Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 25
Filter
1.
J Med Chem ; 65(2): 1302-1312, 2022 01 27.
Article in English | MEDLINE | ID: covidwho-1747278

ABSTRACT

CK2α and CK2α' are paralogous catalytic subunits of CK2, which belongs to the eukaryotic protein kinases. CK2 promotes tumorigenesis and the spread of pathogenic viruses like SARS-CoV-2 and is thus an attractive drug target. Efforts to develop selective CK2 inhibitors binding offside the ATP site had disclosed the αD pocket in CK2α; its occupation requires large conformational adaptations of the helix αD. As shown here, the αD pocket is accessible also in CK2α', where the necessary structural plasticity can be triggered with suitable ligands even in the crystalline state. A CK2α' structure with an ATP site and an αD pocket ligand guided the design of the bivalent CK2 inhibitor KN2. It binds to CK2 with low nanomolar affinity, is cell-permeable, and suppresses the intracellular phosphorylation of typical CK2 substrates. Kinase profiling revealed a high selectivity of KN2 for CK2 and emphasizes the selectivity-promoting potential of the αD pocket.


Subject(s)
Casein Kinase II/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Adenosine Triphosphate/metabolism , Casein Kinase II/chemistry , Casein Kinase II/metabolism , Crystallization , HEK293 Cells , HeLa Cells , Humans , Ligands , Phosphorylation , Protein Conformation , Substrate Specificity
2.
FASEB J ; 36(3): e22199, 2022 03.
Article in English | MEDLINE | ID: covidwho-1684809

ABSTRACT

Spike trimer plays a key role in SARS-CoV-2 infection and vaccine development. It consists of a globular head and a flexible stalk domain that anchors the protein into the viral membrane. While the head domain has been extensively studied, the properties of the adjoining stalk are poorly understood. Here, we characterize the coiled-coil formation and thermodynamic stability of the stalk domain and its segments. We find that the N-terminal segment of the stalk does not form coiled-coils and remains disordered in solution. The C-terminal stalk segment forms a trimeric coiled-coil in solution, which becomes significantly stabilized in the context of the full-length stalk. Its crystal structure reveals a novel antiparallel tetramer coiled-coil with an unusual combination of a-d and e-a-d hydrophobic core packing. Structural analysis shows that a subset of hydrophobic residues stabilizes different coiled-coil structures: trimer, tetramer, and heterohexamer, underscoring a highly polymorphic nature of the SARS-CoV-2 stalk sequence.


Subject(s)
COVID-19/virology , Models, Molecular , Protein Domains , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Amino Acid Sequence , Crystallization , Crystallography, X-Ray , Humans , Hydrophobic and Hydrophilic Interactions , Protein Stability , Protein Structure, Secondary , Scattering, Small Angle , Temperature , X-Ray Diffraction
3.
STAR Protoc ; 3(1): 101158, 2022 03 18.
Article in English | MEDLINE | ID: covidwho-1650422

ABSTRACT

The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography. For complete details on the use and execution of this protocol, please refer to Durdagi et al. (2021).


Subject(s)
Coronavirus 3C Proteases/chemistry , Models, Molecular , SARS-CoV-2/enzymology , Coronavirus 3C Proteases/genetics , Crystallization , Crystallography, X-Ray , Humans
4.
Commun Biol ; 4(1): 1240, 2021 10 29.
Article in English | MEDLINE | ID: covidwho-1493232

ABSTRACT

Circular tandem repeat proteins ('cTRPs') are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , Protein Engineering/methods , Proteins/chemistry , Proteins/metabolism , SARS-CoV-2/metabolism , Tandem Repeat Sequences , Amino Acid Sequence , COVID-19/virology , Computer Simulation , Crystallization , HEK293 Cells , Humans , Models, Molecular , Neutralization Tests , Protein Binding , Protein Domains , Protein Folding , Protein Structure, Secondary , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
5.
Acta Crystallogr F Struct Biol Commun ; 77(Pt 10): 348-355, 2021 Oct 01.
Article in English | MEDLINE | ID: covidwho-1450488

ABSTRACT

Human coronavirus NL63 (HCoV-NL63), which belongs to the genus Alphacoronavirus, mainly infects children and the immunocompromized and is responsible for a series of clinical manifestations, including cough, fever, rhinorrhoea, bronchiolitis and croup. HCoV-NL63, which was first isolated from a seven-month-old child in 2004, has led to infections worldwide and accounts for 10% of all respiratory illnesses caused by etiological agents. However, effective antivirals against HCoV-NL63 infection are currently unavailable. The HCoV-NL63 main protease (Mpro), also called 3C-like protease (3CLpro), plays a vital role in mediating viral replication and transcription by catalyzing the cleavage of replicase polyproteins (pp1a and pp1ab) into functional subunits. Moreover, Mpro is highly conserved among all coronaviruses, thus making it a prominent drug target for antiviral therapy. Here, four crystal structures of HCoV-NL63 Mpro in the apo form at different pH values are reported at resolutions of up to 1.78 Å. Comparison with Mpro from other human betacoronaviruses such as SARS-CoV-2 and SARS-CoV reveals common and distinct structural features in different genera and extends knowledge of the diversity, function and evolution of coronaviruses.


Subject(s)
Coronavirus NL63, Human/chemistry , Crystallization/methods , Crystallography, X-Ray/methods , Humans , Hydrogen-Ion Concentration , Protein Conformation
6.
Nat Rev Nephrol ; 17(9): 572, 2021 09.
Article in English | MEDLINE | ID: covidwho-1428876
7.
J Med Chem ; 65(2): 1302-1312, 2022 01 27.
Article in English | MEDLINE | ID: covidwho-1331359

ABSTRACT

CK2α and CK2α' are paralogous catalytic subunits of CK2, which belongs to the eukaryotic protein kinases. CK2 promotes tumorigenesis and the spread of pathogenic viruses like SARS-CoV-2 and is thus an attractive drug target. Efforts to develop selective CK2 inhibitors binding offside the ATP site had disclosed the αD pocket in CK2α; its occupation requires large conformational adaptations of the helix αD. As shown here, the αD pocket is accessible also in CK2α', where the necessary structural plasticity can be triggered with suitable ligands even in the crystalline state. A CK2α' structure with an ATP site and an αD pocket ligand guided the design of the bivalent CK2 inhibitor KN2. It binds to CK2 with low nanomolar affinity, is cell-permeable, and suppresses the intracellular phosphorylation of typical CK2 substrates. Kinase profiling revealed a high selectivity of KN2 for CK2 and emphasizes the selectivity-promoting potential of the αD pocket.


Subject(s)
Casein Kinase II/antagonists & inhibitors , Protein Kinase Inhibitors/pharmacology , Adenosine Triphosphate/metabolism , Casein Kinase II/chemistry , Casein Kinase II/metabolism , Crystallization , HEK293 Cells , HeLa Cells , Humans , Ligands , Phosphorylation , Protein Conformation , Substrate Specificity
8.
Chem Biol Drug Des ; 98(4): 604-619, 2021 10.
Article in English | MEDLINE | ID: covidwho-1273079

ABSTRACT

3CLpro is essential for SARS-CoV-2 replication and infection; its inhibition using small molecules is a potential therapeutic strategy. In this study, a comprehensive crystallography-guided fragment-based drug discovery approach was employed to design new inhibitors for SARS-CoV-2 3CLpro. All small molecules co-crystallized with SARS-CoV-2 3CLpro with structures deposited in the Protein Data Bank were used as inputs. Fragments sitting in the binding pocket (87) were grouped into eight geographical types. They were interactively coupled using various synthetically reasonable linkers to generate larger molecules with divalent binding modes taking advantage of two different fragments' interactions. In total, 1,251 compounds were proposed, and 7,158 stereoisomers were screened using Glide (standard precision and extra precision), AutoDock Vina, and Prime MMGBSA. The top 22 hits having conformations approaching the linear combination of their constituent fragments were selected for MD simulation on Desmond. MD simulation suggested 15 of these did adopt conformations very close to their constituent pieces with far higher binding affinity than either constituent domain alone. These structures could provide a starting point for the further design of SARS-CoV-2 3CLpro inhibitors with improved binding, and structures are provided.


Subject(s)
Antiviral Agents/chemistry , COVID-19/drug therapy , SARS-CoV-2/drug effects , Viral Protease Inhibitors/chemistry , Viral Proteases/metabolism , Antiviral Agents/pharmacology , Crystallization , Drug Design , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Multivariate Analysis , Protein Binding , Protein Conformation , Stereoisomerism , Structure-Activity Relationship , Viral Protease Inhibitors/pharmacology
9.
Molecules ; 26(9)2021 May 03.
Article in English | MEDLINE | ID: covidwho-1238921

ABSTRACT

Chitosan has many useful intrinsic properties (e.g., non-toxicity, antibacterial properties, and biodegradability) and can be processed into high-surface-area nanofiber constructs for a broad range of sustainable research and commercial applications. These nanofibers can be further functionalized with bioactive agents. In the food industry, for example, edible films can be formed from chitosan-based composite fibers filled with nanoparticles, exhibiting excellent antioxidant and antimicrobial properties for a variety of products. Processing 'pure' chitosan into nanofibers can be challenging due to its cationic nature and high crystallinity; therefore, chitosan is often modified or blended with other materials to improve its processability and tailor its performance to specific needs. Chitosan can be blended with a variety of natural and synthetic polymers and processed into fibers while maintaining many of its intrinsic properties that are important for textile, cosmeceutical, and biomedical applications. The abundance of amine groups in the chemical structure of chitosan allows for facile modification (e.g., into soluble derivatives) and the binding of negatively charged domains. In particular, high-surface-area chitosan nanofibers are effective in binding negatively charged biomolecules. Recent developments of chitosan-based nanofibers with biological activities for various applications in biomedical, food packaging, and textiles are discussed herein.


Subject(s)
Chitosan/chemistry , Cosmeceuticals/chemistry , Food Packaging , Textiles , Amines/chemistry , Animals , Anti-Bacterial Agents/chemistry , Anti-Infective Agents/chemistry , Antioxidants/chemistry , Crystallization , Edible Films , Humans , Nanofibers/chemistry , Nanoparticles/chemistry , Polymers , Regeneration , Skin/pathology , Skin, Artificial , Solubility , Tissue Engineering , Wound Healing
10.
J Colloid Interface Sci ; 600: 1-13, 2021 Oct 15.
Article in English | MEDLINE | ID: covidwho-1237742

ABSTRACT

HYPOTHESIS: The droplets ejected from an infected host during expiratory events can get deposited as fomites on everyday use surfaces. Recognizing that these fomites can be a secondary route for disease transmission, exploring the deposition pattern of such sessile respiratory droplets on daily-use substrates thus becomes crucial. EXPERIMENTS: The used surrogate respiratory fluid is composed of a water-based salt-protein solution, and its precipitation dynamics is studied on four different substrates (glass, ceramic, steel, and PET). For tracking the final deposition of viruses in these droplets, 100 nm virus emulating particles (VEP) are used and their distribution in dried-out patterns is identified using fluorescence and SEM imaging techniques. FINDINGS: The final precipitation pattern and VEP deposition strongly depend on the interfacial transport processes, edge evaporation, and crystallization dynamics. A constant contact radius mode of evaporation with a mixture of capillary and Marangoni flows results in spatio-temporally varying edge deposits. Dendritic and cruciform-shaped crystals are majorly seen in all substrates except on steel, where regular cubical crystals are formed. The VEP deposition is higher near the three-phase contact line and crystal surfaces. The results showed the role of interfacial processes in determining the initiation of fomite-type infection pathways in the context of COVID-19.


Subject(s)
COVID-19 , Fomites , Crystallization , Humans , SARS-CoV-2 , Sodium Chloride
11.
ACS Appl Mater Interfaces ; 13(14): 16084-16096, 2021 Apr 14.
Article in English | MEDLINE | ID: covidwho-1164786

ABSTRACT

As COVID-19 exemplifies, respiratory diseases transmitted through aerosols or droplets are global threats to public health, and respiratory protection measures are essential first lines of infection prevention and control. However, common face masks are single use and can cause cross-infection due to the accumulated infectious pathogens. We developed salt-based formulations to coat membrane fibers to fabricate antimicrobial filters. Here, we report a mechanistic study on salt-induced pathogen inactivation. The salt recrystallization following aerosol exposure was characterized over time on sodium chloride (NaCl), potassium sulfate (K2SO4), and potassium chloride (KCl) powders and coatings, which revealed that NaCl and KCl start to recrystallize within 5 min and K2SO4 within 15 min. The inactivation kinetics observed for the H1N1 influenza virus and Klebsiella pneumoniae matched the salt recrystallization well, which was identified as the main destabilizing mechanism. Additionally, the salt-coated filters were prepared with different methods (with and without a vacuum process), which led to salt coatings with different morphologies for diverse applications. Finally, the salt-coated filters caused a loss of pathogen viability independent of transmission mode (aerosols or droplets), against both DI water and artificial saliva suspensions. Overall, these findings increase our understanding of the salt-recrystallization-based technology to develop highly versatile antimicrobial filters.


Subject(s)
Filtration/instrumentation , Influenza A Virus, H1N1 Subtype/drug effects , Klebsiella pneumoniae/drug effects , Masks , Potassium Chloride/chemistry , Sodium Chloride/chemistry , Sulfates/chemistry , Aerosols , Air Filters , Crystallization , Kinetics , Membranes, Artificial , Polypropylenes , Powders , Respiratory Protective Devices , Temperature , X-Ray Diffraction
12.
J Chem Inf Model ; 60(12): 5803-5814, 2020 12 28.
Article in English | MEDLINE | ID: covidwho-1065781

ABSTRACT

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for creating Mpro complexes. We make these tools and models freely available. iMD-VR provides an immersive environment in which users can interact with MD simulations and so build protein complexes in a physically rigorous and flexible way. Recently, we have demonstrated that iMD-VR is an effective method for interactive, flexible docking of small molecule drugs into their protein targets (Deeks et al. PLoS One 2020, 15, e0228461). Here, we apply this approach to both an Mpro inhibitor and an oligopeptide substrate, using experimentally determined crystal structures. For the oligopeptide, we test against a crystallographic structure of the original SARS Mpro. Docking with iMD-VR gives models in agreement with experimentally observed (crystal) structures. The docked structures are also tested in MD simulations and found to be stable. Different protocols for iMD-VR docking are explored, e.g., with and without restraints on protein backbone, and we provide recommendations for its use. We find that it is important for the user to focus on forming binding interactions, such as hydrogen bonds, and not to rely on using simple metrics (such as RMSD), in order to create realistic, stable complexes. We also test the use of apo (uncomplexed) crystal structures for docking and find that they can give good results. This is because of the flexibility and dynamic response allowed by the physically rigorous, atomically detailed simulation approach of iMD-VR. We make our models (and interactive simulations) freely available. The software framework that we use, Narupa, is open source, and uses commodity VR hardware, so these tools are readily accessible to the wider research community working on Mpro (and other COVID-19 targets). These should be widely useful in drug development, in education applications, e.g., on viral enzyme structure and function, and in scientific communication more generally.


Subject(s)
Antiviral Agents/chemistry , Benzeneacetamides/chemistry , COVID-19/metabolism , Coronavirus 3C Proteases/metabolism , Imidazoles/chemistry , SARS-CoV-2/enzymology , Viral Protease Inhibitors/chemistry , Antiviral Agents/pharmacokinetics , Antiviral Agents/pharmacology , Benzeneacetamides/pharmacokinetics , Benzeneacetamides/pharmacology , Coronavirus 3C Proteases/genetics , Crystallization , Cyclohexylamines , Drug Design , Humans , Hydrogen Bonding , Imidazoles/pharmacokinetics , Imidazoles/pharmacology , Molecular Docking Simulation , Molecular Dynamics Simulation , Mutation , Oligopeptides/chemistry , Oligopeptides/metabolism , Protein Conformation , Pyridines , Structure-Activity Relationship , Viral Protease Inhibitors/pharmacokinetics , Viral Protease Inhibitors/pharmacology
13.
Appl Environ Microbiol ; 86(23)2020 11 10.
Article in English | MEDLINE | ID: covidwho-1020865

ABSTRACT

Emerging outbreaks of airborne pathogenic infections worldwide, such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, have raised the need to understand parameters affecting the airborne survival of microbes in order to develop measures for effective infection control. We report a novel experimental strategy, TAMBAS (tandem approach for microphysical and biological assessment of airborne microorganism survival), to explore the synergistic interactions between the physicochemical and biological processes that impact airborne microbe survival in aerosol droplets. This innovative approach provides a unique and detailed understanding of the processes taking place from aerosol droplet generation through to equilibration and viability decay in the local environment, elucidating decay mechanisms not previously described. The impact of evaporation kinetics, solute hygroscopicity and concentration, particle morphology, and equilibrium particle size on airborne survival are reported, using Escherichia coli MRE162 as a benchmark system. For this system, we report that (i) particle crystallization does not directly impact microbe longevity, (ii) bacteria act as crystallization nuclei during droplet drying and equilibration, and (iii) the kinetics of size and compositional change appear to have a larger effect on microbe longevity than the equilibrium solute concentration.IMPORTANCE A transformative approach to identify the physicochemical processes that impact the biological decay rates of bacteria in aerosol droplets is described. It is shown that the evaporation process and changes in the phase and morphology of the aerosol particle during evaporation impact microorganism viability. The equilibrium droplet size was found to affect airborne bacterial viability. Furthermore, the presence of Escherichia coli MRE162 in a droplet does not affect aerosol growth/evaporation but influences the dynamic behavior of the aerosol by processing the culture medium prior to aerosolization, affecting the hygroscopicity of the culture medium; this highlights the importance of the inorganic and organic chemical composition within the aerosolized droplets that impact hygroscopicity. Bacteria also act as crystallization nuclei. The novel approach and data have implications for increased mechanistic understanding of aerosol survival and infectivity in bioaerosol studies spanning the medical, veterinary, farming, and agricultural fields, including the role of microorganisms in atmospheric processing and cloud formation.


Subject(s)
Aerosols , Air Microbiology , Coronavirus Infections/transmission , Escherichia coli Infections/transmission , Infection Control/methods , Pneumonia, Viral/transmission , Betacoronavirus/physiology , COVID-19 , Cough/microbiology , Crystallization , Escherichia coli/physiology , Humans , Microbial Viability , Pandemics , Particle Size , SARS-CoV-2 , Sneezing/physiology
14.
J R Soc Interface ; 18(174): 20200591, 2021 01.
Article in English | MEDLINE | ID: covidwho-1010695

ABSTRACT

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has no publicly available vaccine or antiviral drugs at the time of writing. An attractive coronavirus drug target is the main protease (Mpro, also known as 3CLpro) because of its vital role in the viral cycle. A significant body of work has been focused on finding inhibitors which bind and block the active site of the main protease, but little has been done to address potential non-competitive inhibition, targeting regions other than the active site, partly because the fundamental biophysics of such allosteric control is still poorly understood. In this work, we construct an elastic network model (ENM) of the SARS-CoV-2 Mpro homodimer protein and analyse its dynamics and thermodynamics. We found a rich and heterogeneous dynamical structure, including allosterically correlated motions between the homodimeric protease's active sites. Exhaustive 1-point and 2-point mutation scans of the ENM and their effect on fluctuation free energies confirm previously experimentally identified bioactive residues, but also suggest several new candidate regions that are distant from the active site, yet control the protease function. Our results suggest new dynamically driven control regions as possible candidates for non-competitive inhibiting binding sites in the protease, which may assist the development of current fragment-based binding screens. The results also provide new insights into the active biophysical research field of protein fluctuation allostery and its underpinning dynamical structure.


Subject(s)
COVID-19/virology , SARS-CoV-2/metabolism , Viral Proteases/chemistry , Computer Simulation , Crystallization , Humans , Models, Molecular , Protein Conformation , SARS-CoV-2/enzymology , Thermodynamics , Viral Proteases/drug effects , Viral Proteases/metabolism
15.
Emerg Microbes Infect ; 10(1): 66-80, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-979439

ABSTRACT

Coronaviruses (CoVs) are potential pandemic pathogens that can infect a variety of hosts and cause respiratory, enteric, hepatic and neurological diseases. Nonstructural protein 3 (nsp3), an essential component of the replication/transcription complex, is one of the most important antiviral targets. Here, we report the first crystal structure of multiple functional domains from porcine delta-coronavirus (PDCoV) nsp3, including the macro domain (Macro), ubiquitin-like domain 2 (Ubl2) and papain-like protease (PLpro) catalytic domain. In the asymmetric unit, two of the subunits form the head-to-tail homodimer with an interaction interface between Macro and PLpro. However, PDCoV Macro-Ubl2-PLpro mainly exists as a monomer in solution. Then, we conducted fluorescent resonance energy transfer-based protease assays and found that PDCoV PLpro can cleave a peptide by mimicking the cognate nsp2/nsp3 cleavage site in peptide substrates and exhibits deubiquitinating and de-interferon stimulated gene(deISGylating) activities by hydrolysing ubiquitin-7-amino-4-methylcoumarin (Ub-AMC) and ISG15-AMC substrates. Moreover, the deletion of Macro or Macro-Ubl2 decreased the enzyme activity of PLpro, indicating that Macro and Ubl2 play important roles in maintaining the stability of the PLpro domain. Two active sites of PLpro, Cys260 and His398, were determined; unexpectedly, the conserved site Asp412 was not the third active site. Furthermore, the motif "NGYDT" (amino acids 409-413) was important for stabilizing the enzyme activity of PLpro, and the N409A mutant significantly decreased the enzyme activity of PLpro. These results provide novel insights into the replication mechanism of CoV and new clues for future drug design.


Subject(s)
Coronavirus Papain-Like Proteases/chemistry , Catalytic Domain , Coronavirus Papain-Like Proteases/physiology , Crystallization , HeLa Cells , Humans , Protein Domains , Protein Multimerization , Ubiquitination
16.
Immunity ; 53(6): 1272-1280.e5, 2020 12 15.
Article in English | MEDLINE | ID: covidwho-967824

ABSTRACT

Most antibodies isolated from individuals with coronavirus disease 2019 (COVID-19) are specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, COVA1-16 is a relatively rare antibody that also cross-neutralizes SARS-CoV. Here, we determined a crystal structure of the COVA1-16 antibody fragment (Fab) with the SARS-CoV-2 receptor-binding domain (RBD) and negative-stain electron microscopy reconstructions with the spike glycoprotein trimer to elucidate the structural basis of its cross-reactivity. COVA1-16 binds a highly conserved epitope on the SARS-CoV-2 RBD, mainly through a long complementarity-determining region (CDR) H3, and competes with the angiotensin-converting enzyme 2 (ACE2) receptor because of steric hindrance rather than epitope overlap. COVA1-16 binds to a flexible up conformation of the RBD on the spike and relies on antibody avidity for neutralization. These findings, along with the structural and functional rationale for epitope conservation, provide insights for development of more universal SARS-like coronavirus vaccines and therapies.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Antibodies, Viral/metabolism , COVID-19 Vaccines/immunology , COVID-19/immunology , SARS Virus/immunology , SARS-CoV-2/immunology , Antibodies, Viral/genetics , Broadly Neutralizing Antibodies/genetics , Broadly Neutralizing Antibodies/metabolism , Conserved Sequence/genetics , Cross Reactions , Crystallization , Epitope Mapping , Epitopes, B-Lymphocyte/genetics , Epitopes, B-Lymphocyte/metabolism , Humans , Immunoglobulin Fab Fragments/genetics , Immunoglobulin Fab Fragments/metabolism , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs/genetics
17.
Molecules ; 25(23)2020 Nov 28.
Article in English | MEDLINE | ID: covidwho-948909

ABSTRACT

AIMS: Angiotensin-converting enzyme 2 (ACE2) plays an important role in the entry of coronaviruses into host cells. The current paper described how carnosine, a naturally occurring supplement, can be an effective drug candidate for coronavirus disease (COVID-19) on the basis of molecular docking and modeling to host ACE2 cocrystallized with nCoV spike protein. METHODS: First, the starting point was ACE2 inhibitors and their structure-activity relationship (SAR). Next, chemical similarity (or diversity) and PubMed searches made it possible to repurpose and assess approved or experimental drugs for COVID-19. Parallel, at all stages, the authors performed bioactivity scoring to assess potential repurposed inhibitors at ACE2. Finally, investigators performed molecular docking and modeling of the identified drug candidate to host ACE2 with nCoV spike protein. RESULTS: Carnosine emerged as the best-known drug candidate to match ACE2 inhibitor structure. Preliminary docking was more optimal to ACE2 than the known typical angiotensin-converting enzyme 1 (ACE1) inhibitor (enalapril) and quite comparable to known or presumed ACE2 inhibitors. Viral spike protein elements binding to ACE2 were retained in the best carnosine pose in SwissDock at 1.75 Angstroms. Out of the three main areas of attachment expected to the protein-protein structure, carnosine bound with higher affinity to two compared to the known ACE2 active site. LibDock score was 92.40 for site 3, 90.88 for site 1, and inside the active site 85.49. CONCLUSION: Carnosine has promising inhibitory interactions with host ACE2 and nCoV spike protein and hence could offer a potential mitigating effect against the current COVID-19 pandemic.


Subject(s)
Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme Inhibitors/pharmacology , Angiotensin-Converting Enzyme 2/metabolism , Angiotensin-Converting Enzyme Inhibitors/chemistry , Antiviral Agents/pharmacology , Biological Availability , COVID-19/drug therapy , Carnosine/chemistry , Carnosine/metabolism , Carnosine/pharmacology , Catalytic Domain , Crystallization , Humans , Molecular Docking Simulation , Protein Interaction Domains and Motifs/drug effects , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Structure-Activity Relationship
19.
Nature ; 581(7808): 252-255, 2020 05.
Article in English | MEDLINE | ID: covidwho-831180

Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/chemistry , Betacoronavirus/immunology , Drug Design , Viral Proteins/antagonists & inhibitors , Viral Proteins/chemistry , Viral Vaccines , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/pharmacology , Adenosine Monophosphate/therapeutic use , Alanine/analogs & derivatives , Alanine/pharmacology , Alanine/therapeutic use , Angiotensin-Converting Enzyme 2 , Animals , Antiviral Agents/chemistry , Azoles/pharmacology , Betacoronavirus/drug effects , Betacoronavirus/enzymology , COVID-19 Vaccines , China , Coronavirus 3C Proteases , Coronavirus Infections/immunology , Coronavirus Infections/prevention & control , Coronavirus Papain-Like Proteases , Coronavirus RNA-Dependent RNA Polymerase , Cryoelectron Microscopy , Crystallization , Crystallography, X-Ray , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/metabolism , Drug Evaluation, Preclinical , Germany , High-Throughput Screening Assays , Humans , Isoindoles , Mice , National Institutes of Health (U.S.)/economics , National Institutes of Health (U.S.)/organization & administration , Organoselenium Compounds/pharmacology , Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/metabolism , Protease Inhibitors/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Synchrotrons , Time Factors , United Kingdom , United States , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Proteins/immunology
20.
Sci Rep ; 10(1): 13875, 2020 08 17.
Article in English | MEDLINE | ID: covidwho-720847

ABSTRACT

Respiratory protection is key in infection prevention of airborne diseases, as highlighted by the COVID-19 pandemic for instance. Conventional technologies have several drawbacks (i.e., cross-infection risk, filtration efficiency improvements limited by difficulty in breathing, and no safe reusability), which have yet to be addressed in a single device. Here, we report the development of a filter overcoming the major technical challenges of respiratory protective devices. Large-pore membranes, offering high breathability but low bacteria capture, were functionalized to have a uniform salt layer on the fibers. The salt-functionalized membranes achieved high filtration efficiency as opposed to the bare membrane, with differences of up to 48%, while maintaining high breathability (> 60% increase compared to commercial surgical masks even for the thickest salt filters tested). The salt-functionalized filters quickly killed Gram-positive and Gram-negative bacteria aerosols in vitro, with CFU reductions observed as early as within 5 min, and in vivo by causing structural damage due to salt recrystallization. The salt coatings retained the pathogen inactivation capability at harsh environmental conditions (37 °C and a relative humidity of 70%, 80% and 90%). Combination of these properties in one filter will lead to the production of an effective device, comprehensibly mitigating infection transmission globally.


Subject(s)
Air Filters/microbiology , Anti-Bacterial Agents/chemistry , Betacoronavirus , Coronavirus Infections/prevention & control , Masks/microbiology , Membranes, Artificial , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Respiratory Protective Devices/microbiology , Sodium Chloride/chemistry , Aerosols , Anti-Bacterial Agents/pharmacology , COVID-19 , Coronavirus Infections/transmission , Coronavirus Infections/virology , Crystallization , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effects , Hot Temperature , Humans , Humidity , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , SARS-CoV-2 , Sodium Chloride/pharmacology
SELECTION OF CITATIONS
SEARCH DETAIL