-T5 ( Supplementary Figures S5B, S5C ).…”

Section: Resultsmentioning

confidence: 99%

“…Differences in binding energies between the thiosemicarbazones, caused by the individual phenolic substitution patterns, were reduced for the compound extension by the addition of the second phenol ring. As a result, the extended compounds will most likely not only possess an increased binding affinity but also an increased inhibitory potential as the separate phenolic fragments alone were already shown to inhibit deubiquitination by PLpro ( Srinivasan et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease

et al. 2022

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The papain-like protease (PLpro) of SARS-CoV-2 is essential for viral propagation and, additionally, dysregulation of the host innate immune system. Using a library of 40 potential metal-chelating compounds we performed an X-ray crystallographic screening against PLpro. As outcome we identified six compounds binding to the target protein. Here we describe the interaction of one hydrazone (H1) and five thiosemicarbazone (T1-T5) compounds with the two distinct natural substrate binding sites of PLpro for ubiquitin and ISG15. H1 binds to a polar groove at the S1 binding site by forming several hydrogen bonds with PLpro. T1-T5 bind into a deep pocket close to the polyubiquitin and ISG15 binding site S2. Their interactions are mainly mediated by multiple hydrogen bonds and further hydrophobic interactions. In particular compound H1 interferes with natural substrate binding by sterical hindrance and induces conformational changes in protein residues involved in substrate binding, while compounds T1-T5 could have a more indirect effect. Fluorescence based enzyme activity assay and complementary thermal stability analysis reveal only weak inhibition properties in the high micromolar range thereby indicating the need for compound optimization. Nevertheless, the unique binding properties involving strong hydrogen bonding and the various options for structural optimization make the compounds ideal lead structures. In combination with the inexpensive and undemanding synthesis, the reported hydrazone and thiosemicarbazones represent an attractive scaffold for further structure-based development of novel PLpro inhibitors by interrupting protein-protein interactions at the S1 and S2 site.

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SARS-CoV-2 papain-like protease PLpro in complex with natural compounds reveal allosteric sites for antiviral drug design

Cited by 4 publications

References 58 publications

Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease

Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease

Inhibitors of SARS-CoV-2 PLpro

Hydrazones and Thiosemicarbazones Targeting Protein-Protein-Interactions of SARS-CoV-2 Papain-like Protease

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