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1.
Pol Arch Intern Med ; 130(5): 420-430, 2020 05 29.
Article in English | MEDLINE | ID: covidwho-621657

ABSTRACT

The outbreak of the coronavirus disease 2019 (COVID­19) pandemic has become the biggest challenge for the whole human community since many years. It seems that the proper identification of all people infected with severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) is the best strategy to limit the transmission. However, in a significant proportion of patients, there are no clinical manifestations of the disease, and symptoms may be very mild or atypical. There is a growing body of evidence that digestive manifestations of COVID­19 are frequently reported and may precede typical respiratory symptoms. Moreover, SARS­CoV­2 particles were found in the gastrointestinal epithelial cells, and viral RNA was detected in the feces of patients with COVID­19. These data suggest that gastrointestinal symptoms in COVID­19 are not accidental findings and they may result from direct digestive involvement. Patients with new­onset diarrhea, abdominal pain, nausea, and vomiting without any other evident etiological factors should be tested for SARS­CoV­2 infection. Gastroenterologists and members of other medical specialties should also remember that the current epidemiological situation has changed diagnostic and therapeutic algorithms in the management of several gastrointestinal and liver disorders. This review article summarizes the currently available data on multiple gastroenterological aspects of COVID­19 and provides information on practical recommendations and position statements of the most prominent associations in the field of gastroenterology, which appeared in response to the emergence of the pandemic.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/complications , Digestive System Diseases/virology , Digestive System/virology , Pneumonia, Viral/complications , Coronavirus/metabolism , Coronavirus Infections/diagnosis , Coronavirus Infections/drug therapy , Coronavirus Infections/therapy , Digestive System/metabolism , Humans , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/therapy
2.
Int J Mol Sci ; 21(14)2020 Jul 11.
Article in English | MEDLINE | ID: covidwho-646270

ABSTRACT

A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.


Subject(s)
Magnetic Resonance Spectroscopy/methods , Valinomycin/chemistry , Betacoronavirus/chemistry , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Carbon Isotopes/chemistry , Coronavirus Infections/pathology , Coronavirus Infections/virology , Crystallography , Hydrogen Bonding , Nitrogen Isotopes/chemistry , Pandemics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Valinomycin/metabolism
3.
Oral Oncol ; 108: 104821, 2020 09.
Article in English | MEDLINE | ID: covidwho-753019

ABSTRACT

Outbreak pneumonia announced in Wuhan, China, in December 2019, had its causative factor classified as a new coronavirus (SARS-CoV-2). Since saliva can host several viruses including SARS-CoV-2, the transmission chance of viruses through saliva, particularly those causing respiratory infections, is unavoidable. COVID-19 can be detected through salivary diagnostic testing which has lots of advantages for medical care professionals and patients. It should be noted that not only does saliva offer an ecological niche for the colonization and development of oral microorganisms, but it also prevents the overgrowth of particular pathogens such as viral factors. The aim of this study is to gather all the information about saliva and its association with COVID-19 for the whole health care professionals across the world.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Saliva/immunology , Saliva/virology , Sialadenitis/diagnosis , Aged , Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Dental Care , Dentists/psychology , Diagnostic Tests, Routine/methods , Female , Humans , Immunity, Innate , Infection Control/methods , Male , Middle Aged , Pandemics , Patient Safety , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Practice Patterns, Dentists' , Reverse Transcriptase Polymerase Chain Reaction , Salivary Gland Neoplasms/diagnosis , Salivary Glands/metabolism , Salivary Glands/virology , Salivary Proteins and Peptides/immunology , Sialadenitis/virology , Telemedicine/methods , Xerostomia
4.
Sci Rep ; 10(1): 14179, 2020 08 25.
Article in English | MEDLINE | ID: covidwho-741695

ABSTRACT

A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development.


Subject(s)
Betacoronavirus/immunology , Computational Biology , Coronavirus Infections/immunology , Coronavirus Infections/virology , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/immunology , Host-Pathogen Interactions/immunology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Viral Proteins/immunology , Amino Acid Sequence , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Betacoronavirus/classification , Betacoronavirus/genetics , Betacoronavirus/metabolism , Computational Biology/methods , Coronavirus Infections/metabolism , Epitopes, B-Lymphocyte/chemistry , Epitopes, T-Lymphocyte/chemistry , Genome, Viral , Genomics/methods , Humans , Models, Molecular , Pandemics , Peptides/chemistry , Peptides/immunology , Phylogeny , Pneumonia, Viral/metabolism , Structure-Activity Relationship , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Vaccines, Subunit/immunology , Viral Proteins/chemistry , Viral Vaccines/immunology
5.
J Virol ; 94(17)2020 08 17.
Article in English | MEDLINE | ID: covidwho-740271

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus first identified in December 2019. Notable features that make SARS-CoV-2 distinct from most other previously identified betacoronaviruses include a receptor binding domain and a unique insertion of 12 nucleotides or 4 amino acids (PRRA) at the S1/S2 boundary. In this study, we identified two deletion variants of SARS-CoV-2 that either directly affect the polybasic cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN). These deletions were verified by multiple sequencing methods. In vitro results showed that the deletion of NSPRRAR likely does not affect virus replication in Vero and Vero-E6 cells; however, the deletion of QTQTN may restrict late-phase viral replication. The deletion of QTQTN was detected in 3 of 68 clinical samples and 12 of 24 in vitro-isolated viruses, while the deletion of NSPRRAR was identified in 3 in vitro-isolated viruses. Our data indicate that (i) there may be distinct selection pressures on SARS-CoV-2 replication or infection in vitro and in vivo; (ii) an efficient mechanism for deleting this region from the viral genome may exist, given that the deletion variant is commonly detected after two rounds of cell passage; and (iii) the PRRA insertion, which is unique to SARS-CoV-2, is not fixed during virus replication in vitro These findings provide information to aid further investigation of SARS-CoV-2 infection mechanisms and a better understanding of the NSPRRAR deletion variant observed here.IMPORTANCE The spike protein determines the infectivity and host range of coronaviruses. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has two unique features in its spike protein, the receptor binding domain and an insertion of 12 nucleotides at the S1/S2 boundary resulting in a furin-like cleavage site. Here, we identified two deletion variants of SARS-CoV-2 that either directly affect the furin-like cleavage site itself (NSPRRAR) or a flanking sequence (QTQTN), and we investigated these deletions in cell isolates and clinical samples. The absence of the polybasic cleavage site in SARS-CoV-2 did not affect virus replication in Vero or Vero-E6 cells. Our data indicate the PRRAR sequence and the flanking QTQTN sequence are not fixed in vitro; thus, there appears to be distinct selection pressures on SARS-CoV-2 sequences in vitro and in vivo Further investigation of the mechanism of generating these deletion variants and their infectivity in different animal models would improve our understanding of the origin and evolution of this virus.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/metabolism , Sequence Deletion , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/isolation & purification , Amino Acid Sequence , Animals , Base Sequence , Cell Line , Chlorocebus aethiops , Coronavirus Infections/virology , Furin/metabolism , Genome, Viral , Host Specificity , Kinetics , Models, Molecular , Pandemics , Pneumonia, Viral/virology , Protein Conformation , Sequence Analysis , Spike Glycoprotein, Coronavirus/chemistry , Vero Cells , Virus Replication
7.
Anal Chem ; 92(16): 11305-11309, 2020 08 18.
Article in English | MEDLINE | ID: covidwho-733550

ABSTRACT

The SARS-CoV-2 pandemic has created an unprecedented need for rapid diagnostic testing to enable the efficient treatment and mitigation of COVID-19. The primary diagnostic tool currently employed is reverse transcription polymerase chain reaction (RT-PCR), which can have good sensitivity and excellent specificity. Unfortunately, implementation costs and logistical problems with reagents during the global SARS-CoV-2 pandemic have hindered its universal on demand adoption. Lateral flow assays (LFAs) represent a class of diagnostic that, if sufficiently clinically sensitive, may fill many of the gaps in the current RT-PCR testing regime, especially in low- and middle-income countries (LMICs). To date, many serology LFAs have been developed, though none meet the performance requirements necessary for diagnostic use cases, primarily due to the relatively long delay between infection and seroconversion. However, on the basis of previously reported results from SARS-CoV-1, antigen-based SARS-CoV-2 assays may have significantly better clinical sensitivity than serology assays. To date, only a very small number of antigen-detecting LFAs have been developed. Development of a half-strip LFA is a useful first step in the development of any LFA format. In this work, we present a half-strip LFA using commercially available antibodies for the detection of SARS-CoV-2. We have tested this LFA in buffer and measured an LOD of 0.65 ng/mL (95% CI of 0.53 to 0.77 ng/mL) ng/mL with recombinant antigen using an optical reader with sensitivity equivalent to a visual read. Further development, including evaluating the appropriate sample matrix, will be required for this assay approach to be made useful in a point of care setting, though this half-strip LFA may serve as a useful starting point for others developing similar tests.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/diagnosis , Immunoassay/methods , Nucleocapsid/immunology , Pneumonia, Viral/diagnosis , Point-of-Care Systems , Antibodies, Viral/blood , Antigens/immunology , Betacoronavirus/isolation & purification , Coronavirus Infections/virology , Humans , Limit of Detection , Pandemics , Pneumonia, Viral/virology
8.
Nat Commun ; 11(1): 4303, 2020 08 27.
Article in English | MEDLINE | ID: covidwho-733523

ABSTRACT

The novel highly transmissible human coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Thus far, there is no approved therapeutic drug specifically targeting this emerging virus. Here we report the isolation and characterization of a panel of human neutralizing monoclonal antibodies targeting the SARS-CoV-2 receptor binding domain (RBD). These antibodies were selected from a phage display library constructed using peripheral circulatory lymphocytes collected from patients at the acute phase of the disease. These neutralizing antibodies are shown to recognize distinct epitopes on the viral spike RBD. A subset of the antibodies exert their inhibitory activity by abrogating binding of the RBD to the human ACE2 receptor. The human monoclonal antibodies described here represent a promising basis for the design of efficient combined post-exposure therapy for SARS-CoV-2 infection.


Subject(s)
Antibodies, Monoclonal/immunology , Antibodies, Neutralizing/immunology , Betacoronavirus/immunology , Spike Glycoprotein, Coronavirus/immunology , Animals , Antibodies, Monoclonal/metabolism , Antibodies, Neutralizing/metabolism , Antibodies, Viral/immunology , Antibodies, Viral/metabolism , Betacoronavirus/metabolism , Chlorocebus aethiops , Epitope Mapping , Epitopes , Humans , Peptide Library , Peptidyl-Dipeptidase A/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Vero Cells
9.
Open Biol ; 10(8): 200208, 2020 08.
Article in English | MEDLINE | ID: covidwho-733298

ABSTRACT

COVID-19 management guidelines have largely attributed critically ill patients who develop acute respiratory distress syndrome, to a systemic overproduction of pro-inflammatory cytokines. Cardiovascular dysfunction may also represent a primary phenomenon, with increasing data suggesting that severe COVID-19 reflects a confluence of vascular dysfunction, thrombosis and dysregulated inflammation. Here, we first consolidate the information on localized microvascular inflammation and disordered cytokine release, triggering vessel permeability and prothrombotic conditions that play a central role in perpetuating the pathogenic COVID-19 cascade. Secondly, we seek to clarify the gateways which SARS-CoV-2, the causative COVID-19 virus, uses to enter host vascular cells. Post-mortem examinations of patients' tissues have confirmed direct viral endothelial infection within several organs. While there have been advances in single-cell RNA sequencing, endothelial cells across various vascular beds express low or undetectable levels of those touted SARS-CoV-2 entry factors. Emerging studies postulate alternative pathways and the apicobasal distribution of host cell surface factors could influence endothelial SARS-CoV-2 entry and replication. Finally, we provide experimental considerations such as endothelial polarity, cellular heterogeneity in organoids and shear stress dynamics in designing cellular models to facilitate research on viral-induced endothelial dysfunctions. Understanding the vascular underpinning of COVID-19 pathogenesis is crucial to managing outcomes and mortality.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/pathology , Endothelial Cells/pathology , Inflammation/pathology , Pneumonia, Viral/pathology , Thrombosis/pathology , Capillary Permeability/physiology , Comorbidity , Coronavirus Infections/immunology , Coronavirus Infections/mortality , Cytokine Release Syndrome/immunology , Cytokine Release Syndrome/pathology , Cytokines/blood , Endothelial Cells/virology , Humans , Pandemics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/immunology , Pneumonia, Viral/mortality , Respiratory Distress Syndrome, Adult/immunology , Respiratory Distress Syndrome, Adult/pathology , Severity of Illness Index , Virus Internalization
10.
J Transl Med ; 18(1): 321, 2020 08 24.
Article in English | MEDLINE | ID: covidwho-727282

ABSTRACT

BACKGROUND: The outbreak of coronavirus disease (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), through its surface spike glycoprotein (S-protein) recognition on the receptor Angiotensin-converting enzyme 2 (ACE2) in humans. However, it remains unclear how genetic variations in ACE2 may affect its function and structure, and consequently alter the recognition by SARS-CoV-2. METHODS: We have systemically characterized missense variants in the gene ACE2 using data from the Genome Aggregation Database (gnomAD; N = 141,456). To investigate the putative deleterious role of missense variants, six existing functional prediction tools were applied to evaluate their impact. We further analyzed the structural flexibility of ACE2 and its protein-protein interface with the S-protein of SARS-CoV-2 using our developed Legion Interfaces Analysis (LiAn) program. RESULTS: Here, we characterized a total of 12 ACE2 putative deleterious missense variants. Of those 12 variants, we further showed that p.His378Arg could directly weaken the binding of catalytic metal atom to decrease ACE2 activity and p.Ser19Pro could distort the most important helix to the S-protein. Another seven missense variants may affect secondary structures (i.e. p.Gly211Arg; p.Asp206Gly; p.Arg219Cys; p.Arg219His, p.Lys341Arg, p.Ile468Val, and p.Ser547Cys), whereas p.Ile468Val with AF = 0.01 is only present in Asian. CONCLUSIONS: We provide strong evidence of putative deleterious missense variants in ACE2 that are present in specific populations, which could disrupt the function and structure of ACE2. These findings provide novel insight into the genetic variation in ACE2 which may affect the SARS-CoV-2 recognition and infection, and COVID-19 susceptibility and treatment.


Subject(s)
Betacoronavirus/physiology , Mutation, Missense , Peptidyl-Dipeptidase A/genetics , Protein Interaction Domains and Motifs/genetics , Spike Glycoprotein, Coronavirus/metabolism , Amino Acid Substitution , Betacoronavirus/metabolism , Binding Sites/genetics , Coronavirus Infections/ethnology , Coronavirus Infections/genetics , Coronavirus Infections/virology , DNA Mutational Analysis/methods , Databases, Genetic , Genetic Predisposition to Disease/ethnology , Genetic Variation , Geography , Humans , Models, Molecular , Molecular Docking Simulation , Pandemics , Peptidyl-Dipeptidase A/chemistry , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/ethnology , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , Polymorphism, Single Nucleotide , Protein Binding , Protein Structure, Secondary/genetics , Spike Glycoprotein, Coronavirus/chemistry , Virus Internalization
11.
Int J Mol Sci ; 21(17)2020 Aug 20.
Article in English | MEDLINE | ID: covidwho-725462

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor, angiotensin-converting enzyme 2 (ACE2), transmembrane protease serine 2 (TMPRSS2), and furin, which promote entry of the virus into the host cell, have been identified as determinants of SARS-CoV-2 infection. Dorsal tongue and gingiva, saliva, and tongue coating samples were examined to determine the presence of these molecules in the oral cavity. Immunohistochemical analyses showed that ACE2 was expressed in the stratified squamous epithelium of the dorsal tongue and gingiva. TMPRSS2 was strongly expressed in stratified squamous epithelium in the keratinized surface layer and detected in the saliva and tongue coating samples via Western blot. Furin was localized mainly in the lower layer of stratified squamous epithelium and detected in the saliva but not tongue coating. ACE2, TMPRSS2, and furin mRNA expression was observed in taste bud-derived cultured cells, which was similar to the immunofluorescence observations. These data showed that essential molecules for SARS-CoV-2 infection were abundant in the oral cavity. However, the database analysis showed that saliva also contains many protease inhibitors. Therefore, although the oral cavity may be the entry route for SARS-CoV-2, other factors including protease inhibitors in the saliva that inhibit viral entry should be considered.


Subject(s)
Betacoronavirus/metabolism , Furin/metabolism , Mouth Mucosa/metabolism , Peptidyl-Dipeptidase A/metabolism , Serine Endopeptidases/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Coronavirus Infections/metabolism , Gingiva/metabolism , Humans , Pandemics , Pneumonia, Viral/metabolism , Saliva/metabolism , Tongue/metabolism , Virus Internalization
12.
Mar Drugs ; 18(7)2020 Jun 28.
Article in English | MEDLINE | ID: covidwho-724325

ABSTRACT

Four new indolyl diketopiperazines, aspamides A-E (1-4) and two new diketopiperazines, aspamides F-G (5-6), along with 11 known diketopiperazines and intermediates were isolated from the solid culture of Aspergillus versicolor, which is an endophyte with the sea crab (Chiromantes haematocheir). Further chiral high-performance liquid chromatography resolution gave enantiomers (+)- and (-)-4, respectively. The structures and absolute configurations of compounds 1-6 were determined by the comprehensive analyses of nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), and electronic circular dichroism (ECD) calculation. All isolated compounds were selected for the virtual screening on the coronavirus 3-chymoretpsin-like protease (Mpro) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and the docking scores of compounds 1-2, 5, 6, 8 and 17 were top among all screened molecules, may be helpful in fighting with Corona Virus Disease-19 (COVID-19) after further studies.


Subject(s)
Antiviral Agents , Aquatic Organisms/chemistry , Aspergillus/chemistry , Cysteine Endopeptidases/metabolism , Diketopiperazines/chemistry , Diketopiperazines/metabolism , Viral Nonstructural Proteins/metabolism , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Betacoronavirus/metabolism , Chromatography, High Pressure Liquid , Cysteine Endopeptidases/chemistry , Drug Evaluation, Preclinical , Magnetic Resonance Spectroscopy , Mass Spectrometry , Molecular Docking Simulation , Stereoisomerism , User-Computer Interface , Viral Nonstructural Proteins/chemistry
14.
Int J Mol Sci ; 21(16)2020 Aug 13.
Article in English | MEDLINE | ID: covidwho-717745

ABSTRACT

While SARS-CoV-2 uses angiotensin converting enzyme 2 (ACE2) as the receptor for cell entry, it is important to examine other potential interactions between the virus and other cell receptors. Based on the clinical observation of low prevalence of smoking among hospitalized COVID-19 patients, we examined and identified a "toxin-like" amino acid (aa) sequence in the Receptor Binding Domain of the Spike Glycoprotein of SARS-CoV-2 (aa 375-390), which is homologous to a sequence of the Neurotoxin homolog NL1, one of the many snake venom toxins that are known to interact with nicotinic acetylcholine receptors (nAChRs). We present the 3D structural location of this "toxin-like" sequence on the Spike Glycoprotein and the superposition of the modelled structure of the Neurotoxin homolog NL1 and the SARS-CoV-2 Spike Glycoprotein. We also performed computational molecular modelling and docking experiments using 3D structures of the SARS-CoV-2 Spike Glycoprotein and the extracellular domain of the nAChR α9 subunit. We identified a main interaction between the aa 381-386 of the SARS-CoV-2 Spike Glycoprotein and the aa 189-192 of the extracellular domain of the nAChR α9 subunit, a region which forms the core of the "toxin-binding site" of the nAChRs. The mode of interaction is very similar to the interaction between the α9 nAChR and α-bungarotoxin. A similar interaction was observed between the pentameric α7 AChR chimera and SARS-CoV-2 Spike Glycoprotein. The findings raise the possibility that SARS-CoV-2 may interact with nAChRs, supporting the hypothesis of dysregulation of the nicotinic cholinergic system being implicated in the pathophysiology of COVID-19. Nicotine and other nicotinic cholinergic agonists may protect nAChRs and thus have therapeutic value in COVID-19 patients.


Subject(s)
Betacoronavirus/metabolism , Receptors, Nicotinic/genetics , Receptors, Nicotinic/metabolism , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Amino Acid Sequence/genetics , Computational Biology , Coronavirus Infections/physiopathology , Humans , Molecular Docking Simulation , Neurotoxins/genetics , Neurotoxins/metabolism , Pandemics , Pneumonia, Viral/physiopathology , Protein Structure, Tertiary/genetics , Sequence Alignment , Snake Venoms/genetics
15.
J Chem Inf Model ; 60(8): 3910-3934, 2020 08 24.
Article in English | MEDLINE | ID: covidwho-714258

ABSTRACT

Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.


Subject(s)
Drug Design , Drug Discovery , Protein Interaction Maps/drug effects , Small Molecule Libraries/pharmacology , Algorithms , Betacoronavirus/drug effects , Betacoronavirus/metabolism , Coronavirus Infections/drug therapy , Coronavirus Infections/metabolism , Databases, Protein , Humans , Ligands , Machine Learning , Molecular Docking Simulation , Molecular Targeted Therapy , Pandemics , Pneumonia, Viral/drug therapy , Pneumonia, Viral/metabolism , Proteins/chemistry , Proteins/metabolism , Small Molecule Libraries/chemistry
16.
Int J Mol Sci ; 21(16)2020 Aug 09.
Article in English | MEDLINE | ID: covidwho-713065

ABSTRACT

The pandemic evolution of SARS-CoV-2 infection is forcing the scientific community to unprecedented efforts to explore all possible approaches against COVID-19. In this context, targeting virus entry is a promising antiviral strategy for controlling viral infections. The main strategies pursued to inhibit the viral entry are considering both the virus and the host factors involved in the process. Primarily, direct-acting antivirals rely on inhibition of the interaction between ACE2 and the receptor binding domain (RBD) of the Spike (S) protein or targeting the more conserved heptad repeats (HRs), involved in the membrane fusion process. The inhibition of host TMPRSS2 and cathepsins B/L may represent a complementary strategy to be investigated. In this review, we discuss the development entry inhibitors targeting the S protein, as well as the most promising host targeting strategies involving TMPRSS2 and CatB/L, which have been exploited so far against CoVs and other related viruses.


Subject(s)
Angiotensin-Converting Enzyme Inhibitors/pharmacology , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Serine Proteinase Inhibitors/pharmacology , Virus Internalization/drug effects , Animals , Betacoronavirus/metabolism , Betacoronavirus/physiology , Humans , Spike Glycoprotein, Coronavirus/metabolism
17.
J Infect Dis ; 222(5): 734-745, 2020 08 04.
Article in English | MEDLINE | ID: covidwho-711823

ABSTRACT

Clinical manifestations of coronavirus disease 2019 (COVID-19) vary from asymptomatic virus shedding, nonspecific pharyngitis, to pneumonia with silent hypoxia and respiratory failure. Dendritic cells and macrophages are sentinel cells for innate and adaptive immunity that affect the pathogenesis of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). The interplay between SARS-CoV-2 and these cell types remains unknown. We investigated infection and host responses of monocyte-derived dendritic cells (moDCs) and macrophages (MDMs) infected by SARS-CoV-2. MoDCs and MDMs were permissive to SARS-CoV-2 infection and protein expression but did not support productive virus replication. Importantly, SARS-CoV-2 launched an attenuated interferon response in both cell types and triggered significant proinflammatory cytokine/chemokine expression in MDMs but not moDCs. Investigations suggested that this attenuated immune response to SARS-CoV-2 in moDCs was associated with viral antagonism of STAT1 phosphorylation. These findings may explain the mild and insidious course of COVID-19 until late deterioration.


Subject(s)
Betacoronavirus/physiology , Coronavirus Infections/immunology , Dendritic Cells/immunology , Interferons/immunology , Monocytes/immunology , Pneumonia, Viral/immunology , STAT1 Transcription Factor/antagonists & inhibitors , Adaptive Immunity , Animals , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , Betacoronavirus/metabolism , Chemokines/metabolism , Chlorocebus aethiops , Coronavirus Infections/metabolism , Coronavirus Infections/virology , Cytokines/metabolism , Dendritic Cells/metabolism , Dendritic Cells/virology , Humans , Macrophages/immunology , Macrophages/virology , Monocytes/virology , Pandemics , Phosphorylation , Pneumonia, Viral/metabolism , Pneumonia, Viral/virology , STAT1 Transcription Factor/immunology , STAT1 Transcription Factor/metabolism , Vero Cells , Virus Replication/physiology , Virus Shedding
18.
J Exp Med ; 217(12)2020 12 07.
Article in English | MEDLINE | ID: covidwho-709757

ABSTRACT

Severe acute respiratory syndrome-coronavirus 2 (SARS-Cov-2) has caused over 13,000,000 cases of coronavirus disease (COVID-19) with a significant fatality rate. Laboratory mice have been the stalwart of therapeutic and vaccine development; however, they do not support infection by SARS-CoV-2 due to the virus's inability to use the mouse orthologue of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis, these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno-associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and exhibit pathological findings found in COVID-19 patients. Moreover, we show that type I interferons do not control SARS-CoV-2 replication in vivo but are significant drivers of pathological responses. Thus, the AAV-hACE2 mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds.


Subject(s)
Betacoronavirus/metabolism , Coronavirus Infections/metabolism , Disease Models, Animal , Interferon Type I/metabolism , Mice/genetics , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/metabolism , Animals , Cell Line, Tumor , Coronavirus Infections/pathology , Coronavirus Infections/virology , Dependovirus/genetics , Female , Humans , Inflammation/metabolism , Lung/pathology , Lung/virology , Male , Mice, Inbred C57BL , Mice, Transgenic , Pandemics , Parvoviridae Infections/metabolism , Parvoviridae Infections/virology , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Signal Transduction/genetics , Virus Replication/genetics
19.
Blood ; 136(4): 489-500, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-704282

ABSTRACT

Patients with coronavirus disease 2019 (COVID-19) have elevated D-dimer levels. Early reports describe high venous thromboembolism (VTE) and disseminated intravascular coagulation (DIC) rates, but data are limited. This multicenter retrospective study describes the rate and severity of hemostatic and thrombotic complications of 400 hospital-admitted COVID-19 patients (144 critically ill) primarily receiving standard-dose prophylactic anticoagulation. Coagulation and inflammatory parameters were compared between patients with and without coagulation-associated complications. Multivariable logistic models examined the utility of these markers in predicting coagulation-associated complications, critical illness, and death. The radiographically confirmed VTE rate was 4.8% (95% confidence interval [CI], 2.9-7.3), and the overall thrombotic complication rate was 9.5% (95% CI, 6.8-12.8). The overall and major bleeding rates were 4.8% (95% CI, 2.9-7.3) and 2.3% (95% CI, 1.0-4.2), respectively. In the critically ill, radiographically confirmed VTE and major bleeding rates were 7.6% (95% CI, 3.9-13.3) and 5.6% (95% CI, 2.4-10.7), respectively. Elevated D-dimer at initial presentation was predictive of coagulation-associated complications during hospitalization (D-dimer >2500 ng/mL, adjusted odds ratio [OR] for thrombosis, 6.79 [95% CI, 2.39-19.30]; adjusted OR for bleeding, 3.56 [95% CI, 1.01-12.66]), critical illness, and death. Additional markers at initial presentation predictive of thrombosis during hospitalization included platelet count >450 × 109/L (adjusted OR, 3.56 [95% CI, 1.27-9.97]), C-reactive protein (CRP) >100 mg/L (adjusted OR, 2.71 [95% CI, 1.26-5.86]), and erythrocyte sedimentation rate (ESR) >40 mm/h (adjusted OR, 2.64 [95% CI, 1.07-6.51]). ESR, CRP, fibrinogen, ferritin, and procalcitonin were higher in patients with thrombotic complications than in those without. DIC, clinically relevant thrombocytopenia, and reduced fibrinogen were rare and were associated with significant bleeding manifestations. Given the observed bleeding rates, randomized trials are needed to determine any potential benefit of intensified anticoagulant prophylaxis in COVID-19 patients.


Subject(s)
Betacoronavirus/metabolism , Blood Coagulation , Coronavirus Infections/blood , Hemorrhage/blood , Pneumonia, Viral/blood , Thrombosis/blood , Adult , Aged , Aged, 80 and over , Biomarkers/blood , C-Reactive Protein/metabolism , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Coronavirus Infections/therapy , Female , Fibrin Fibrinogen Degradation Products/metabolism , Hemorrhage/epidemiology , Hemorrhage/therapy , Hospitalization , Humans , Male , Middle Aged , Pandemics , Platelet Count , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Pneumonia, Viral/therapy , Thrombosis/epidemiology , Thrombosis/therapy
20.
Am J Physiol Heart Circ Physiol ; 318(5): H1084-H1090, 2020 05 01.
Article in English | MEDLINE | ID: covidwho-707207

ABSTRACT

The novel SARS coronavirus SARS-CoV-2 pandemic may be particularly deleterious to patients with underlying cardiovascular disease (CVD). The mechanism for SARS-CoV-2 infection is the requisite binding of the virus to the membrane-bound form of angiotensin-converting enzyme 2 (ACE2) and internalization of the complex by the host cell. Recognition that ACE2 is the coreceptor for the coronavirus has prompted new therapeutic approaches to block the enzyme or reduce its expression to prevent the cellular entry and SARS-CoV-2 infection in tissues that express ACE2 including lung, heart, kidney, brain, and gut. ACE2, however, is a key enzymatic component of the renin-angiotensin-aldosterone system (RAAS); ACE2 degrades ANG II, a peptide with multiple actions that promote CVD, and generates Ang-(1-7), which antagonizes the effects of ANG II. Moreover, experimental evidence suggests that RAAS blockade by ACE inhibitors, ANG II type 1 receptor antagonists, and mineralocorticoid antagonists, as well as statins, enhance ACE2 which, in part, contributes to the benefit of these regimens. In lieu of the fact that many older patients with hypertension or other CVDs are routinely treated with RAAS blockers and statins, new clinical concerns have developed regarding whether these patients are at greater risk for SARS-CoV-2 infection, whether RAAS and statin therapy should be discontinued, and the potential consequences of RAAS blockade to COVID-19-related pathologies such as acute and chronic respiratory disease. The current perspective critically examines the evidence for ACE2 regulation by RAAS blockade and statins, the cardiovascular benefits of ACE2, and whether ACE2 blockade is a viable approach to attenuate COVID-19.


Subject(s)
Betacoronavirus/physiology , Cardiovascular Diseases/enzymology , Cardiovascular Diseases/virology , Coronavirus Infections/enzymology , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/enzymology , Animals , Betacoronavirus/metabolism , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Humans , Male , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Rats , Rats, Inbred Lew , Virus Internalization
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