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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 93,254 bioRxiv papers from 397,991 authors.

Most downloaded bioRxiv papers, since beginning of last month

in category biochemistry

3,084 results found. For more information, click each entry to expand.

1: Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design
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Posted to bioRxiv 29 Apr 2020

Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design
1,403 downloads biochemistry

Wioletta Rut, Zongyang Lv, Mikolaj Zmudzinski, Stephanie Patchett, Digant Nayak, Scott J Snipas, Farid El Oualid, Tony T. Huang, Miklos Bekes, Marcin Drag, Shaun K Olsen

In December 2019, the first cases of a novel coronavirus infection causing COVID-19 were diagnosed in Wuhan, China. Viral Papain-Like cysteine protease (PLpro, NSP3) is essential for SARS-CoV-2 replication and represents a promising target for the development of antiviral drugs. Here, we used a combinatorial substrate library containing natural and a wide variety of nonproteinogenic amino acids and performed comprehensive activity profiling of SARS-CoV-2-PLpro. On the scaffold of best hits from positional scanning we designed optimal fluorogenic substrates and irreversible inhibitors with a high degree of selectivity for SARS PLpro variants versus other proteases. We determined crystal structures of two of these inhibitors (VIR250 and VIR251) in complex with SARS-CoV-2-PLpro which reveals their inhibitory mechanisms and provides a structural basis for the observed substrate specificity profiles. Lastly, we demonstrate that SARS-CoV-2-PLpro harbors deISGylating activities similar to SARS-CoV-1-PLpro but its ability to hydrolyze K48-linked Ub chains is diminished, which our sequence and structure analysis provides a basis for. Altogether this work has revealed the molecular rules governing PLpro substrate specificity and provides a framework for development of inhibitors with potential therapeutic value or drug repositioning. ### Competing Interest Statement F.E.O. declares competing financial interests as co-founders and shareholder of UbiQ Bio BV. M.B. is an employee and shareholder of Arvinas, Inc. The remaining authors declare no competing interests.

2: Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor
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Posted to bioRxiv 26 Jun 2020

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor
1,246 downloads biochemistry

Peng Zhao, Jeremy L Praissman, Oliver C. Grant, Yongfei Cai, Tianshu Xiao, Katelyn E Rosenbalm, Kazuhiro Aoki, Benjamin P. Kellman, Robert Bridger, Dan H. Barouch, Melinda A. Brindley, Nathan E. Lewis, Michael Tiemeyer, Bing Chen, Robert J. Woods, Lance Wells

The current COVID-19 pandemic is caused by the SARS-CoV-2 betacoronavirus, which utilizes its highly glycosylated trimeric Spike protein to bind to the cell surface receptor ACE2 glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer Spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatic analyses of natural variants and with existing 3D-structures of both glycoproteins to generate molecular dynamics simulations of each glycoprotein alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation that, taken together, can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection. ### Competing Interest Statement The authors have declared no competing interest.

3: N and O glycosylation of the SARS-CoV-2 spike protein
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Posted to bioRxiv 06 Jul 2020

N and O glycosylation of the SARS-CoV-2 spike protein
788 downloads biochemistry

Miloslav Sanda, Lindsay Morrison, Radoslav Goldman

Covid-19 pandemic outbreak is the reason of the current world health crisis. The development of effective antiviral compounds and vaccines requires detailed descriptive studies of the SARS-CoV-2 proteins. The SARS-CoV-2 spike (S) protein mediates virion binding to the human cells through its interaction with the ACE2 cell surface receptor and is one of the prime immunization targets. A functional virion is composed of three S1 and three S2 subunits created by furin cleavage of the spike protein at R682, a polybasic cleavage sites that differs from the SARS-CoV spike protein of 2002. We observe that the spike protein is O-glycosylated on a threonine (T678) near the furin cleavage site occupied by core-1 and core-2 structures. In addition, we have identified eight additional O-glycopeptides on the spike glycoprotein and we confirmed that the spike protein is heavily N-glycosylated. Our recently developed LC-MS/MS methodology allowed us to identify LacdiNAc structural motives on all occupied N-glycopeptides and polyLacNAc structures on six glycopeptides of the spike protein. In conclusion, our study substantially expands the current knowledge of the spike protein’s glycosylation and enables the investigation of the influence of the O-glycosylation on its proteolytic activation. ### Competing Interest Statement The authors have declared no competing interest.

4: The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2
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Posted to bioRxiv 17 Mar 2020

The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2
776 downloads biochemistry

Erik Procko

The rapid and escalating spread of SARS coronavirus 2 (SARS-CoV-2) poses an immediate public health emergency. The viral spike protein S binds ACE2 on host cells to initiate molecular events that release the viral genome intracellularly. Soluble ACE2 inhibits entry of both SARS and SARS-2 coronaviruses by acting as a decoy for S binding sites, and is a candidate for therapeutic, prophylactic and diagnostic development. Using deep mutagenesis, variants of ACE2 are identified with increased binding to the receptor binding domain of S. Mutations are found across the interface, in the N90-glycosylation motif, and at buried sites where they are predicted to enhance local folding and presentation of the interaction epitope. When single substitutions are combined, large increases in binding can be achieved. The mutational landscape offers a blueprint for engineering high affinity proteins and peptides that block receptor binding sites on S to meet this unprecedented challenge. ### Competing Interest Statement E.P. is the inventor on a provisional patent filing by the University of Illinois claiming mutations in ACE2 described here that enhance binding to S. E.P. is a cofounder of Orthogonal Biologics Inc, which has a license from the University of Illinois.

5: Structure of the full SARS-CoV-2 RNA genome in infected cells
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Posted to bioRxiv 30 Jun 2020

Structure of the full SARS-CoV-2 RNA genome in infected cells
756 downloads biochemistry

Tammy C. T. Lan, Matthew F. Allan, Lauren E. Malsick, Stuti Khandwala, Sherry S. Y. Nyeo, Mark Bathe, Anthony Griffiths, Silvi Rouskin

SARS-CoV-2 is a betacoronavirus with a single-stranded, positive-sense, 30-kilobase RNA genome responsible for the ongoing COVID-19 pandemic. Currently, there are no antiviral drugs or vaccines with proven efficacy, and development of these treatments are hampered by our limited understanding of the molecular and structural biology of the virus. Like many other RNA viruses, RNA structures in coronaviruses regulate gene expression and are crucial for viral replication. Although genome and transcriptome data were recently reported, there is to date little experimental data on predicted RNA structures in SARS-CoV-2 and most putative regulatory sequences are uncharacterized. Here we report the secondary structure of the entire SARS-CoV-2 genome in infected cells at single nucleotide resolution using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq). Our results reveal previously undescribed structures within critical regulatory elements such as the genomic transcription-regulating sequences (TRSs). Contrary to previous studies, our in-cell data show that the structure of the frameshift element, which is a major drug target, is drastically different from prevailing in vitro models. The genomic structure detailed here lays the groundwork for coronavirus RNA biology and will guide the design of SARS-CoV-2 RNA-based therapeutics. ### Competing Interest Statement The authors have declared no competing interest.

6: Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
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Posted to bioRxiv 20 Jul 2020

Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome
685 downloads biochemistry

Kaiming Zhang, Ivan N. Zheludev, Rachel J. Hagey, Marie Teng-Pei Wu, Raphael Haslecker, Yixuan J. Hou, Rachael C. Kretsch, Grigore Pintilie, Ramya Rangan, Wipapat Kladwang, Shanshan Li, Edward A. Pham, Claire Bernardin-Souibgui, Ralph S. Baric, Timothy P. Sheahan, Victoria D′Souza, Jeffrey S Glenn, Wah Chiu, Rhiju Das

Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome. The frameshift stimulation element (FSE) of the SARS-CoV-2 genome is required for balanced expression of essential viral proteins and is highly conserved, making it a potential candidate for antiviral targeting by small molecules and oligonucleotides. To aid global efforts focusing on SARS-CoV-2 frameshifting, we report exploratory results from frameshifting and cellular replication experiments with locked nucleic acid (LNA) antisense oligonucleotides (ASOs), which support the FSE as a therapeutic target but highlight difficulties in achieving strong inactivation. To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA nanostructure tagging method. This is the smallest macromolecule (88 nt; 28 kDa) resolved by single-particle cryo-EM at subnanometer resolution to date. The tertiary structure model, defined to an estimated accuracy of 5.9 Å, presents a topologically complex fold in which the 5′ end threads through a ring formed inside a three-stem pseudoknot. Our results suggest an updated model for SARS-CoV-2 frameshifting as well as binding sites that may be targeted by next generation ASOs and small molecules. ### Competing Interest Statement The authors have declared no competing interest.

7: Distinct conformational states of SARS-CoV-2 spike protein
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Posted to bioRxiv 17 May 2020

Distinct conformational states of SARS-CoV-2 spike protein
678 downloads biochemistry

Yongfei Cai, Jun Zhang, Tianshu Xiao, Hanqin Peng, Sarah M. Sterling, Richard M. Walsh, Shaun Rawson, Sophia Rits-Volloch, Bing Chen

The ongoing SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic has created urgent needs for intervention strategies to control the crisis. The spike (S) protein of the virus forms a trimer and catalyzes fusion between viral and target cell membranes - the first key step of viral infection. Here we report two cryo-EM structures, both derived from a single preparation of the full-length S protein, representing the prefusion (3.1Å resolution) and postfusion (3.3Å resolution) conformations, respectively. The spontaneous structural transition to the postfusion state under mild conditions is independent of target cells. The prefusion trimer forms a tightly packed structure with three receptor-binding domains clamped down by a segment adjacent to the fusion peptide, significantly different from recently published structures of a stabilized S ectodomain trimer. The postfusion conformation is a rigid tower-like trimer, but decorated by N-linked glycans along its long axis with almost even spacing, suggesting possible involvement in a mechanism protecting the virus from host immune responses and harsh external conditions. These findings advance our understanding of how SARS-CoV-2 enters a host cell and may guide development of vaccines and therapeutics. ### Competing Interest Statement The authors have declared no competing interest.

8: Structure of Mpro from COVID-19 virus and discovery of its inhibitors
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Posted to bioRxiv 27 Feb 2020

Structure of Mpro from COVID-19 virus and discovery of its inhibitors
664 downloads biochemistry

Zhenming Jin, Xiaoyu Du, H. Eric Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng, Yinkai Duan, Jing Yu, Lin Wang, Kailin Yang, Fengjiang Liu, Rendi Jiang, Xinglou Yang, Tian You, Xiaoce Liu, Xiuna Yang, Fang Bai, Hong Liu, Xiang Liu, Luke W. Guddat, Wenqing Xu, Gengfu Xiao, Chengfeng Qin, Zhengli Shi, Hualiang Jiang, Zihe Rao, Haitao Yang

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][1]–[4][2]. 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 virus[5][3],[6][4]. 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. [1]: #ref-1 [2]: #ref-4 [3]: #ref-5 [4]: #ref-6

9: SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors
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Posted to bioRxiv 30 Jul 2020

SARS-CoV-2 Spike Protein Interacts with Multiple Innate Immune Receptors
653 downloads biochemistry

Chao Gao, Junwei Zeng, Nan Jia, Kathrin Stavenhagen, Yasuyuki Matsumoto, Hua Zhang, Jiang Li, Adam J Hume, Elke Mühlberger, Irma van Die, Julian Kwan, Kelan Tantisira, Andrew Emili, Richard D. Cummings

The spike (S) glycoprotein in the envelope of SARS-CoV-2 is densely glycosylated but the functions of its glycosylation are unknown. Here we demonstrate that S is recognized in a glycan-dependent manner by multiple innate immune receptors including the mannose receptor MR/CD206, DC-SIGN/CD209, L-SIGN/CD209L, and MGL/CLEC10A/CD301. Single-cell RNA sequencing analyses indicate that such receptors are highly expressed in innate immune cells in tissues susceptible to SARS-CoV-2 infection. Binding of the above receptors to S is characterized by affinities in the picomolar range and consistent with S glycosylation analysis demonstrating a variety of N- and O-glycans as receptor ligands. These results indicate multiple routes for SARS-CoV-2 to interact with human cells and suggest alternative strategies for therapeutic intervention. ### Competing Interest Statement The authors have declared no competing interest.

10: An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19
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Posted to bioRxiv 23 Jun 2020

An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19
643 downloads biochemistry

Jonathan H. Shrimp, Stephen C. Kales, Philip E. Sanderson, Anton Simeonov, Min Shen, Matthew D. Hall

SARS-CoV-2 is the viral pathogen causing the COVID19 global pandemic. Consequently, much research has gone into the development of pre-clinical assays for the discovery of new or repurposing of FDA-approved therapies. Preventing viral entry into a host cell would be an effective antiviral strategy. One mechanism for SARS-CoV-2 entry occurs when the spike protein on the surface of SARS-CoV-2 binds to an ACE2 receptor followed by cleavage at two cut sites (priming) that causes a conformational change allowing for viral and host membrane fusion. TMPRSS2 has an extracellular protease domain capable of cleaving the spike protein to initiate membrane fusion. A validated inhibitor of TMPRSS2 protease activity would be a valuable tool for studying the impact TMPRSS2 has in viral entry and potentially be an effective antiviral therapeutic. To enable inhibitor discovery and profiling of FDA-approved therapeutics, we describe an assay for the biochemical screening of recombinant TMPRSS2 suitable for high throughput application. We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat and gabexate, clinically approved agents in Japan. Also, we profiled a camostat metabolite, FOY-251, and bromhexine hydrochloride, an FDA-approved mucolytic cough suppressant. The rank order potency for the compounds tested are: nafamostat (IC50 = 0.27 nM), camostat (IC50 = 6.2 nM), FOY-251 (IC50 = 33.3 nM) and gabexate (IC50 = 130 nM). Bromhexine hydrochloride showed no inhibition of TMPRSS2. Further profiling of camostat, nafamostat and gabexate against a panel of recombinant proteases provides insight into selectivity and potency. ### Competing Interest Statement The authors have declared no competing interest.

11: Sybodies targeting the SARS-CoV-2 receptor-binding domain
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Posted to bioRxiv 18 Apr 2020

Sybodies targeting the SARS-CoV-2 receptor-binding domain
628 downloads biochemistry

Justin D Walter, Cedric A.J. Hutter, Iwan Zimmermann, Marianne Wyss, Pascal Egloff, Michèle Sorgenfrei, Lea M. Hürlimann, Imre Gonda, Gianmarco Meier, Sille Remm, Sujani Thavarasah, Philippe Plattet, Markus A Seeger

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has resulted in a global health and economic crisis of unprecedented scale. The high transmissibility of SARS-CoV-2, combined with a lack of population immunity and prevalence of severe clinical outcomes, urges the rapid development of effective therapeutic countermeasures. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2. In an expeditious process taking only twelve working days, sybodies were selected entirely in vitro from three large combinatorial libraries, using ribosome and phage display. We obtained six strongly enriched sybody pools against the isolated RBD and identified 63 unique anti-RBD sybodies which also interact in the context of the full-length SARS-CoV-2 spike ectodomain. Among the selected sybodies, six were found to bind to the viral spike with double-digit nanomolar affinity, and five of these also showed substantial inhibition of RBD interaction with human angiotensin-converting enzyme 2 (ACE2). Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. It is anticipated that compact binders such as these sybodies could feasibly be developed into an inhalable drug that can be used as a convenient prophylaxis against COVID-19. Moreover, generation of polyvalent antivirals, via fusion of anti-RBD sybodies to additional small binders recognizing secondary epitopes, could enhance the therapeutic potential and guard against escape mutants. We present full sequence information and detailed protocols for the identified sybodies, as a freely accessible resource. ### Competing Interest Statement Iwan Zimmermann, Pascal Egloff and Markus A. Seeger are founders and shareholders of Linkster Therapeutics AG.

12: Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity
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Posted to bioRxiv 17 Jul 2020

Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity
611 downloads biochemistry

A. Sofia F. Oliveira, Amaurys Avila Ibarra, Isabel Bermudez, Lorenzo Casalino, Zied Gaieb, Deborah K. Shoemark, Timothy Gallagher, Richard B. Sessions, Rommie E. Amaro, Adrian J. Mulholland

Changeux et al. recently suggested that the SARS-CoV-2 spike (S) protein may interact with nicotinic acetylcholine receptors (nAChRs). Such interactions may be involved in pathology and infectivity. Here, we use molecular simulations of validated atomically detailed structures of nAChRs, and of the S protein, to investigate this "nicotinic hypothesis". We examine the binding of the Y674-R685 loop of the S protein to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγδ receptor from Tetronarce californica . Our results indicate that Y674-R685 has affinity for nAChRs and the region responsible for binding contains the PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. In particular, R682 has a key role in the stabilisation of the complexes as it forms interactions with loops A, B and C in the receptors binding pocket. The conformational behaviour of the bound Y674-R685 region is highly dependent on the receptor subtype, adopting extended conformations in the α4β2 and α7 complexes and more compact ones when bound to the muscle-like receptor. In the α4β2 and αβγδ complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket where it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1 and TyrC2. Estimates of binding energy suggest that Y674-R685, forms stable complexes with all three nAChR subtypes, but has highest affinity for the muscle-type receptor. Analyses of the simulations of the full-length S protein show that the Y674-R685 region is accessible for binding, and suggest a potential binding orientation of the S protein with nAChRs. ### Competing Interest Statement The authors have declared no competing interest.

13: Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein
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Posted to bioRxiv 18 Jun 2020

Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein
610 downloads biochemistry

Christine Toelzer, Kapil Gupta, Sathish KN Yadav, Ufuk Borucu, Frederic Garzoni, Oskar Staufer, Julien Capin, Joachim Spatz, Daniel Fitzgerald, Imre Berger, Christiane Schaffitzel

COVID-19, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. Our cryo-EM structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains (RBDs) tightly and specifically bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The pocket also appears to be present in the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. Lipid metabolome remodeling is a key feature of coronavirus infection, with LA at its core. LA metabolic pathways are central to inflammation, immune modulation and membrane fluidity. Our structure directly links LA and S, setting the stage for interventions targeting LA binding and metabolic remodeling by SARS-CoV-2. ### Competing Interest Statement I.B. and D.F. report shareholding in Geneva Biotech SARL unrelated to this Correspondence. I.B and F.G. report shareholding in Imophoron Ltd. unrelated to this Correspondence. A patent application describing drug discovery methods and therapeutic interventions based on the present observations has been filed.

14: The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding.
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Posted to bioRxiv 02 Mar 2020

The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding.
607 downloads biochemistry

Courtney Mycroft-West, Dunhao Su, Stefano Elli, Yong Li, Scott Guimond, Gavin Miller, Jeremy E Turnbull, Edwin Yates, Marco Guerrini, David Fernig, Marcelo Lima, Mark A. Skidmore

Many pathogens take advantage of the dependence of the host on the interaction of hundreds of extracellular proteins with the glycosaminoglycans heparan sulphate to regulate homeostasis and use heparan sulphate as a means to adhere and gain access to cells. Moreover, mucosal epithelia such as that of the respiratory tract are protected by a layer of mucin polysaccharides, which are usually sulphated. Consequently, the polydisperse, natural products of heparan sulphate and the allied polysaccharide, heparin have been found to be involved and prevent infection by a range of viruses including S-associated coronavirus strain HSR1. Here we use surface plasmon resonance and circular dichroism to measure the interaction between the SARS-CoV- 2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) and heparin. The data demonstrate an interaction between the recombinant surface receptor binding domain and the polysaccharide. This has implications for the rapid development of a first-line therapeutic by repurposing heparin and for next-generation, tailor-made, GAG-based antivirals. ### Competing Interest Statement The authors have declared no competing interest.

15: Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein
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Posted to bioRxiv 29 Jun 2020

Phosphorylation modulates liquid-liquid phase separation of the SARS-CoV-2 N protein
586 downloads biochemistry

Christopher R. Carlson, Jonathan B. Asfaha, Chloe M. Ghent, Conor J. Howard, Nairi Hartooni, David O. Morgan

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription in the infected cell. The N protein contains two globular RNA-binding domains surrounded by regions of intrinsic disorder. Phosphorylation of the central disordered region is required for normal viral genome transcription, which occurs in a cytoplasmic structure called the replication transcription complex (RTC). It is not known how phosphorylation controls N protein function. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates. Unmodified N protein forms partially ordered gel-like structures that depend on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces a subset of these interactions, generating a more liquid-like droplet. We speculate that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing. Inhibitors of N protein phosphorylation could therefore serve as antiviral therapy. ### Competing Interest Statement The authors have declared no competing interest.

16: Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of COVID-19 Spike pseudotype virus
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Posted to bioRxiv 22 Jun 2020

Chloroquine and hydroxychloroquine as ACE2 blockers to inhibit viropexis of COVID-19 Spike pseudotype virus
585 downloads biochemistry

Nan Wang, Shengli Han, Rui Liu, Liesu Meng, Huaizhen He, Yongjing Zhang, Cheng Wang, Yanni Lv, Jue Wang, Xiaowei Li, Yuanyuan Ding, Jia Fu, Yajing Hou, Wen Lu, Weina Ma, Yingzhuan Zhan, Bingling Dai, Jie Zhang, Xiaoyan Pan, Shiling Hu, Jiapan Gao, Qianqian Jia, Liyang Zhang, Shuai Ge, Saisai Wang, Peida Liang, Tian Hu, Jiayu Lu, Xiangjun Wang, Huaxin Zhou, Wenjing Ta, Yuejin Wang, Shemin Lu, Langchong He

Background: COVID-19 has been affecting global health since the end of 2019 and so far, no any sign shows the relief of the pandemic. The major issue for controlling the infection disease is lacking efficient prevention and therapeutic approaches. Chloroquine (CQ) and Hydroxychloroquine (HCQ) has been reported to treat the disease, but underlying mechanism still keeps controversial. Purpose: The objective of this study was to investigate whether CQ and HCQ could be an ACE2 blocker to inhibit COVID-19 infection. Methods: In our study, we used CCK-8 stain, flow cytometry and immunofluorescent stain to evaluated the toxicity and autophagy of CQ and HCQ respectively on ACE2 high expressed HEK293T cells (ACE2h cells). We further analyzed the binding character of CQ and HCQ to ACE2 by molecular docking, surface plasmon resonance (SPR) assays and molecule docking, and COVID-19 spike pseudotype virus was also used to observe the viropexis effect of CQ and HCQ in ACEh cells. Results: Results showed that HCQ is slightly more toxic to ACE2h cells than CQ, both CQ and HCQ could bind to ACE2 with KD (7.31±0.62)e-7 and (4.82±0.87)e-7, respectively. They also exhibit equivalent suppression effect for the entrance of COVID-19 spike pseudotype virus into ACE2h cells. Conclusions: CQ and HCQ both inhibite the entrance COVID-19 virus into cell by blocking the binding of the virus with ACE2. Our finding provides a novel insight into the molecular mechanism of CQ and HCQ treatment effect on the virus infection. ### Competing Interest Statement The authors have declared no competing interest.

17: High Affinity Nanobodies Block SARS-CoV-2 Spike Receptor Binding Domain Interaction with Human Angiotensin Converting Enzyme
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Posted to bioRxiv 24 Jul 2020

High Affinity Nanobodies Block SARS-CoV-2 Spike Receptor Binding Domain Interaction with Human Angiotensin Converting Enzyme
574 downloads biochemistry

Thomas J. Esparza, David L. Brody

There are currently no approved effective treatments for SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Nanobodies are 12-15 kDa single-domain antibody fragments that are more stable and amenable to large-scale production compared to conventional antibodies. Nanobodies can also be administered in an inhaled form directly to the lungs. We have isolated several nanobodies that bind to the SARS-CoV-2 spike protein receptor binding domain and block spike protein interaction with the angiotensin converting enzyme 2 (ACE2) receptor. The SARS-CoV-2 spike protein is responsible for viral entry into human cells via interaction with ACE2 on the cell surface. The lead therapeutic candidate, NIH-CoVnb-112, binds to the SARS-CoV-2 spike protein receptor binding domain at approximately 5 nM affinity, and blocks spike protein interaction with the human ACE2 receptor at approximately 0.02 micrograms/mL EC50 (1.1 nM). The affinity and blocking potency of NIH-CoVnb-112 are substantially better than previously reported candidate nanobody therapeutics for SARS CoV-2, and bind to a distinct site. Furthermore, NIH-CoVnb-112 blocks interaction between ACE2 and several high affinity variant forms of the spike protein. When multimerized or combined with other nanobodies, the effective affinity and blocking interactions may be even more potent, as has been well described for other nanobody therapeutics. These resulting nanobodies have therapeutic, preventative, and diagnostic potential. ### Competing Interest Statement The authors have declared no competing interest.

18: Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
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Posted to bioRxiv 12 Jun 2020

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate
559 downloads biochemistry

Christiane Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis, Christopher Y. Park, Avinash Boppana, Ethan Fritch, Yixuan J. Hou, Chandra Theesfeld, Olga G. Troyanskaya, Ralph S. Baric, Timothy P. Sheahan, Kevin Weeks, Amy S. Gladfelter

A mechanistic understanding of the SARS-CoV-2 viral replication cycle is essential to develop new therapies for the COVID-19 global health crisis. In this study, we show that the SARS-CoV-2 nucleocapsid protein (N-protein) undergoes liquid-liquid phase separation (LLPS) with the viral genome, and propose a model of viral packaging through LLPS. N-protein condenses with specific RNA sequences in the first 1000 nts (5'-End) under physiological conditions and is enhanced at human upper airway temperatures. N-protein condensates exclude non-packaged RNA sequences. We comprehensively map sites bound by N-protein in the 5'-End and find preferences for single-stranded RNA flanked by stable structured elements. Liquid-like N-protein condensates form in mammalian cells in a concentration-dependent manner and can be altered by small molecules. Condensation of N-protein is sequence and structure specific, sensitive to human body temperature, and manipulatable with small molecules thus presenting screenable processes for identifying antiviral compounds effective against SARS-CoV-2. ### Competing Interest Statement K.M.W. is an advisor to and holds equity in Ribometrix, to which mutational profiling (MaP) technologies have been licensed. All other authors declare that they have no competing interests.

19: Stabilizing the Closed SARS-CoV-2 Spike Trimer
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Posted to bioRxiv 10 Jul 2020

Stabilizing the Closed SARS-CoV-2 Spike Trimer
559 downloads biochemistry

Jarek Juraszek, Lucy Rutten, Sven Blokland, Pascale Bouchier, Richard Voorzaat, Tina Ritschel, Mark J.G. Bakkers, Ludovic L.R. Renault, Johannes P.M. Langedijk

The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers, with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify two regions in the S-protein critical for the protein's stability: the heptad repeat region 1 of the S2 subunit and subunit domain 1 at the interface with S2. We combined a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics. ### Competing Interest Statement The authors have declared no competing interest.

20: Enhancing Colorimetric LAMP Amplification Speed and Sensitivity with Guanidine Chloride
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Posted to bioRxiv 04 Jun 2020

Enhancing Colorimetric LAMP Amplification Speed and Sensitivity with Guanidine Chloride
553 downloads biochemistry

Yinhua Zhang, Guoping Ren, Jackson Buss, Andrew J. Barry, Gregory C. Patton, Nathan A Tanner

Loop-mediated isothermal amplification (LAMP) is a versatile technique for detection of target DNA and RNA, enabling rapid molecular diagnostic assays with minimal equipment. The global SARS-CoV-2 pandemic has presented an urgent need for new and better diagnostic methods, with colorimetric LAMP utilized in numerous studies for SARS-CoV-2 detection. However, the sensitivity of colorimetric LAMP in early reports has been below that of the standard RT-qPCR tests, and we sought to improve performance. Here we report the use of guanidine hydrochloride and combined primer sets to increase speed and sensitivity in colorimetric LAMP, bringing this simple method up to the standards of sophisticated technique and enabling accurate and high-throughput diagnostics. ### Competing Interest Statement The authors are employees of New England Biolabs, manufacturer of reagents described in the manuscript.

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