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1.
SLAS Discovery ; 2022.
Article in English | ScienceDirect | ID: covidwho-1586501

ABSTRACT

Effective small molecule therapies to combat the SARS-CoV-2 infection are still lacking as the COVID-19 pandemic continues globally. High throughput screening assays are needed for lead discovery and optimization of small molecule SARS-CoV-2 inhibitors. In this work, we have applied viral pseudotyping to establish a cell-based SARS-CoV-2 entry assay. Here, the pseudotyped particles (PP) contain SARS-CoV-2 spike in a membrane enveloping both the murine leukemia virus (MLV) gag-pol polyprotein and luciferase reporter RNA. Upon addition of PP to HEK293-ACE2 cells, the SARS-CoV-2 spike protein binds to the ACE2 receptor on the cell surface, resulting in priming by host proteases to trigger endocytosis of these particles, and membrane fusion between the particle envelope and the cell membrane. The internalized luciferase reporter gene is then expressed in cells, resulting in a luminescent readout as a surrogate for spike-mediated entry into cells. This SARS-CoV-2 PP entry assay can be executed in a biosafety level 2 containment lab for high throughput screening. From a collection of 5,158 approved drugs and drug candidates, our screening efforts identified 7 active compounds that inhibited the SARS-CoV-2-S PP entry. Of these seven, six compounds were active against live replicating SARS-CoV-2 virus in a cytopathic effect assay. Our results demonstrated the utility of this assay in the discovery and development of SARS-CoV-2 entry inhibitors as well as the mechanistic study of anti-SARS-CoV-2 compounds. Additionally, particles pseudotyped with spike proteins from SARS-CoV-2 B.1.1.7 and B.1.351 variants were prepared and used to evaluate the therapeutic effects of viral entry inhibitors.

2.
Front Med (Lausanne) ; 8: 783646, 2021.
Article in English | MEDLINE | ID: covidwho-1581284

ABSTRACT

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been basically under control in China since March 2020, but the import of domestic SARS-CoV-2 has begun to increase. This study reported the first case of asymptomatic SARS-CoV-2 infection imported from Spain into Sichuan Province, China, on March 11, 2020. The infected male had a body temperature of 37.5°C, normal blood oxygen saturation levels, and a computed tomography (CT) examination showed that his lungs had no shadows. However, a throat swab from the subject tested positive for SARS-CoV-2 using qPCR assay. In this study, we conducted transcriptome sequencing on respiratory throat swabs from the subject and found that the dominant SARS-CoV-2 sequence (Gene Bank ID: MW301121) was a spike protein D614G mutant strain, which is currently popular throughout world. We downloaded and analyzed SARS-CoV-2 sequences collected from cases in China and Spain for comparison and tracing purposes. After March 11, 2020, the Chinese domestic clade was naturally divided into the imported SARS-CoV-2 D614G mutant strain and evolutionarily-related similar sequences and that of sequences collected in the original Wuhan area. The sequence reported in this study was located on a small branch, far from the evolution of Wuhan sequences. As expected, the identified sequence was closely related to the evolution of the SARS-CoV-2 D614G mutant strain circulating in Spain.

3.
Preprint | EuropePMC | ID: ppcovidwho-296676

ABSTRACT

The cell entry of SARS-CoV-2 has emerged as an attractive drug development target. We previously reported that the entry of SARS-CoV-2 depends on the cell surface heparan sulfate proteoglycan (HSPG) and the cortex actin, which can be targeted by therapeutic agents identified by conventional drug repurposing screens. However, this drug identification strategy requires laborious library screening, which is time-consuming and often limited number of compounds can be screened. As an alternative approach, we developed and trained a graph convolutional network (GCN)-based classification model using information extracted from experimentally identified HSPG and actin inhibitors. This method allowed us to virtually screen 170,000 compounds, resulting in ~2000 potential hits. A hit confirmation assay with the uptake of a fluorescently labeled HSPG cargo further shortlisted 256 active compounds. Among them, 16 compounds had modest to strong inhibitory activities against the entry of SARS-CoV-2 pseudotyped particles into Vero E6 cells. These results establish a GCN-based virtual screen workflow for rapid identification of new small molecule inhibitors against validated drug targets.

4.
Preprint in English | [Unspecified Source] | ID: ppcovidwho-292816

ABSTRACT

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emphasized the urgency to develop effective therapeutics. Drug repurposing screening is regarded as one of the most practical and rapid approaches for the discovery of such therapeutics. The 3C like protease (3CL (pro) ), or main protease (M (pro) ) of SARS-CoV-2 is a valid drug target as it is a specific viral enzyme and plays an essential role in viral replication. We performed a quantitative high throughput screening (qHTS) of 10,755 compounds consisting of approved and investigational drugs, and bioactive compounds using a SARS-CoV-2 3CL (pro) assay. Twenty-three small molecule inhibitors of SARS-CoV-2 3CL (pro) have been identified with IC50s ranging from 0.26 to 28.85 μM. Walrycin B (IC (50) = 0.26 µM), Hydroxocobalamin (IC (50) = 3.29 µM), Suramin sodium (IC (50) = 6.5 µM), Z-DEVD-FMK (IC (50) = 6.81 µM), LLL-12 (IC (50) = 9.84 µM), and Z-FA-FMK (IC (50) = 11.39 µM) are the most potent 3CL (pro) inhibitors. The activities of anti-SARS-CoV-2 viral infection was confirmed in 7 of 23 compounds using a SARS-CoV-2 cytopathic effect assay. The results demonstrated a set of SARS-CoV-2 3CL (pro) inhibitors that may have potential for further clinical evaluation as part of drug combination therapies to treating COVID-19 patients, and as starting points for chemistry optimization for new drug development.

6.
ACS Pharmacol Transl Sci ; 4(5): 1675-1688, 2021 Oct 08.
Article in English | MEDLINE | ID: covidwho-1450269

ABSTRACT

The National Center for Advancing Translational Sciences (NCATS) has been actively generating SARS-CoV-2 high-throughput screening data and disseminates it through the OpenData Portal (https://opendata.ncats.nih.gov/covid19/). Here, we provide a hybrid approach that utilizes NCATS screening data from the SARS-CoV-2 cytopathic effect reduction assay to build predictive models, using both machine learning and pharmacophore-based modeling. Optimized models were used to perform two iterative rounds of virtual screening to predict small molecules active against SARS-CoV-2. Experimental testing with live virus provided 100 (∼16% of predicted hits) active compounds (efficacy > 30%, IC50 ≤ 15 µM). Systematic clustering analysis of active compounds revealed three promising chemotypes which have not been previously identified as inhibitors of SARS-CoV-2 infection. Further investigation resulted in the identification of allosteric binders to host receptor angiotensin-converting enzyme 2; these compounds were then shown to inhibit the entry of pseudoparticles bearing spike protein of wild-type SARS-CoV-2, as well as South African B.1.351 and UK B.1.1.7 variants.

7.
Brief Bioinform ; 2021 Sep 01.
Article in English | MEDLINE | ID: covidwho-1393161

ABSTRACT

Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of Minimal Information for Chemosensitivity Assays (MICHA), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies as well as six recently conducted COVID-19 studies. With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.

8.
Chem Sci ; 12(38): 12600-12609, 2021 Oct 06.
Article in English | MEDLINE | ID: covidwho-1387506

ABSTRACT

SARS-CoV-2, the cause of the COVID-19 pandemic, exploits host cell proteins for viral entry into human lung cells. One of them, the protease TMPRSS2, is required to activate the viral spike protein (S). Even though two inhibitors, camostat and nafamostat, are known to inhibit TMPRSS2 and block cell entry of SARS-CoV-2, finding further potent therapeutic options is still an important task. In this study, we report that a late-stage drug candidate, otamixaban, inhibits SARS-CoV-2 cell entry. We show that otamixaban suppresses TMPRSS2 activity and SARS-CoV-2 infection of a human lung cell line, although with lower potency than camostat or nafamostat. In contrast, otamixaban inhibits SARS-CoV-2 infection of precision cut lung slices with the same potency as camostat. Furthermore, we report that otamixaban's potency can be significantly enhanced by (sub-) nanomolar nafamostat or camostat supplementation. Dominant molecular TMPRSS2-otamixaban interactions are assessed by extensive 109 µs of atomistic molecular dynamics simulations. Our findings suggest that combinations of otamixaban with supplemental camostat or nafamostat are a promising option for the treatment of COVID-19.

9.
ACS Med Chem Lett ; 12(8): 1267-1274, 2021 Aug 12.
Article in English | MEDLINE | ID: covidwho-1358337

ABSTRACT

SARS-CoV-2 entry into host cells relies on the spike (S) protein binding to the human ACE2 receptor. In this study, we investigated the structural dynamics of the viral S protein at the fusion peptide (FP) domain and small molecule binding for therapeutics development. Following comparative modeling analysis and docking studies of our previously identified fusion inhibitor chlorcyclizine, we performed a pharmacophore-based virtual screen and identified two novel chemotypes of entry inhibitors targeting the FP. The compounds were evaluated in the pseudoparticle viral entry assay and SARS-CoV-2 cytopathic effect assay and showed single-digital micromole inhibition against SARS-CoV-2 as well as SARS-CoV-1 and MERS. The characterization of the FP binding site of SARS-CoV-2 S protein provides a promising target for the structure-based development of small molecule entry inhibitors as drug candidates for the treatment of COVID-19.

10.
Nano Life ; : 1, 2021.
Article in English | Academic Search Complete | ID: covidwho-1261216

ABSTRACT

Aim: To develop a nursing early warning system in children’s hospital during the outbreak of the novel coronavirus pneumonia, and to accomplish the construction and application of this system, so as to provide decision-support of the prevention and control for COVID-19 in children’s medical institutions. Method: Children’s hospital nursing early warning system was divided into three modules: hospital nursing early warning platform includes internal and external early warning platform, nursing staff early warning program includes protection, human resources early warning plan and patient early warning program includes outpatient, emergency and ward early warning plan. The data of epidemic training, assessment, prevention and control screening from January to June 2020 were collected from the nursing early warning system to evaluate the application effect of the system. Results: A total of 18 procedures and specifications were formulated, nine hospital-level trainings and about 1000 department-level trainings were organized, two hospital-level assessments (pass rate 95.6% and 98.2%), and 78 nurses were reserved, and 10 popular science articles, five popular science videos were published during the application of the nursing early warning system. A total of 583,435 children and 139,308 caregivers were screened in outpatient, emergency and wards during pre-checks, 2385 suspected cases of novel coronavirus pneumonia were confirmed (0.41%) after the screening and 1 case (0.0002%) was finally confirmed. Conclusion: The nursing early warning system of children’s hospital can prevent and control the novel coronavirus pneumonia epidemic from each module, ensure early warning and triage of suspected infected patients, reduce the risk of cross-infection in hospital and improve the safety of the children’s hospital medical environment. [ABSTRACT FROM AUTHOR] Copyright of Nano Life is the property of World Scientific Publishing Company and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

11.
The FASEB Journal ; 35(S1), 2021.
Article in English | Wiley | ID: covidwho-1233926

ABSTRACT

Understanding the SARS-CoV-2 virus? routes of infection, virus?host?protein interactions, and mechanisms of virus-induced cytopathic effects will greatly aid in the discovery and design of new therapeutics to treat COVID-19. Chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including alkalizing lysosomes and blocking autophagy as well as exhibiting dose-limiting toxicities in patients. To identify an alternative lysosome-based drug repurposing opportunity we evaluated additional lysosomotropic compounds . We found that six of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero E6 cells with half-maximal effective concentration (EC50) values ranging from 2.0 to 13 ?M and selectivity indices (SIs;SI = CC50/EC50) ranging from 1.5- to >10-fold. We demonstrate how the compounds (1) blocked lysosome functioning and autophagy, (2) prevented pseudotyped particle entry, (3) increased lysosomal pH, and (4) that ROC-325 reduced viral titers in the EpiAirway 3D tissue model. Consistent with these findings, the siRNA knockdown of ATP6V0D1 blocked the HCoV-NL63 cytopathic effect in LLC-MK2 cells. Moreover, an analysis of SARS-CoV-2 infected Vero E6 cell lysate revealed significant dysregulation of autophagy and lysosomal function, suggesting a contribution of the lysosome to the life cycle of SARS-CoV-2. Our findings support targeting the lysosome to combat SARS-CoV-2 infections and inhibitors of lysosomal function could become an important component of drug combination therapies aimed at improving treatment and outcomes for COVID-19.

12.
ACS Pharmacol Transl Sci ; 4(3): 1124-1135, 2021 Jun 11.
Article in English | MEDLINE | ID: covidwho-1233687

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has prompted researchers to pivot their efforts to finding antiviral compounds and vaccines. In this study, we focused on the human host cell transmembrane protease serine 2 (TMPRSS2), which plays an important role in the viral life cycle by cleaving the spike protein to initiate membrane fusion. TMPRSS2 is an attractive target and has received attention for the development of drugs against SARS and Middle East respiratory syndrome. Starting with comparative structural modeling and a binding model analysis, we developed an efficient pharmacophore-based approach and applied a large-scale in silico database screening for small-molecule inhibitors against TMPRSS2. The hits were evaluated in the TMPRSS2 biochemical assay and the SARS-CoV-2 pseudotyped particle entry assay. A number of novel inhibitors were identified, providing starting points for the further development of drug candidates for the treatment of coronavirus disease 2019.

14.
Bioorg Med Chem ; 38: 116119, 2021 05 15.
Article in English | MEDLINE | ID: covidwho-1157155

ABSTRACT

In response to the pandemic caused by SARS-CoV-2, we constructed a hybrid support vector machine (SVM) classification model using a set of publicly posted SARS-CoV-2 pseudotyped particle (PP) entry assay repurposing screen data to identify novel potent compounds as a starting point for drug development to treat COVID-19 patients. Two different molecular descriptor systems, atom typing descriptors and 3D fingerprints (FPs), were employed to construct the SVM classification models. Both models achieved reasonable performance, with the area under the curve of receiver operating characteristic (AUC-ROC) of 0.84 and 0.82, respectively. The consensus prediction outperformed the two individual models with significantly improved AUC-ROC of 0.91, where the compounds with inconsistent classifications were excluded. The consensus model was then used to screen the 173,898 compounds in the NCATS annotated and diverse chemical libraries. Of the 255 compounds selected for experimental confirmation, 116 compounds exhibited inhibitory activities in the SARS-CoV-2 PP entry assay with IC50 values ranged between 0.17 µM and 62.2 µM, representing an enrichment factor of 3.2. These 116 active compounds with diverse and novel structures could potentially serve as starting points for chemistry optimization for COVID-19 drug discovery.


Subject(s)
Antiviral Agents/pharmacology , SARS-CoV-2/drug effects , Support Vector Machine/statistics & numerical data , Virus Internalization/drug effects , Area Under Curve , Databases, Chemical/statistics & numerical data , Drug Repositioning , HEK293 Cells , Humans , Microbial Sensitivity Tests , ROC Curve , Small Molecule Libraries/pharmacology
15.
Bioorg Med Chem Lett ; 40: 127906, 2021 05 15.
Article in English | MEDLINE | ID: covidwho-1118337

ABSTRACT

Zika virus has emerged as a potential threat to human health globally. A previous drug repurposing screen identified the approved anthelminthic drug niclosamide as a small molecule inhibitor of Zika virus infection. However, as antihelminthic drugs are generally designed to have low absorption when dosed orally, the very limited bioavailability of niclosamide will likely hinder its potential direct repurposing as an antiviral medication. Here, we conducted SAR studies focusing on the anilide and salicylic acid regions of niclosamide to improve physicochemical properties such as microsomal metabolic stability, permeability and solubility. We found that the 5-bromo substitution in the salicylic acid region retains potency while providing better drug-like properties. Other modifications in the anilide region with 2'-OMe and 2'-H substitutions were also advantageous. We found that the 4'-NO2 substituent can be replaced with a 4'-CN or 4'-CF3 substituents. Together, these modifications provide a basis for optimizing the structure of niclosamide to improve systemic exposure for application of niclosamide analogs as drug lead candidates for treating Zika and other viral infections. Indeed, key analogs were also able to rescue cells from the cytopathic effect of SARS-CoV-2 infection, indicating relevance for therapeutic strategies targeting the COVID-19 pandemic.


Subject(s)
Antiviral Agents/pharmacology , Niclosamide/analogs & derivatives , Niclosamide/pharmacology , SARS-CoV-2/drug effects , Zika Virus/drug effects , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/metabolism , Binding Sites , Chlorocebus aethiops , Drug Stability , Humans , Microbial Sensitivity Tests , Microsomes, Liver/metabolism , Molecular Docking Simulation , Molecular Structure , Niclosamide/metabolism , Protein Binding , Rats , Serine Endopeptidases/chemistry , Serine Endopeptidases/metabolism , Structure-Activity Relationship , Vero Cells , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism
16.
Front Pharmacol ; 11: 592737, 2020.
Article in English | MEDLINE | ID: covidwho-1090410

ABSTRACT

Drug repurposing is a rapid approach to identify therapeutics for the treatment of emerging infectious diseases such as COVID-19. To address the urgent need for treatment options, we carried out a quantitative high-throughput screen using a SARS-CoV-2 cytopathic assay with a compound collection of 8,810 approved and investigational drugs, mechanism-based bioactive compounds, and natural products. Three hundred and nineteen compounds with anti-SARS-CoV-2 activities were identified and confirmed, including 91 approved drugs and 49 investigational drugs. The anti-SARS-CoV-2 activities of 230 of these confirmed compounds, of which 38 are approved drugs, have not been previously reported. Chlorprothixene, methotrimeprazine, and piperacetazine were the three most potent FDA-approved drugs with anti-SARS-CoV-2 activities. These three compounds have not been previously reported to have anti-SARS-CoV-2 activities, although their antiviral activities against SARS-CoV and Ebola virus have been reported. These results demonstrate that this comprehensive data set is a useful resource for drug repurposing efforts, including design of new drug combinations for clinical trials for SARS-CoV-2.

17.
Neurosci Lett ; 743: 135567, 2021 01 19.
Article in English | MEDLINE | ID: covidwho-1087171

ABSTRACT

Coronavirus disease 2019 (COVID-19) usually leads to a mild infectious disease course in children, but serious complications may occur in conjunction with both acute infection and associated phenomena such as the multisystem inflammatory syndrome in children (MIS-C). Neurological symptoms, which have been predominantly reported in adults, range from mild headache to seizure, peripheral neuropathy, stroke, demyelinating disorders, and encephalopathy. Similar to respiratory and cardiac manifestations of COVID-19, neurological complications present differently based on age and underlying comorbidities. This review provides a concise overview of the neurological conditions seen in the context of COVID-19, as well as potential mechanisms and long-term implications of COVID-19 in the pediatric population from literature reviews and primary data collected at NewYork-Presbyterian Morgan Stanley Children's Hospital.


Subject(s)
COVID-19/complications , Nervous System Diseases/virology , Child , Child, Preschool , Female , Humans , Male , SARS-CoV-2
18.
JMIR Biomed Eng ; 5(1): e24388, 2020.
Article in English | MEDLINE | ID: covidwho-1059612

ABSTRACT

Background: Due to the COVID-19 pandemic, the demand for remote electrocardiogram (ECG) monitoring has increased drastically in an attempt to prevent the spread of the virus and keep vulnerable individuals with less severe cases out of hospitals. Enabling clinicians to set up remote patient ECG monitoring easily and determining how to classify the ECG signals accurately so relevant alerts are sent in a timely fashion is an urgent problem to be addressed for remote patient monitoring (RPM) to be adopted widely. Hence, a new technique is required to enable routine and widespread use of RPM, as is needed due to COVID-19. Objective: The primary aim of this research is to create a robust and easy-to-use solution for personalized ECG monitoring in real-world settings that is precise, easily configurable, and understandable by clinicians. Methods: In this paper, we propose a Personalized Monitoring Model (PMM) for ECG data based on motif discovery. Motif discovery finds meaningful or frequently recurring patterns in patient ECG readings. The main strategy is to use motif discovery to extract a small sample of personalized motifs for each individual patient and then use these motifs to predict abnormalities in real-time readings of that patient using an artificial logical network configured by a physician. Results: Our approach was tested on 30 minutes of ECG readings from 32 patients. The average diagnostic accuracy of the PMM was always above 90% and reached 100% for some parameters, compared to 80% accuracy for the Generalized Monitoring Models (GMM). Regardless of parameter settings, PMM training models were generated within 3-4 minutes, compared to 1 hour (or longer, with increasing amounts of training data) for the GMM. Conclusions: Our proposed PMM almost eliminates many of the training and small sample issues associated with GMMs. It also addresses accuracy and computational cost issues of the GMM, caused by the uniqueness of heartbeats and training issues. In addition, it addresses the fact that doctors and nurses typically do not have data science training and the skills needed to configure, understand, and even trust existing black box machine learning models.

20.
World J Clin Cases ; 8(24): 6252-6263, 2020 Dec 26.
Article in English | MEDLINE | ID: covidwho-1005656

ABSTRACT

BACKGROUND: Understanding a virus shedding patterns in body fluids/secretions is important to determine the samples to be used for diagnosis and to formulate infection control measures. AIM: To investigate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding patterns and its risk factors. METHODS: All laboratory-confirmed coronavirus disease 2019 patients with complete medical records admitted to the Shenzhen Third People's Hospital from January 28, 2020 to March 8, 2020 were included. Among 145 patients (54.5% males; median age, 46.1 years), three (2.1%) died. The bronco-alveolar lavage fluid (BALF) had the highest virus load compared with the other samples. The viral load peaked at admission (3.3 × 108 copies) and sharply decreased 10 d after admission. RESULTS: The viral load was associated with prolonged intensive care unit (ICU) duration. Patients in the ICU had significantly longer shedding time compared to those in the wards (P < 0.0001). Age > 60 years [hazard ratio (HR) = 0.6; 95% confidence interval (CI): 0.4-0.9] was an independent risk factor for SARS-CoV-2 shedding, while chloroquine (HR = 22.8; 95%CI: 2.3-224.6) was a protective factor. CONCLUSION: BALF had the highest SARS-CoV-2 load. Elderly patients had higher virus loads, which was associated with a prolonged ICU stay. Chloroquine was associated with shorter shedding duration and increased the chance of viral negativity.

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