scholarly journals A genetic trap in yeast for inhibitors of SARS-CoV-2 main protease

2021 ◽  
Author(s):  
Hanna Alalam ◽  
Sunniva Sigurdardóttir ◽  
Catarina Bourgard ◽  
Ievgeniia A. Tiukova ◽  
Ross D King ◽  
...  

The ongoing COVID-19 pandemic urges searches for antiviral agents that can block infection or ameliorate its symptoms. Using dissimilar search strategies for new antivirals will improve our overall chances of finding effective treatments. Here, we have established an experimental platform for screening of small molecule inhibitors of SARS-CoV-2 main protease in Saccharomyces cerevisiae cells, genetically engineered to enhance cellular uptake of small molecules in the environment. The system consists of a fusion of the E. coli toxin MazF and its antitoxin MazE, with insertion of a protease cleavage site in the linker peptide connecting the MazE and MazF moieties. Expression of the viral protease confers cleavage of the MazEF fusion, releasing the MazF toxin from its antitoxin, resulting in growth inhibition. In the presence of a small molecule inhibiting the protease, cleavage is blocked and the MazF toxin remains inhibited, promoting growth. The system thus allows positive selection for inhibitors. The engineered yeast strain is tagged with a fluorescent marker protein, allowing precise monitoring of its growth in the presence or absence of inhibitor. We detect an established main protease inhibitor down to 10 μM by a robust growth increase. The system is suitable for robotized large-scale screens. It allows in vivo evaluation of drug candidates, and is rapidly adaptable for new variants of the protease with deviant site specificities.

2010 ◽  
Vol 107 (43) ◽  
pp. 18342-18347 ◽  
Author(s):  
C. Samara ◽  
C. B. Rohde ◽  
C. L. Gilleland ◽  
S. Norton ◽  
S. J. Haggarty ◽  
...  

2020 ◽  
Vol 4 (14) ◽  
pp. 3357-3367 ◽  
Author(s):  
Rafet Basar ◽  
May Daher ◽  
Nadima Uprety ◽  
Elif Gokdemir ◽  
Abdullah Alsuliman ◽  
...  

Abstract Virus-specific T cells have proven highly effective for the treatment of severe and drug-refractory infections after hematopoietic stem cell transplant (HSCT). However, the efficacy of these cells is hindered by the use of glucocorticoids, often given to patients for the management of complications such as graft-versus-host disease. To address this limitation, we have developed a novel strategy for the rapid generation of good manufacturing practice (GMP)–grade glucocorticoid-resistant multivirus-specific T cells (VSTs) using clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) gene-editing technology. We have shown that deleting the nuclear receptor subfamily 3 group C member 1 (NR3C1; the gene encoding for the glucocorticoid receptor) renders VSTs resistant to the lymphocytotoxic effect of glucocorticoids. NR3C1-knockout (KO) VSTs kill their targets and proliferate successfully in the presence of high doses of dexamethasone both in vitro and in vivo. Moreover, we developed a protocol for the rapid generation of GMP-grade NR3C1 KO VSTs with high on-target activity and minimal off-target editing. These genetically engineered VSTs promise to be a novel approach for the treatment of patients with life-threatening viral infections post-HSCT on glucocorticoid therapy.


2015 ◽  
Vol 6 (5) ◽  
pp. 2795-2801 ◽  
Author(s):  
Catherine M. Clavel ◽  
Patrycja Nowak-Sliwinska ◽  
Emilia Păunescu ◽  
Arjan W. Griffioen ◽  
Paul J. Dyson

Hyperthermia used as an adjuvant with chemotherapy is highly promising in the treatment of certain cancers.


2020 ◽  
Author(s):  
Mikolaj Zmudzinski ◽  
Wioletta Rut ◽  
Kamila Olech ◽  
Jarosław Granda ◽  
Mirosław Giurg ◽  
...  

AbstractProteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage - a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and anti-viral assays. In this study, we screened a collection of 23 ebselen derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Our work shows that ebselen constitutes a promising platform for development of new antiviral agents targeting both SARS-CoV-2 PLpro and Mpro.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 266-266
Author(s):  
Shan Lin ◽  
Clement Larrue ◽  
Nastassja K. Scheidegger ◽  
Bo Kyung A. Seong ◽  
Neekesh V Dharia ◽  
...  

Abstract First-generation, large-scale functional genomic screens have revealed hundreds of potential genetic vulnerabilities in acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival. Because these large-scale genetic screens were primarily performed in vitro in established AML cell lines, their translational relevance has been debated. Therefore, we established a protocol for CRISPR screening in orthotopic xenograft models of human AML, including patient-derived-xenograft (PDX) models that are tractable for CRISPR-editing. We first defined experimental conditions necessary for an optimal in vivo screen via barcoding experiments. We determined that sub-lethal irradiation was necessary for improved barcode representation in bone marrow and to reduce mouse-to-mouse variation. Moreover, it was critical to combine samples from multiple mice to achieve complete in vivo library representation. Next, using the Broad DepMap and other publicly available functional genomic screen data, we identified 200 genes that were stronger dependencies in AML cell lines compared to all other cancer types screened. Using this list, we created a secondary library and performed parallel in vivo and in vitro screens using the MV4-11 and U937 cell lines and a PDX model. In vitro and in vivo hits were surprisingly well correlated, although a modest number of targets did not score well in vivo. Notably, dependencies identified across AML cell line models were strongly recapitulated in the PDX model, validating the application of AML cell lines for dependency discovery. Our in vivo screens nominated the mitochondria-localized RING-type ubiquitin E3 ligase MARCH5 as a potential therapeutic target in AML. Using CRISPR, we first validated this in vitro dependency on MARCH5 and determined that MARCH5 is a critical guardian to prevent apoptosis in AML. MARCH5 depletion activates the canonical mitochondrial apoptosis pathway in a BAX/BAK1-dependent manner. Multiple genome-wide screens revealed that a dependency on MARCH5 is strongly correlated with a dependency on MCL1, but not other anti-apoptotic BCL2-family members, across the AML cell lines in the screen. As observed with MCL1 inhibition, MARCH5 depletion sensitized AML cells to venetoclax, a BCL2-specific inhibitor FDA-approved in combination with a hypomethylating agent for the treatment of older adults with AML. Importantly, MARCH5 depletion diminished the venetoclax resistance induced by MCL1 overexpression but not that caused by BCLXL overexpression. Altogether, these results suggest that MARCH5 is required for maintaining MCL1 activity specifically. Since there are no small molecule inhibitors directed against MARCH5, we deployed a dTAG system as an approximation of pharmacological inhibition. This approach uses a hetero-bifunctional small molecule that binds the FKBP12 F36V-fused MARCH5 and the E3 ligase VHL, leading to the ubiquitination and proteasome-mediated degradation of the fusion protein. dTAG-MARCH5 cells were established via deleting endogenous MARCH5 by CRISPR and expressing exogenous FKBP-tagged MARCH5 protein. MARCH5 degradation with the dTAG molecule dTAG V-1 markedly impaired cell growth in vitro. Additionally, we demonstrated the utility of dTAG system in vivo using a PDX model. The combination treatment of dTAG V-1 and venetoclax elicited a much stronger anti-leukemic effect compared to the treatment with only venetoclax or dTAG V-1, further highlighting MARCH5 as a promising synergistic target for enhancing the efficacy of venetoclax in AML. Taken together, our in vivo screening approach, coupled with CRISPR-competent PDX models and dTAG-directed protein degradation, constitute a useful platform for prioritizing AML targets emerging from in vitro screens to serve as the starting point for therapy development. Disclosures Dharia: Genentech: Current Employment. Piccioni: Merck Research Laboratories: Current Employment. Stegmaier: Bristol Myers Squibb: Consultancy; KronosBio: Consultancy; AstraZeneca: Consultancy; Auron Therapeutics: Consultancy, Current equity holder in publicly-traded company; Novartis: Research Funding.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3484-3484 ◽  
Author(s):  
Harald Herrmann ◽  
Katharina Blatt ◽  
Junwei Shi ◽  
Amy R. Rappaport ◽  
Karoline V. Gleixner ◽  
...  

Abstract Abstract 3484 Acute myeloid leukemia (AML) is a stem cell-derived malignancy characterized by uncontrolled proliferation and accumulation of myeloblasts in hematopoietic tissues. The clinical course and prognosis in AML vary depending on deregulated genes, cell type(s) involved, and the biological properties of the clone. In most variants of AML, the complexity and heterogeneity of oncogenomes pose a challenge for the development of effective targeted therapeutics. However, diverse genetic aberrations in AML typically converge functionally to dysregulate the same cellular core processes. One key event is the corruption of myeloid cell-fate programs resulting in the generation of aberrantly self-renewing leukemia stem cells (LSC), which maintain and propagate the disease and are often resistant to conventional chemotherapy. Hence, strategies aimed at terminating aberrant self-renewal and eradicating LSC are considered as key for the development of more effective AML therapies. In an effort to systematically probe genes involved in chromatin regulation as potential therapeutic targets, we recently employed an unbiased screening approach combining AML mouse models and new in-vivo RNAi technologies, through which we identified the epigenetic ‘reader' BRD4 as new candidate drug target in AML (Zuber et al., Nature, in press). Inhibition of BRD4 using RNAi or a new small-molecule inhibitor (JQ1) blocking BRD4 binding to acetylated histones, showed profound antileukemic effects in AML mouse models, in all human AML cell lines tested (n=8) as well as in primary AML cells. In all models tested, BRD4 suppression was found to trigger apoptosis as well as terminal myeloid differentiation, and potently suppressed expression programs previously associated with LSC. As one key target, we observed a dramatic transcriptional repression of MYC, which recently has been discussed as core component of an LSC associated transcriptional module. To further evaluate suppression of BRD4 as a potential therapeutic approach to eradicate LSC in human AML, we analyzed the effects of JQ1 in primary AML cells obtained from 17 patients with freshly diagnosed or relapsed/refractory AML (females, n=5, males, n=12, median age: 54 years; range: 21–80 years). In unfractionated primary AML cells, submicromolar doses of JQ1 were found to induce major growth-inhibitory effects (IC50 between 0.05 and 0.5 μM) in a broad spectrum of AML subtypes. No differences in IC50 values were seen when comparing drug effects in AML cells kept in the presence or absence of growth-stimulating cytokines (G-CSF, IL-3, SCF). In addition, JQ1 treatment effectively triggered apoptosis in all patients tested, with similar anti-leukemic activities observed in newly diagnosed pts and refractory/relapsed AML. To further evaluate the clinical value of BRD4 as a clinically relevant target in AML, we analyzed the effect of JQ1 on AML LSC. In these experiments, JQ1 effectively induced apoptosis in CD34+/CD38+ progenitor cells as well as in CD34+/CD38− AML stem cells in all donors examined as evidenced by combined surface/Annexin-V staining. Furthermore, JQ1 was found to induce morphologic signs of maturation in 6 of 7 patients examined, thereby confirming our previous data obtained in mouse AML cells. Finally, we were able to show that JQ1 synergizes with Ara-C in inducing growth inhibition in HL60 cells and KG-1 cells. In summary, our data show that small-molecule inhibition of BRD4 has strong anti-leukemic effects in a broad range of AML subtypes. Furthermore, our results support the notion that JQ1's ability to suppress LSC specific transcriptional modules may translate into a therapeutic entry point for eradicating LSC in primary AML. While a more extensive in vivo evaluation of these effects, as well as the development of pharmacologically improved compounds will be required, all existing data unambiguously highlight small-molecule inhibition of BRD4 as a new promising concept in AML therapy. Disclosures: No relevant conflicts of interest to declare.


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