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in category biochemistry

6,535 results found. For more information, click each entry to expand.

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

Structure of Mpro from COVID-19 virus and discovery of its inhibitors
26,672 downloads bioRxiv biochemistry

Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Suwen 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 William Guddat, Wenqing Xu, Gengfu Xiao, Chengfeng Qin, Zhengli Shi, Ruotian 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

2: SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
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Posted 21 Dec 2021

SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
23,709 downloads bioRxiv biochemistry

Dhiraj Mannar, James W. Saville, Xing Zhu, Shanti S. Srivastava, Alison M. Berezuk, Katharine Tuttle, Citliali Marquez, Inna Sekirov, Sriram Subramaniam

The newly reported Omicron variant is poised to replace Delta as the most rapidly spread SARS-CoV-2 variant across the world. Cryo-EM structural analysis of the Omicron variant spike protein in complex with human ACE2 reveals new salt bridges and hydrogen bonds formed by mutated residues R493, S496 and R498 in the RBD with ACE2. These interactions appear to compensate for other Omicron mutations such as K417N known to reduce ACE2 binding affinity, explaining our finding of similar biochemical ACE2 binding affinities for Delta and Omicron variants. Neutralization assays show that pseudoviruses displaying the Omicron spike protein exhibit increased antibody evasion, with greater evasion observed in sera obtained from unvaccinated convalescent patients as compared to doubly vaccinated individuals (8- vs 3-fold). The retention of strong interactions at the ACE2 interface and the increase in antibody evasion are molecular factors that likely contribute to the increased transmissibility of the Omicron variant.

3: SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
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Posted 06 Jan 2021

SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
21,142 downloads bioRxiv biochemistry

Jiri Zahradnik, Shir Marciano, Maya Shemesh, Eyal Zoler, Jeanne Chiaravalli, Bjorn Meyer, Yinon Rudich, Orly Dym, Nadav Elad, Gideon Schreiber

SARS-CoV-2 is continually evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2 resulted in the more contagious mutations, S477N, E484K, and N501Y, to be among the first selected, explaining the convergent evolution of the European (20E-EU1), British (501.V1), South African (501.V2), and Brazilian variants (501.V3). Plotting the binding affinity to ACE2 of all RBD mutations against their incidence in the population shows a strong correlation between the two. Further in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity. For example, Q498R epistatic to N501Y. Nevertheless, the high-affinity RBD is also an efficient drug, inhibiting SARS-CoV-2 infection. The 2.9A Cryo-EM structure of the high-affinity complex, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.

4: An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation
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Posted 10 Aug 2020

An ultra-potent synthetic nanobody neutralizes SARS-CoV-2 by locking Spike into an inactive conformation
20,755 downloads bioRxiv biochemistry

Michael Schoof, Bryan Faust, Reuben A. Saunders, Smriti Sangwan, Veronica Rezelj, Nicholas Hoppe, Morgane Boone, Christian B. Billesbølle, Cristina Puchades, Caleigh M. Azumaya, Huong T Kratochvil, Marcell Zimanyi, Ishan Deshpande, Jiahao Liang, Sasha Dickinson, Henry Nguyen, Cynthia M Chio, Gregory E Merz, Michael C Thompson, Devan Diwanji, Kaitlin Schaefer, Aditya A. Anand, Niv Dobzinski, Beth Shoshana Zha, Camille R. Simoneau, Kristoffer E Leon, Kris White, Un Seng Chio, Meghna Gupta, Mingliang Jin, Fei Li, Yanxin Liu, Kaihua Zhang, David Bulkley, Ming Sun, Amber Smith, Alexandrea N. Rizo, Frank Russell Moss, Axel F. Britol, Sergei Pourmal, Raphael Trenker, Thomas Pospiech, Sayan Gupta, Benjamin Barsi-Rhyne, Vladislav Belyy, Andrew W. Barile-Hill, Silke Nock, Yuwei Liu, Nevan J. Krogan, Corie Y. Ralston, Danielle L Swaney, Adolfo García-Sastre, Melanie Ott, Marco Vignuzzi, QCRG Structural Biology Consortium, Peter Walter, Aashish Manglik

Without an effective prophylactic solution, infections from SARS-CoV-2 continue to rise worldwide with devastating health and economic costs. SARS-CoV-2 gains entry into host cells via an interaction between its Spike protein and the host cell receptor angiotensin converting enzyme 2 (ACE2). Disruption of this interaction confers potent neutralization of viral entry, providing an avenue for vaccine design and for therapeutic antibodies. Here, we develop single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. By screening a yeast surface-displayed library of synthetic nanobody sequences, we identified a panel of nanobodies that bind to multiple epitopes on Spike and block ACE2 interaction via two distinct mechanisms. Cryogenic electron microscopy (cryo-EM) revealed that one exceptionally stable nanobody, Nb6, binds Spike in a fully inactive conformation with its receptor binding domains (RBDs) locked into their inaccessible down-state, incapable of binding ACE2. Affinity maturation and structure-guided design of multivalency yielded a trivalent nanobody, mNb6-tri, with femtomolar affinity for SARS-CoV-2 Spike and picomolar neutralization of SARS-CoV-2 infection. mNb6-tri retains stability and function after aerosolization, lyophilization, and heat treatment. These properties may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century. ### Competing Interest Statement M.Schoof, B.Faust, R.Saunders, N.Hoppe, P.Walter, and A.Manglik are inventors on a provisional patent describing anti-Spike nanobodies described in this manuscript.

5: Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
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Posted 20 Feb 2020

Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein
15,651 downloads bioRxiv biochemistry

Alexandra C Walls, Young-Jun Park, M. Alexandra Tortorici, Abigail Wall, Andrew McGuire, David Veesler

The recent emergence of a novel coronavirus associated with an ongoing outbreak of pneumonia (Covid-2019) resulted in infections of more than 72,000 people and claimed over 1,800 lives. Coronavirus spike (S) glycoprotein trimers promote entry into cells and are the main target of the humoral immune response. We show here that SARS-CoV-2 S mediates entry in VeroE6 cells and in BHK cells transiently transfected with human ACE2, establishing ACE2 as a functional receptor for this novel coronavirus. We further demonstrate that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, which correlates with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and other SARS-related CoVs. We determined a cryo-electron microscopy structure of the SARS-CoV-2 S ectodomain trimer, demonstrating spontaneous opening of the receptor-binding domain, and providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal sera potently inhibited SARS-CoV-2 S-mediated entry into target cells, thereby indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.

6: Visual Interpretation of the Meaning of kcat/KM in Enzyme Kinetics
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Posted 10 Dec 2021

Visual Interpretation of the Meaning of kcat/KM in Enzyme Kinetics
14,716 downloads bioRxiv biochemistry

Chiwook Park

kcat and kcat/KM are the two fundamental kinetic parameters in enzyme kinetics. kcat is the first-order rate constant that determines the reaction rate when the enzyme is fully occupied at a saturating concentration of the substrate. kcat/KM is the second-order rate constant that determines the reaction rate when the enzyme is mostly free at a very low concentration of the substrate. Both parameters provide critical information on how the enzyme lowers the energy barriers along the reaction pathway for catalysis. However, it is surprising how often kcat/KM is used inappropriately as a composite parameter derived by dividing kcat with KM to assess both catalytic power and affinity to the substrate of the enzyme. The main challenge in explaining the true meaning of kcat/KM is the difficulty to demonstrate how the reaction energetics of enzyme catalysis determines kcat/KM in a simple way. Here, I report a step-by-step demonstration on how to visualize the meaning of kcat/KM on the reaction energy diagram. By using the reciprocal form of the expression of kcat/KM with the elementary rate constants in kinetic models, I show that kcat/KM is a harmonic sum of several kinetic terms that correspond to the heights of the transition states relative to the free enzyme. Then, I demonstrate that the height of the highest transition state has the dominant influence on kcat/KM, i. e. the step with the highest transition state is the limiting step for kcat/KM. The visualization of the meaning of kcat/KM on the reaction energy diagram offers an intuitive way to understand all the known properties of kcat/KM, including the Haldane relationship.

7: Structure of dimeric full-length human ACE2 in complex with B0AT1
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Posted 18 Feb 2020

Structure of dimeric full-length human ACE2 in complex with B0AT1
14,684 downloads bioRxiv biochemistry

Renhong Yan, Yuanyuan Zhang, Yaning Li, Lu Xia, Qiang Zhou

Angiotensin-converting enzyme 2 (ACE2) is the surface receptor for SARS coronavirus (SARS-CoV) through interaction with its spike glycoprotein (S protein). ACE2 is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome. BAT1 (SLC6A19) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2. Here we present the 2.9 Å resolution cryo-EM structure of full-length human ACE2 in complex with BAT1. The complex, assembled as a dimer of ACE2-BAT1 heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains of ACE2. A newly resolved Collectrin-like domain (CLD) on ACE2 mediates homo-dimerization. The extended TM7 in each BAT1 clamps CLD of ACE2. Structural analysis suggests that the ACE2-BAT1 complex can bind two S proteins simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection.

8: Substrate specificity profiling of SARS-CoV-2 main protease enables design of activity-based probes for patient-sample imaging
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Posted 08 Mar 2020

Substrate specificity profiling of SARS-CoV-2 main protease enables design of activity-based probes for patient-sample imaging
14,550 downloads bioRxiv biochemistry

Wioletta Rut, Katarzyna Groborz, Linlin Zhang, Xinyuanyuan Sun, Mikolaj Zmudzinski, Bartlomiej Pawlik, Wojciech Młynarski, Rolf Hilgenfeld, Marcin Drag

In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed in Wuhan, China. Due to international travel and human-to-human transmission, the virus spread rapidly inside and outside of China. Currently, there is no effective antiviral treatment for coronavirus disease 2019 (COVID-19); therefore, research efforts are focused on the rapid development of vaccines and antiviral drugs. The SARS-CoV-2 main protease constitutes one of the most attractive antiviral drug targets. To address this emerging problem, we have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases, using natural and a large panel of unnatural amino acids. On the basis of these findings, we designed and synthesized an inhibitor and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. Using this approach we visualized SARS-CoV-2 active Mpro within nasopharyngeal epithelial cells of a patient with active COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents or diagnostic tests. ### Competing Interest Statement Wroclaw University of Science and Technology has filed a patent application covering compounds: Ac-Abu-Tle-Leu-Gln-VS, Biotin-PEG(4)-Abu-Tle-Leu-Gln-VS and Cy5-PEG(4)-Abu-Tle-Leu-Gln-VS as well as related compounds with W.R. and M.D. as inventors.

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

The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding.
12,860 downloads bioRxiv biochemistry

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

10: Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate
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Posted 16 Nov 2020

Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate
11,638 downloads bioRxiv biochemistry

Juliane Brun, Snezana Vasiljevic, Bevin Gangadharan, Mario Hensen, Anu V. Chandran, Michelle Hill, J. L. Kiappes, Raymond A. Dwek, Dominic S. Alonzi, Weston B. Struwe, Nicole Zitzmann

Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralisation. Immunogen integrity is therefore important for glycoprotein-based vaccine candidates. Here we show how site-specific glycosylation differs between virus-derived spikes and spike proteins derived from a viral vectored SARS-CoV-2 vaccine candidate. We show that their cellular secretion pathways are unique, resulting in different protein glycosylation and secretion, which may have implications for the resulting immune response and future vaccine design. ### Competing Interest Statement W.B.S. is a shareholder and consultant to Refeyn Ltd. All other authors declare no conflict of interest.

11: Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
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Posted 31 Dec 2021

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
11,447 downloads bioRxiv biochemistry

Matthew McCallum, Nadine Czudnochowski, Laura E. Rosen, Samantha K Zepeda, John E. Bowen, Josh R. Dillen, Abigail Powell, Tristan Croll, Jay Nix, Herbert W Virgin, Davide Corti, Gyorgy Snell, David Veesler

The SARS-CoV-2 Omicron variant of concern evades antibody mediated immunity with an unprecedented magnitude due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and X-ray crystal structures of the spike and RBD bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a structural framework for understanding the marked reduction of binding of all other therapeutic mAbs leading to dampened neutralizing activity. We reveal electrostatic remodeling of the interactions within the spike and those formed between the Omicron RBD and human ACE2, likely explaining enhanced affinity for the host receptor relative to the prototypic virus.

12: 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 29 Apr 2020

Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design
11,295 downloads bioRxiv 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.

13: Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target
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Posted 17 Mar 2020

Structure of RNA-dependent RNA polymerase from 2019-nCoV, a major antiviral drug target
11,160 downloads bioRxiv biochemistry

Yan Gao, Liming Yan, Yucen Huang, Fengjiang Liu, Suwen Zhao, Lin Cao, Tao Wang, Qianqian Sun, Zhenhua Ming, Lianqi Zhang, Ji Ge, Litao Zheng, Ying Zhang, Haofeng Wang, Yan Zhu, Chen Zhu, Tianyu Hu, Tian Hua, Bing Zhang, Xiuna Yang, Jun Li, Haitao Yang, Zhijie Liu, Wenqing Xu, Luke William Guddat, Quan Wang, Zhiyong Lou, Zihe Rao

A novel coronavirus (2019-nCoV) outbreak has caused a global pandemic resulting in tens of thousands of infections and thousands of deaths worldwide. The RNA-dependent RNA polymerase (RdRp, also named nsp12), which catalyzes the synthesis of viral RNA, is a key component of coronaviral replication/transcription machinery and appears to be a primary target for the antiviral drug, remdesivir. Here we report the cryo-EM structure of 2019-nCoV full-length nsp12 in complex with cofactors nsp7 and nsp8 at a resolution of 2.9-Å. Additional to the conserved architecture of the polymerase core of the viral polymerase family and a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain featured in coronaviral RdRp, nsp12 possesses a newly identified β-hairpin domain at its N-terminal. Key residues for viral replication and transcription are observed. A comparative analysis to show how remdesivir binds to this polymerase is also provided. This structure provides insight into the central component of coronaviral replication/transcription machinery and sheds light on the design of new antiviral therapeutics targeting viral RdRp. One Sentence Summary Structure of 2019-nCov RNA polymerase. ### Competing Interest Statement

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

The sequence of human ACE2 is suboptimal for binding the S spike protein of SARS coronavirus 2
10,970 downloads bioRxiv 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.

15: The meaning of the Michaelis-Menten constant: Km describes a steady-state
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Posted 13 Apr 2019

The meaning of the Michaelis-Menten constant: Km describes a steady-state
10,568 downloads bioRxiv biochemistry

Enric I. Canela, Gemma Navarro, José Luis Beltrán, Rafael Franco

Often, in vitro or in vivo enzyme-mediated catalytic events occur far from equilibrium and, therefore, substrate affinity measured as the inverse of ES ⇄ E+S dissociation equilibrium constant ( Kd ) has a doubtful physiological meaning; in practice it is almost impossible to determine Kd (except using stopped-flow or other sophisticated methodologies). The Michaelis-Menten constant ( Km ), the concentration of substrate ([S]) providing half of enzyme maximal activity, is not the ( Kd ). In the simple E+S ⇄ ES → E+P or in more complex models describing S conversion into P, Km must be considered the constant defining the steady state at any substrate concentration. Enzyme kinetics is based on initial rate determination, i.e. in the linear part of the S to P conversion when the concentration of [ES] remains constant while steady state occurs. We also show that Systems Biology issues such as the time required to respond to a system perturbation, is more dependent on k 1, the kinetic constant defining substrateenzyme association, than on Km . Whereas Km is instrumental for biochemical basic and applied approaches, in any physiological condition, an important parameter to be considered is the substrate association rate ( k1 ).

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

Structure of the full SARS-CoV-2 RNA genome in infected cells
10,364 downloads bioRxiv 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.

17: Modified TCA/acetone precipitation of plant proteins for proteomic analysis
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Posted 01 Aug 2018

Modified TCA/acetone precipitation of plant proteins for proteomic analysis
9,807 downloads bioRxiv biochemistry

Liangjie Niu, Hang Zhang, Zhaokun Wu, Wei Wang, Hui Liu, Xiaolin Wu, Wei Wang

Protein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.

18: Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells
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Posted 16 Jan 2018

Homology Directed Repair by Cas9:Donor Co-localization in Mammalian Cells
9,641 downloads bioRxiv biochemistry

Philip JR Roche, Heidi Gytz, Faiz Hussain, Christopher JF Cameron, Denis Paquette, Mathieu Blanchette, Josée Dostie, Bhushan Nagar, Uri David Akavia

Homology directed repair (HDR) induced by site specific DNA double strand breaks (DSB) with CRISPR/Cas9 is a precision gene editing approach that occurs at low frequency in comparison to indel forming non homologous end joining (NHEJ). In order to obtain high HDR percentages in mammalian cells, we engineered Cas9 protein fused to a high-affinity monoavidin domain to deliver biotinylated donor DNA to a DSB site. In addition, we used the cationic polymer, polyethylenimine, to deliver Cas9 RNP-donor DNA complex into the cell. Combining these strategies improved HDR percentages of up to 90% in three tested loci (CXCR4, EMX1, and TLR) in standard HEK293 cells. Our approach offers a cost effective, simple and broadly applicable gene editing method, thereby expanding the CRISPR/Cas9 genome editing toolbox.

19: Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics
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Posted 30 Oct 2020

Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics
9,127 downloads bioRxiv biochemistry

The COVID Moonshot Initiative, Hagit Achdout, Anthony Aimon, Elad Bar-David, Haim Barr, Amir Ben-Shmuel, James Bennett, Vitaliy A. Bilenko, Melissa L. Boby, Bruce Borden, Gregory R. Bowman, Juliane Brun, Sarma BVNBS, Mark Calmiano, Anna Carbery, Daniel Carney, Emma Cattermole, Edcon Chang, Eugene Chernyshenko, John D Chodera, Austin Clyde, Joseph E. Coffland, Galit Cohen, Jason Cole, Alessandro Contini, Lisa Cox, Milan Cvitkovic, Alex Dias, Kim Donckers, David L Dotson, Alice Douangamath, Shirly Duberstein, Tim Dudgeon, Louise E Dunnett, Peter K. Eastman, Noam Erez, Charles J. Eyermann, Michael Fairhead, Gwen Fate, Daren Fearon, Oleg Fedorov, Matteo Ferla, Rafaela S. Fernandes, Lori Ferrins, Richard Foster, Holly Foster, Ronen Gabizon, Adolfo García-Sastre, Victor O Gawriljuk, Paul Gehrtz, Carina Gileadi, Charline Giroud, William G. Glass, Robert Glen, Itai Glinert, Andre Schutzer Godoy, Marian Gorichko, Tyler Gorrie-Stone, Ed J. Griffen, Storm Hassell Hart, Jag Heer, Michael Henry, Michelle Hill, Sam Horrell, Victor D. Huliak, Matthew F.D. Hurley, Tomer Israely, Andrew Jajack, Jitske Jansen, Eric Jnoff, Dirk Jochmans, Tobias John, Steven De Jonghe, Anastassia L. Kantsadi, Peter W. Kenny, J. L. Kiappes, Serhii O. Kinakh, Lizbe Koekemoer, Boris Kovar, Tobias Krojer, Alpha Lee, Bruce A. Lefker, Haim Levy, Ivan G. Logvinenko, Nir London, Petra Lukacik, Hannah Bruce Macdonald, Beth MacLean, Tika R. Malla, Tatiana Matviiuk, Willam McCorkindale, Briana L. McGovern, Sharon Melamed, Kostiantyn P. Melnykov, Oleg Michurin, Halina Mikolajek, Bruce F. Milne, Aaron Morris, Garrett M. Morris, Melody Jane Morwitzer, Demetri Moustakas, Aline M. Nakamura, Jose Brandao-Neto, Johan Neyts, Luong Nguyen, Gabriela D. Noske, Vladas Oleinikovas, Glaucius Oliva, Gijs J. Overheul, David Owen, Ruby Pai, Jin Pan, Nir Paran, Benjamin Perry, Maneesh Pingle, Jakir Pinjari, Boaz Politi, Alisa Powell, Vladimir Psenak, Reut Puni, Victor Lopes Rangel, Rambabu N. Reddi, St Patrick Reid, Efrat Resnick, Emily Grace Ripka, Matthew C Robinson, Ralph P. Robinson, Jaime Rodriguez-Guerra Pedragal, Romel Rosales, Dominic Rufa, Kadi Saar, Kumar Singh Saikatendu, Christopher J Schofield, Mikhail Shafeev, Aarif Shaikh, Jiye Shi, Khriesto Shurrush, Sukrit Singh, Assa Sittner, Rachael Skyner, Adam Smalley, Bart Smeets, Mihaela D. Smilova, Leonardo J. Solmesky, John Spencer, Claire Strain-Damerell, Vishwanath Swamy, Hadas Tamir, Rachael Tennant, Warren Thompson, Andrew Thompson, Susana Tomasio, Igor S. Tsurupa, Anthony Tumber, Ioannis Vakonakis, Ronald P van Rij, Laura Vangeel, Finny S. Varghese, Mariana Vaschetto, Einat. B. Vitner, Vincent Voelz, Andrea Volkamer, Frank von Delft, Annette von Delft, Martin Walsh, Walter Ward, Charlie Weatherall, Shay Weiss, Kris White, Conor Francis Wild, Matthew Wittmann, Nathan Wright, Yfat Yahalom-Ronen, Daniel Zaidmann, Hadeer Zidane, Nicole Zitzmann

The COVID-19 pandemic is a stark reminder that a barren global antiviral pipeline has grave humanitarian consequences. Future pandemics could be prevented by accessible, easily deployable broad-spectrum oral antivirals and open knowledge bases that derisk and accelerate novel antiviral discovery and development. Here, we report the results of the COVID Moonshot, a fully open-science structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease. We discovered a novel chemical scaffold that is differentiated to current clinical candidates in terms of toxicity and pharmacokinetics liabilities, and developed it into orally-bioavailable inhibitors with clinical potential. Our approach leverages crowdsourcing, high throughput structural biology, machine learning, and exascale molecular simulations. In the process, we generated a detailed map of the structural plasticity of the main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. In a first for a structure-based drug discovery campaign, all compound designs (>18,000 designs), crystallographic data (>500 ligand-bound X-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery.

20: All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
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Posted 21 Mar 2020

All-in-One Dual CRISPR-Cas12a (AIOD-CRISPR) Assay: A Case for Rapid, Ultrasensitive and Visual Detection of Novel Coronavirus SARS-CoV-2 and HIV virus
9,062 downloads bioRxiv biochemistry

Xiong Ding, Kun Yin, Ziyue Li, Changchun Liu

A recent outbreak of novel coronavirus (SARS-CoV-2), the causative agent of COVID-19, has spread rapidly all over the world. Human immunodeficiency virus (HIV) is another deadly virus and causes acquired immunodeficiency syndrome (AIDS). Rapid and early detection of these viruses will facilitate early intervention and reduce disease transmission risk. Here, we present an All-In-One Dual CRISPR-Cas12a (termed "AIOD-CRISPR") assay method for simple, rapid, ultrasensitive, one-pot, and visual detection of coronavirus SARS-CoV-2 and HIV virus. In our AIOD CRISPR assay, a pair of crRNAs was introduced to initiate dual CRISPR-Cas12a detection and improve detection sensitivity. The AIOD-CRISPR assay system was successfully utilized to detect nucleic acids (DNA and RNA) of SARS-CoV-2 and HIV with a sensitivity of few copies. Also, it was evaluated by detecting HIV-1 RNA extracted from human plasma samples, achieving a comparable sensitivity with real-time RT-PCR method. Thus, our method has a great potential for developing next-generation point-of-care molecular diagnostics.

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