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1.
Int J Mol Sci ; 22(20)2021 Oct 12.
Article in English | MEDLINE | ID: covidwho-1480791

ABSTRACT

Novel xanthine and imidazolone derivatives were synthesized based on oxazolone derivatives 2a-c as a key intermediate. The corresponding xanthine 3-5 and imidazolone derivatives 6-13 were obtained via reaction of oxazolone derivative 2a-c with 5,6-diaminouracils 1a-e under various conditions. Xanthine compounds 3-5 were obtained by cyclocondensation of 5,6-diaminouracils 1a-c with different oxazolones in glacial acetic acid. Moreover, 5,6-diaminouracils 1a-e were reacted with oxazolones 2a-c in presence of drops of acetic acid under fused condition yielding the imidazolone derivatives 6-13. Furthermore, Schiff base of compounds 14-16 were obtained by condensing 5,6-diaminouracils 1a,b,e with 4-dimethylaminobenzaldehyde in acetic acid. The structural identity of the resulting compounds was resolved by IR, 1H-, 13C-NMR and Mass spectral analyses. The novel synthesized compounds were screened for their antifungal and antibacterial activities. Compounds 3, 6, 13 and 16 displayed the highest activity against Escherichia coli as revealed from the IC50 values (1.8-1.9 µg/mL). The compound 16 displayed a significant antifungal activity against Candia albicans (0.82 µg/mL), Aspergillus flavus (1.2 µg/mL) comparing to authentic antibiotics. From the TEM microgram, the compounds 3, 12, 13 and 16 exhibited a strong deformation to the cellular entities, by interfering with the cell membrane components, causing cytosol leakage, cellular shrinkage and irregularity to the cell shape. In addition, docking study for the most promising antimicrobial tested compounds depicted high binding affinity against acyl carrier protein domain from a fungal type I polyketide synthase (ACP), and Baumannii penicillin- binding protein (PBP). Moreover, compound 12 showed high drug- likeness, and excellent pharmacokinetics, which needs to be in focus for further antimicrobial drug development. The most promising antimicrobial compounds underwent theoretical investigation using DFT calculation.


Subject(s)
Anti-Infective Agents/chemical synthesis , Imidazoles/chemistry , Uracil/chemistry , Xanthines/chemistry , Animals , Anti-Infective Agents/metabolism , Anti-Infective Agents/pharmacology , Binding Sites , Candida albicans/drug effects , Cell Survival/drug effects , Chlorocebus aethiops , DNA Gyrase/chemistry , DNA Gyrase/metabolism , Density Functional Theory , Gram-Negative Bacteria/drug effects , Gram-Positive Bacteria/drug effects , Half-Life , Imidazoles/metabolism , Imidazoles/pharmacology , Microbial Sensitivity Tests , Molecular Docking Simulation , Polyketide Synthases/chemistry , Polyketide Synthases/metabolism , Structure-Activity Relationship , Thermodynamics , Vero Cells
2.
J Phys Chem Lett ; 12(20): 4814-4822, 2021 May 27.
Article in English | MEDLINE | ID: covidwho-1387121

ABSTRACT

Angiotensin converting enzyme 2 (ACE2) plays a key role in renin-angiotensin system regulation and amino acid homeostasis. Human ACE2 acts as the receptor for severe acute respiratory syndrome coronaviruses SARS-CoV and SARS-CoV-2. ACE2 is also widely expressed in epithelial cells of the lungs, heart, kidney, and pancreas. It is considered an important drug target for treating SARS-CoV-2 as well as pulmonary diseases, heart failure, hypertension, renal diseases, and diabetes. Despite the critical importance, the mechanism of ligand binding to the human ACE2 receptor remains unknown. Here, we have addressed this challenge through all-atom simulations using a novel ligand Gaussian accelerated molecular dynamics (LiGaMD) method. Microsecond time scale LiGaMD simulations have unprecedentedly captured multiple times of spontaneous binding and unbinding of a potent inhibitor MLN-4760 in the ACE2 receptor. With ligand far away in the unbound state, the ACE2 receptor samples distinct Open, Partially Open, Closed, and Fully Closed conformations. Upon ligand binding to the active site, conformational ensemble of the ACE2 receptor is biased toward the Closed state as observed in the X-ray experimental structure. The LiGaMD simulations thus suggest a conformational selection mechanism for ligand recognition by the highly flexible ACE2 receptor, which is expected to facilitate rational drug design targeting human ACE2 against coronaviruses and other related human diseases.


Subject(s)
Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Antiviral Agents/chemistry , COVID-19/drug therapy , Imidazoles/chemistry , Leucine/analogs & derivatives , Protease Inhibitors/chemistry , SARS-CoV-2/drug effects , Antiviral Agents/pharmacology , COVID-19/metabolism , Catalytic Domain , Drug Design , Humans , Imidazoles/pharmacology , Leucine/chemistry , Leucine/pharmacology , Ligands , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology , Protein Binding , Protein Conformation , SARS-CoV-2/metabolism
3.
Biomed Res Int ; 2021: 6614000, 2021.
Article in English | MEDLINE | ID: covidwho-1327769

ABSTRACT

Chloroquine (CQ) and hydroxychloroquine (HCQ) have shown the ability to inhibit in vitro viral replications of coronaviridae viruses such as SARS-CoV and SARS-CoV-2. However, clinical trial outcomes have been disparate, suggesting that CQ and HCQ antiviral mechanisms are not fully understood. Based on three-dimensional structural similarities between HCQ and the known ACE2 specific inhibitor MLN-4760, we compared their modulation on ACE2 activity. Here we describe, for the first time, in a cell-free in vitro system that HCQ directly and dose-dependently inhibits the activity of recombinant human ACE2, with a potency similar to the MLN-4760. Further analysis suggests that HCQ binds to a noncompetitive site other than the one occupied by MLN-4760. We also determined that the viral spike glycoprotein segment that comprises the RBD segment has no effect on ACE2 activity but unexpectedly was able to partially reverse the inhibition induced by HCQ but not that by MLN-4760. In summary, here we demonstrate the direct inhibitory action of HCQ over the activity of the enzyme ACE2. Then, by determining the activity of ACE2, we reveal that the interaction with the spike protein of SARS-CoV-2 leads to structural changes that at least partially displace the interaction of the said enzyme with HCQ. These results may help to explain why the effectiveness of HCQ in clinical trials has been so variable. Additionally, this knowledge could be used for to develop techniques for the detection of SARS-CoV-2.


Subject(s)
Angiotensin-Converting Enzyme 2 , Antiviral Agents , COVID-19/drug therapy , Hydroxychloroquine , Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/metabolism , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Humans , Hydroxychloroquine/chemistry , Hydroxychloroquine/metabolism , Hydroxychloroquine/pharmacology , Imidazoles/chemistry , Imidazoles/metabolism , Imidazoles/pharmacology , Leucine/analogs & derivatives , Leucine/chemistry , Leucine/metabolism , Leucine/pharmacology , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
4.
Proteins ; 89(11): 1425-1441, 2021 11.
Article in English | MEDLINE | ID: covidwho-1281247

ABSTRACT

The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug has not been confirmed so far for regular treatment. An important target is the main protease (Mpro ), which plays a major role in replication of the virus. In this study, Gaussian and residue network models are employed to reveal two distinct potential allosteric sites on Mpro that can be evaluated as drug targets besides the active site. Then, Food and Drug Administration (FDA)-approved drugs are docked to three distinct sites with flexible docking using AutoDock Vina to identify potential drug candidates. Fourteen best molecule hits for the active site of Mpro are determined. Six of these also exhibit high docking scores for the potential allosteric regions. Full-atom molecular dynamics simulations with MM-GBSA method indicate that compounds docked to active and potential allosteric sites form stable interactions with high binding free energy (∆Gbind ) values. ∆Gbind values reach -52.06 kcal/mol for the active site, -51.08 kcal/mol for the potential allosteric site 1, and - 42.93 kcal/mol for the potential allosteric site 2. Energy decomposition calculations per residue elucidate key binding residues stabilizing the ligands that can further serve to design pharmacophores. This systematic and efficient computational analysis successfully determines ivermectine, diosmin, and selinexor currently subjected to clinical trials, and further proposes bromocriptine, elbasvir as Mpro inhibitor candidates to be evaluated against SARS-CoV-2 infections.


Subject(s)
Antiviral Agents/metabolism , Benzofurans/chemistry , Coronavirus 3C Proteases/metabolism , Drug Repositioning/methods , Imidazoles/chemistry , Allosteric Site , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Benzofurans/metabolism , Benzofurans/pharmacology , Binding Sites , Bromocriptine/chemistry , Bromocriptine/metabolism , Bromocriptine/pharmacology , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/chemistry , Diosmin/chemistry , Diosmin/metabolism , Hydrazines/chemistry , Hydrazines/metabolism , Hydrazines/pharmacology , Imidazoles/metabolism , Imidazoles/pharmacology , Ivermectin/chemistry , Ivermectin/metabolism , Ivermectin/pharmacology , Ligands , Molecular Docking Simulation , Molecular Dynamics Simulation , Triazoles/chemistry , Triazoles/metabolism , Triazoles/pharmacology , United States , United States Food and Drug Administration
5.
J Pharmacol Sci ; 147(1): 62-71, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1240460

ABSTRACT

Owing to the urgent need for therapeutic interventions against the SARS-coronavirus 2 (SARS-CoV-2) pandemic, we employed an in silico approach to evaluate the SARS-CoV-2 inhibitory potential of newly synthesized imidazoles. The inhibitory potentials of the compounds against SARS-CoV-2 drug targets - main protease (Mpro), spike protein (Spro) and RNA-dependent RNA polymerase (RdRp) were investigated through molecular docking analysis. The binding free energy of the protein-ligand complexes were estimated, pharmacophore models were generated and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of the compounds were determined. The compounds displayed various levels of binding affinities for the SARS-CoV-2 drug targets. Bisimidazole C2 scored highest against all the targets, with its aromatic rings including the two imidazole groups contributing to the binding. Among the phenyl-substituted 1H-imidazoles, C9 scored highest against all targets. C11 scored highest against Spro and C12 against Mpro and RdRp among the thiophene-imidazoles. The compounds interacted with HIS 41 - CYS 145 and GLU 288 - ASP 289 - GLU 290 of Mpro, ASN 501 of Spro receptor binding motif and some active site amino acids of RdRp. These novel imidazole compounds could be further developed as drug candidates against SARS-CoV-2 following lead optimization and experimental studies.


Subject(s)
Computational Biology/methods , Enzyme Inhibitors/pharmacology , Imidazoles/pharmacology , Molecular Docking Simulation/methods , SARS-CoV-2/drug effects , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/metabolism , Humans , Imidazoles/chemistry , Imidazoles/metabolism , Protein Binding/physiology , Protein Structure, Secondary , Protein Structure, Tertiary , SARS-CoV-2/chemistry , SARS-CoV-2/metabolism
6.
Protein Cell ; 12(11): 877-888, 2021 11.
Article in English | MEDLINE | ID: covidwho-1188202

ABSTRACT

A new coronavirus (SARS-CoV-2) has been identified as the etiologic agent for the COVID-19 outbreak. Currently, effective treatment options remain very limited for this disease; therefore, there is an urgent need to identify new anti-COVID-19 agents. In this study, we screened over 6,000 compounds that included approved drugs, drug candidates in clinical trials, and pharmacologically active compounds to identify leads that target the SARS-CoV-2 papain-like protease (PLpro). Together with main protease (Mpro), PLpro is responsible for processing the viral replicase polyprotein into functional units. Therefore, it is an attractive target for antiviral drug development. Here we discovered four compounds, YM155, cryptotanshinone, tanshinone I and GRL0617 that inhibit SARS-CoV-2 PLpro with IC50 values ranging from 1.39 to 5.63 µmol/L. These compounds also exhibit strong antiviral activities in cell-based assays. YM155, an anticancer drug candidate in clinical trials, has the most potent antiviral activity with an EC50 value of 170 nmol/L. In addition, we have determined the crystal structures of this enzyme and its complex with YM155, revealing a unique binding mode. YM155 simultaneously targets three "hot" spots on PLpro, including the substrate-binding pocket, the interferon stimulating gene product 15 (ISG15) binding site and zinc finger motif. Our results demonstrate the efficacy of this screening and repurposing strategy, which has led to the discovery of new drug leads with clinical potential for COVID-19 treatments.


Subject(s)
Coronavirus Papain-Like Proteases/chemistry , High-Throughput Screening Assays/methods , Protease Inhibitors/chemistry , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/therapeutic use , Binding Sites , COVID-19/drug therapy , COVID-19/virology , Coronavirus Papain-Like Proteases/genetics , Coronavirus Papain-Like Proteases/metabolism , Crystallography, X-Ray , Drug Evaluation, Preclinical , Drug Repositioning , Humans , Imidazoles/chemistry , Imidazoles/metabolism , Imidazoles/therapeutic use , Inhibitory Concentration 50 , Molecular Dynamics Simulation , Mutagenesis, Site-Directed , Naphthoquinones/chemistry , Naphthoquinones/metabolism , Naphthoquinones/therapeutic use , Protease Inhibitors/metabolism , Protease Inhibitors/therapeutic use , Protein Structure, Tertiary , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , SARS-CoV-2/isolation & purification
7.
Molecules ; 26(5)2021 Mar 04.
Article in English | MEDLINE | ID: covidwho-1129755

ABSTRACT

A novel, simple, low-cost, and user-friendly potentiometric surfactant sensor based on the new 1,3-dihexadecyl-1H-benzo[d]imidazol-3-ium-tetraphenylborate (DHBI-TPB) ion-pair for the detection of cationic surfactants in personal care products and disinfectants is presented here. The new cationic surfactant DHBI-Br was successfully synthesized and characterized by nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) spectrometry, liquid chromatography-mass spectrometry (LC-MS) and elemental analysis and was further employed for DHBI-TPB ion-pair preparation. The sensor gave excellent response characteristics for CTAB, CPC and Hyamine with a Nernstian slope (57.1 to 59.1 mV/decade) whereas the lowest limit of detection (LOD) value was measured for CTAB (0.3 × 10-6 M). The sensor exhibited a fast dynamic response to dodecyl sulfate (DDS) and TPB. High sensor performances stayed intact regardless of the employment of inorganic and organic cations and in a broad pH range (2-11). Titration of cationic and etoxylated (EO)-nonionic surfactant (NSs) (in Ba2+) mixtures with TPB revealed the first inflexion point for a cationic surfactant and the second for an EO-nonionic surfactant. The increased concentration of EO-nonionic surfactants and the number of EO groups had a negative influence on titration curves and signal change. The sensor was successfully applied for the quantification of technical-grade cationic surfactants and in 12 personal care products and disinfectants. The results showed good agreement with the measurements obtained by a commercial surfactant sensor and by a two-phase titration. A good recovery for the standard addition method (98-102%) was observed.


Subject(s)
Biosensing Techniques/methods , Cations/chemistry , Cosmetics/analysis , Disinfectants/analysis , Imidazoles/chemistry , Potentiometry/methods , Surface-Active Agents/chemistry , Hydrogen-Ion Concentration
8.
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
9.
Virology ; 554: 48-54, 2021 02.
Article in English | MEDLINE | ID: covidwho-989369

ABSTRACT

The COVID-19 pandemic has urged for the repurposing of existing drugs for rapid management and treatment. Renin inhibitors down regulation of ACE2, which is an essential receptor for SARS-CoV-2 infection that is responsible for COVID-19, in addition to their ability to act as protease inhibitors were encouraging aspects for their investigation as possible inhibitors of main protease of SARS-CoV-2 via computational studies. A Pharmacophore model was generated using the newly released SARS-COV-2 main protease inhibitors. Virtual screening was performed on renin inhibitors, and Drug likeness filter identified remikiren and 0IU as hits. Molecular docking for both compounds showed that the orally active renin inhibitor remikiren (Ro 42-5892) of Hoffmann-La Roche exhibited good molecular interaction with Cys145 and His41 in the catalytic site of SARS-CoV-2 main protease. Molecular dynamics simulation suggested that the drug is stable in the active site of the enzyme.


Subject(s)
Coronavirus 3C Proteases/antagonists & inhibitors , Drug Repositioning , Protease Inhibitors/pharmacology , Renin/antagonists & inhibitors , SARS-CoV-2/drug effects , COVID-19/drug therapy , COVID-19/virology , Catalytic Domain , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/metabolism , Imidazoles/chemistry , Imidazoles/metabolism , Imidazoles/pharmacology , Models, Molecular , Protease Inhibitors/chemistry , Protease Inhibitors/metabolism , Protein Binding , SARS-CoV-2/enzymology
10.
Life Sci ; 262: 118469, 2020 Dec 01.
Article in English | MEDLINE | ID: covidwho-779375

ABSTRACT

Because of the fast increase in deaths due to Corona Viral Infection in majority region in the world, the detection of drugs potent of this infection is a major need. With this idea, docking study was executed on eighteen imidazole derivatives based on 7-chloro-4-aminoquinoline against novel Coronavirus (SARS-CoV-2). In this study, we carried out a docking study of these molecules in the active site of SARS-CoV-2 main protease. The result indicate that Molecules N° 3, 7 and 14 have more binding energy with SARS-CoV-2 main protease recently crystallized (pdb code 6LU7) in comparison with the other imidazole derivatives and the two drug; Chloroquine and hydroxychloroquine. Because of the best energy of interaction, these three molecules could have the most potential antiviral treatment of COVID-19 than the other studied compounds. The structures with best affinity in the binding site of the protease have more than 3 cycles and electronegative atoms in the structure. This may increase the binding affinity of these molecules because of formation of π-bonds, halogen interactions and/or Hydrogen bond interactions between compounds and the enzyme. So, compounds with more cycles and electronegative atoms could have a potent inhibition of SARS-CoV-2 main protease.


Subject(s)
Coronavirus 3C Proteases/antagonists & inhibitors , Imidazoles/pharmacology , Molecular Docking Simulation , Protease Inhibitors/pharmacology , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Aminoquinolines/pharmacology , Binding Sites/drug effects , COVID-19/drug therapy , Chloroquine/pharmacology , Hydroxychloroquine/pharmacology , Imidazoles/chemistry , Molecular Structure , Pandemics
11.
Angew Chem Int Ed Engl ; 59(47): 20814-20819, 2020 11 16.
Article in English | MEDLINE | ID: covidwho-739123

ABSTRACT

The catalytic asymmetric synthesis of the anti-COVID-19 drug Remdesivir has been realized by the coupling of the P-racemic phosphoryl chloride with protected nucleoside GS441524. The chiral bicyclic imidazole catalyst used is crucial for the dynamic kinetic asymmetric transformation (DyKAT) to proceed smoothly with high reactivity and excellent stereoselectivity (96 % conv., 22:1 SP :RP ). Mechanistic studies showed that this DyKAT is a first-order visual kinetic reaction dependent on the catalyst concentration. The unique chiral bicyclic imidazole skeleton and carbamate substituent of the catalyst are both required for the racemization process, involving the phosphoryl chloride, and subsequent stereodiscriminating step. A 10 gram scale reaction was also conducted with comparably excellent results, showing its potential for industrial application.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/chemical synthesis , Adenosine Monophosphate/chemical synthesis , Adenosine Monophosphate/chemistry , Alanine/chemical synthesis , Alanine/chemistry , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/virology , Catalysis , Humans , Imidazoles/chemistry , Kinetics , Molecular Conformation , SARS-CoV-2/isolation & purification , Stereoisomerism
12.
Anal Chem ; 92(17): 11543-11547, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-677479

ABSTRACT

Molecular analysis of exhaled breath aerosol (EBA) with simple procedures represents a key step in clinical and point-of-care applications. Due to the crucial health role, a face mask now is a safety device that helps protect the wearer from breathing in hazardous particles such as bacteria and viruses in the air; thus exhaled breath is also blocked to congregate in the small space inside of the face mask. Therefore, direct sampling and analysis of trace constituents in EBA using a face mask can rapidly provide useful insights into human physiologic and pathological information. Herein, we introduce a simple approach to collect and analyze human EBA by combining a face mask with solid-phase microextraction (SPME) fiber. SPME fiber was inserted into a face mask to form SPME-in-mask that covered nose and mouth for in vivo sampling of EBA, and SPME fiber was then coupled with direct analysis in real-time mass spectrometry (DART-MS) to directly analyze the molecular compositions of EBA under ambient conditions. The applicability of SPME-in-mask was demonstrated by direct analysis of drugs and metabolites in oral and nasal EBA. The unique features of SPME-in-mask were also discussed. Our results showed that this method is enabled to analyze volatile and nonvolatile analytes in EBA and is expected to have a significant impact on human EBA analysis in clinical applications. We also hope this method will inspire biomarker screening of some respiratory diseases that usually required wearing of a face mask in daily life.


Subject(s)
Aerosols/chemistry , Biomarkers/analysis , Body Fluids/chemistry , Body Fluids/metabolism , Mass Spectrometry/methods , Organic Chemicals/analysis , Solid Phase Microextraction/methods , Biosensing Techniques , Breath Tests , Exhalation , Humans , Imidazoles/chemistry , In Vitro Techniques , Masks , Metabolomics , Specimen Handling/methods
13.
Mol Inform ; 40(1): e2000113, 2021 01.
Article in English | MEDLINE | ID: covidwho-680516

ABSTRACT

The main protease (Mpro) of the SARS-CoV-2 has been proposed as one of the major drug targets for COVID-19. We have identified the experimental data on the inhibitory activity of compounds tested against the closely related (96 % sequence identity, 100 % active site conservation) Mpro of SARS-CoV. We developed QSAR models of these inhibitors and employed these models for virtual screening of all drugs in the DrugBank database. Similarity searching and molecular docking were explored in parallel, but docking failed to correctly discriminate between experimentally active and inactive compounds, so it was not relied upon for prospective virtual screening. Forty-two compounds were identified by our models as consensus computational hits. Subsequent to our computational studies, NCATS reported the results of experimental screening of their drug collection in SARS-CoV-2 cytopathic effect assay (https://opendata.ncats.nih.gov/covid19/). Coincidentally, NCATS tested 11 of our 42 hits, and three of them, cenicriviroc (AC50 of 8.9 µM), proglumetacin (tested twice independently, with AC50 of 8.9 µM and 12.5 µM), and sufugolix (AC50 12.6 µM), were shown to be active. These observations support the value of our modeling approaches and models for guiding the experimental investigations of putative anti-COVID-19 drug candidates. All data and models used in this study are publicly available via Supplementary Materials, GitHub (https://github.com/alvesvm/sars-cov-mpro), and Chembench web portal (https://chembench.mml.unc.edu/).


Subject(s)
Antiviral Agents , COVID-19 , Coronavirus 3C Proteases , Drug Repositioning , Imidazoles/chemistry , Indoleacetic Acids/chemistry , Molecular Docking Simulation , Protease Inhibitors , SARS-CoV-2/enzymology , Sulfoxides/chemistry , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , COVID-19/drug therapy , COVID-19/enzymology , Catalytic Domain , Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus 3C Proteases/chemistry , Humans , Imidazoles/therapeutic use , Indoleacetic Acids/therapeutic use , Protease Inhibitors/chemistry , Protease Inhibitors/therapeutic use , Quantitative Structure-Activity Relationship , Sulfoxides/therapeutic use
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