Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex

Non-structural protein 1 (Nsp1) is a virulence factor found in all beta coronaviruses (b-CoVs). Recent studies have shown that Nsp1 of SARS-CoV-2 virus interacts with the nuclear export receptor complex, which includes nuclear RNA export factor 1 (NXF1) and nuclear transport factor 2-like export factor 1 (NXT1). The NXF1–NXT1 complex plays a crucial role in the transport of host messenger RNA (mRNA). Nsp1 interferes with the proper binding of NXF1 to mRNA export adaptors and its docking to the nuclear pore complex. We propose that drugs targeting the binding surface between Nsp1 and NXF1–NXT1 may be a useful strategy to restore host antiviral gene expression. Exploring this strategy forms the main goals of this paper. Crystal structures of Nsp1 and the heterodimer of NXF1–NXT1 have been determined. We modeled the docking of Nsp1 to the NXF1–NXT1 complex, and discovered repurposed drugs that may interfere with this binding. To our knowledge, this is the first attempt at drug-repurposing of this complex. We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1–NXT1 complex. The top hit was ganirelix, with a docking score of −14.49. Ganirelix competitively antagonizes the gonadotropin releasing hormone receptor (GNRHR) on pituitary gonadotrophs, and induces rapid, reversible suppression of gonadotropin secretion. The conformations of Nsp1 and GNRHR make it unlikely that they interact with each other. Additional drug leads were inferred from the structural analysis of this complex, which are discussed in the paper. These drugs offer several options for therapeutically blocking Nsp1 binding to NFX1–NXT1, which may normalize nuclear export in COVID-19 infection.

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The Great Escape: mRNA Export through the Nuclear Pore Complex

International Journal of Molecular Sciences ◽

10.3390/ijms222111767 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11767

Author(s):

Paola De Magistris

Keyword(s):

Conformational Changes ◽

Nuclear Pore Complex ◽

Nuclear Export ◽

Messenger Rna ◽

Mrna Export ◽

Protein Translation ◽

Nuclear Pore ◽

Body Of Knowledge ◽

Transport Receptors ◽

Basic Characteristics

Nuclear export of messenger RNA (mRNA) through the nuclear pore complex (NPC) is an indispensable step to ensure protein translation in the cytoplasm of eukaryotic cells. mRNA is not translocated on its own, but it forms ribonuclear particles (mRNPs) in association with proteins that are crucial for its metabolism, some of which; like Mex67/MTR2-NXF1/NXT1; are key players for its translocation to the cytoplasm. In this review, I will summarize our current body of knowledge on the basic characteristics of mRNA export through the NPC. To be granted passage, the mRNP cargo needs to bind transport receptors, which facilitate the nuclear export. During NPC transport, mRNPs undergo compositional and conformational changes. The interactions between mRNP and the central channel of NPC are described; together with the multiple quality control steps that mRNPs undergo at the different rings of the NPC to ensure only proper export of mature transcripts to the cytoplasm. I conclude by mentioning new opportunities that arise from bottom up approaches for a mechanistic understanding of nuclear export.

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Virtual Screening of Potential Drug Molecules Against Covid-19 Targets: A Drug Repurposing Approach

Letters in Applied NanoBioScience ◽

10.33263/lianbs111.29652980 ◽

2021 ◽

Vol 11 (1) ◽

pp. 2965-2980

Keyword(s):

Virtual Screening ◽

Drug Repurposing ◽

Structural Protein ◽

Drug Molecules ◽

Main Protease ◽

The World ◽

Nelfinavir Mesylate ◽

Tenofovir Alafenamide ◽

Approved Drugs ◽

Fda Approved Drugs

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shattered normal life across the world. This deadly virus displays many variants and has claimed many lives in various countries. Spike protein plays a major role in the transmission and infectivity of this virus. The scientific community is trying hard to reign this virus and save human lives. In this effort, drug repurposing has emerged as a reliable tool to screen FDA-approved drugs. In the present study, we did a virtual screening of 265 FDA-approved drugs against two important covid-19 targets (Non-structural protein & main protease) with PDB IDs 6W4H, 6LU7, and 6W63. A comparative analysis of the best drugs based on docking score, binding energy, and effective hits was done against both targets. Out of 265 molecules, the best 7 molecules showed reliable hits against both targets. Best seven drugs namely Saquinavir, Indinavir, Tenofovir Alafenamide, Ritonavir, Nelfinavir mesylate, Cefiderocol and Plazomicin. Our results suggest that these ligands, in combination or individually, can be taken as novel prospects for developing a drug against SARS CoV-2.

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Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression

Science Advances ◽

10.1126/sciadv.abe7386 ◽

2021 ◽

Vol 7 (6) ◽

pp. eabe7386 ◽

Cited By ~ 3

Author(s):

Ke Zhang ◽

Lisa Miorin ◽

Tadashi Makio ◽

Ishmael Dehghan ◽

Shengyan Gao ◽

...

Keyword(s):

Gene Expression ◽

Nuclear Export ◽

Messenger Rna ◽

Mrna Export ◽

Host Gene ◽

Nuclear Pore ◽

Host Gene Expression ◽

Host Interactions ◽

Inhibitory Function ◽

Cellular Mrnas

The ongoing unprecedented severe acute respiratory syndrome caused by the SARS-CoV-2 outbreak worldwide has highlighted the need for understanding viral-host interactions involved in mechanisms of virulence. Here, we show that the virulence factor Nsp1 protein of SARS-CoV-2 interacts with the host messenger RNA (mRNA) export receptor heterodimer NXF1-NXT1, which is responsible for nuclear export of cellular mRNAs. Nsp1 prevents proper binding of NXF1 to mRNA export adaptors and NXF1 docking at the nuclear pore complex. As a result, a significant number of cellular mRNAs are retained in the nucleus during infection. Increased levels of NXF1 rescues the Nsp1-mediated mRNA export block and inhibits SARS-CoV-2 infection. Thus, antagonizing the Nsp1 inhibitory function on mRNA export may represent a strategy to restoring proper antiviral host gene expression in infected cells.

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Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015621118 ◽

2021 ◽

Vol 118 (37) ◽

pp. e2015621118

Author(s):

Yichen Li ◽

Vasilisa Aksenova ◽

Mark Tingey ◽

Jingjie Yu ◽

Ping Ma ◽

...

Keyword(s):

Single Molecule ◽

Nuclear Export ◽

Copy Number ◽

Messenger Rna ◽

High Speed ◽

Three Dimensional ◽

Live Cells ◽

Nuclear Pore ◽

Stoichiometric Ratio

The in vivo characterization of the exact copy number and the specific function of each composite protein within the nuclear pore complex (NPC) remains both desirable and challenging. Through the implementation of live-cell high-speed super-resolution single-molecule microscopy, we first quantified the native copies of nuclear basket (BSK) proteins (Nup153, Nup50, and Tpr) prior to knocking them down in a highly specific manner via an auxin-inducible degron strategy. Second, we determined the specific roles that BSK proteins play in the nuclear export kinetics of model messenger RNA (mRNA) substrates. Finally, the three-dimensional (3D) nuclear export routes of these mRNA substrates through native NPCs in the absence of specific BSK proteins were obtained and further validated via postlocalization computational simulations. We found that these BSK proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs within live cells. The absence of Tpr from the NPC predominantly reduces the probability of nuclear mRNAs entering the NPC for export. Complete depletion of Nup153 and Nup50 results in an mRNA nuclear export efficiency decrease of approximately four folds. mRNAs can gain their maximum successful export efficiency as the copy number of Nup153 increased from zero to only half the full complement natively within the NPC. Lastly, the absence of Tpr or Nup153 seems to alter the 3D export routes of mRNAs as they pass through the NPC. However, the removal of Nup50 alone has almost no impact upon mRNA export route and kinetics.

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Structural Basis of Antisickling Effects of Selected FDA Approved Drugs: A Drug Repurposing Study

Current Computer - Aided Drug Design ◽

10.2174/1573409914666180129163711 ◽

2018 ◽

Vol 14 (2) ◽

pp. 106-116 ◽

Cited By ~ 1

Author(s):

Olujide O. Olubiyi ◽

Maryam O. Olagunju ◽

James O. Oni ◽

Abidemi O. Olubiyi

Keyword(s):

Drug Repurposing ◽

Structural Basis ◽

Approved Drugs ◽

Fda Approved Drugs

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Mex67p of Schizosaccharomyces pombeInteracts with Rae1p in Mediating mRNA Export

Molecular and Cellular Biology ◽

10.1128/mcb.20.23.8767-8782.2000 ◽

2000 ◽

Vol 20 (23) ◽

pp. 8767-8782 ◽

Cited By ~ 52

Author(s):

Jin Ho Yoon ◽

Dona C. Love ◽

Anjan Guhathakurta ◽

John A. Hanover ◽

Ravi Dhar

Keyword(s):

Nuclear Export ◽

Rna Binding ◽

Fluorescent Protein ◽

Synthetic Lethality ◽

Sequence Similarity ◽

Mrna Export ◽

Nuclear Periphery ◽

Nuclear Pore ◽

Multicopy Suppressor ◽

Accessory Factor

ABSTRACT We identified the Schizosaccharomyces pombe mex67 gene (spmex67) as a multicopy suppressor of rae1-167 nup184-1 synthetic lethality and the rae1-167 tsmutation. spMex67p, a 596-amino-acid-long protein, has considerable sequence similarity to the Saccharomyces cerevisiae Mex67p (scMex67p) and human Tap. In contrast toscMEX67, spmex67 is essential for neither growth nor nuclear export of mRNA. However, an spmex67 null mutation (Δmex67) is synthetically lethal with therae1-167 mutation and accumulates poly(A)+ RNA in the nucleus. We identified a central region (149 to 505 amino acids) within spMex67p that associates with a complex containing Rae1p that complements growth and mRNA export defects of therae1-167 Δmex67 synthetic lethality. This region is devoid of RNA-binding, N-terminal nuclear localization, and the C-terminal nuclear pore complex-targeting regions. The (149–505)-green fluorescent protein (GFP) fusion is found diffused throughout the cell. Overexpression of spMex67p inhibits growth and mRNA export and results in the redistribution of the diffused localization of the (149–505)-GFP fusion to the nucleus and the nuclear periphery. These results suggest that spMex67p competes for essential mRNA export factor(s). Finally, we propose that the 149–505 region of spMex67p could act as an accessory factor in Rae1p-dependent transport and that spMex67p participates at various common steps with Rae1p export complexes in promoting the export of mRNA.

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Screening of an FDA-Approved Library for Novel Drugs against Y. pestis

Antibiotics ◽

10.3390/antibiotics10010040 ◽

2021 ◽

Vol 10 (1) ◽

pp. 40

Author(s):

David Gur ◽

Theodor Chitlaru ◽

Emanuelle Mamroud ◽

Ayelet Zauberman

Keyword(s):

Drug Repurposing ◽

Mortality Rates ◽

Systematic Screening ◽

Antibiotic Resistant ◽

Gram Negative ◽

Therapy Initiation ◽

Novel Drugs ◽

Resistant Strains ◽

Approved Drugs ◽

Fda Approved Drugs

Yersinia pestis is a Gram-negative pathogen that causes plague, a devastating disease that kills millions worldwide. Although plague is efficiently treatable by recommended antibiotics, the time of antibiotic therapy initiation is critical, as high mortality rates have been observed if treatment is delayed for longer than 24 h after symptom onset. To overcome the emergence of antibiotic resistant strains, we attempted a systematic screening of Food and Drug Administration (FDA)-approved drugs to identify alternative compounds which may possess antibacterial activity against Y. pestis. Here, we describe a drug-repurposing approach, which led to the identification of two antibiotic-like activities of the anticancer drugs bleomycin sulfate and streptozocin that have the potential for designing novel antiplague therapy approaches. The inhibitory characteristics of these two drugs were further addressed as well as their efficiency in affecting the growth of Y. pestis strains resistant to doxycycline and ciprofloxacin, antibiotics recommended for plague treatment.

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Repurposing of Antimicrobial Agents for Cancer Therapy: What Do We Know?

Cancers ◽

10.3390/cancers13133193 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3193

Author(s):

Christina Pfab ◽

Luisa Schnobrich ◽

Samir Eldnasoury ◽

André Gessner ◽

Nahed El-Najjar

Keyword(s):

Clinical Trials ◽

Antimicrobial Agents ◽

Large Body ◽

Drug Repurposing ◽

Extensive Discussion ◽

Attrition Rates ◽

Beneficial Effects ◽

Stage Of Development ◽

Development Costs ◽

Approved Drugs

The substantial costs of clinical trials, the lengthy timelines of new drug discovery and development, along the high attrition rates underscore the need for alternative strategies for finding quickly suitable therapeutics agents. Given that most approved drugs possess more than one target tightly linked to other diseases, it encourages promptly testing these drugs in patients. Over the past decades, this has led to considerable attention for drug repurposing, which relies on identifying new uses for approved or investigational drugs outside the scope of the original medical indication. The known safety of approved drugs minimizes the possibility of failure for adverse toxicology, making them attractive de-risked compounds for new applications with potentially lower overall development costs and shorter development timelines. This latter case is an exciting opportunity, specifically in oncology, due to increased resistance towards the current therapies. Indeed, a large body of evidence shows that a wealth of non-cancer drugs has beneficial effects against cancer. Interestingly, 335 drugs are currently being evaluated in different clinical trials for their potential activities against various cancers (Redo database). This review aims to provide an extensive discussion about the anti-cancer activities exerted by antimicrobial agents and presents information about their mechanism(s) of action and stage of development/evaluation.

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The crucial roles of N6-methyladenosine (m6A) modification in the carcinogenesis and progression of colorectal cancer

Cell & Bioscience ◽

10.1186/s13578-021-00583-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhihao Fang ◽

Yiqiu Hu ◽

Jinhui Hu ◽

Yanqin Huang ◽

Shu Zheng ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Nuclear Export ◽

Messenger Rna ◽

Regulatory Proteins ◽

Biological Processes ◽

The Past ◽

Common Cancer ◽

Potential Applications ◽

Regulated Gene Expression

AbstractAs the predominant modification in RNA, N6-methyladenosine (m6A) has attracted increasing attention in the past few years since it plays vital roles in many biological processes. This chemical modification is dynamic, reversible and regulated by several methyltransferases, demethylases and proteins that recognize m6A modification. M6A modification exists in messenger RNA and affects their splicing, nuclear export, stability, decay, and translation, thereby modulating gene expression. Besides, the existence of m6A in noncoding RNAs (ncRNAs) could also directly or indirectly regulated gene expression. Colorectal cancer (CRC) is a common cancer around the world and of high mortality. Increasing evidence have shown that the changes of m6A level and the dysregulation of m6A regulatory proteins have been implicated in CRC carcinogenesis and progression. However, the underlying regulation laws of m6A modification to CRC remain elusive and better understanding of these mechanisms will benefit the diagnosis and therapy. In the present review, the latest studies about the dysregulation of m6A and its regulators in CRC have been summarized. We will focus on the crucial roles of m6A modification in the carcinogenesis and development of CRC. Moreover, we will also discuss the potential applications of m6A modification in CRC diagnosis and therapeutics.

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