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1.
J Med Chem ; 65(19): 13328-13342, 2022 10 13.
Article in English | MEDLINE | ID: covidwho-2050247

ABSTRACT

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic. The main protease (Mpro, 3CLpro) of SARS-CoV-2 is a key enzyme that processes polyproteins translated from the viral RNA. Mpro is therefore an attractive target for the design of inhibitors that block viral replication. We report the diastereomeric resolution of the previously designed SARS-CoV-2 Mpro α-ketoamide inhibitor 13b. The pure (S,S,S)-diastereomer, 13b-K, displays an IC50 of 120 nM against the Mpro and EC50 values of 0.8-3.4 µM for antiviral activity in different cell types. Crystal structures have been elucidated for the Mpro complexes with each of the major diastereomers, the active (S,S,S)-13b (13b-K), and the nearly inactive (R,S,S)-13b (13b-H); results for the latter reveal a novel binding mode. Pharmacokinetic studies show good levels of 13b-K after inhalative as well as after peroral administration. The active inhibitor (13b-K) is a promising candidate for further development as an antiviral treatment for COVID-19.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases , Cysteine Endopeptidases/metabolism , Humans , Pandemics , Polyproteins , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , RNA, Viral , Viral Nonstructural Proteins/metabolism
2.
BMC Pulm Med ; 22(1): 339, 2022 Sep 07.
Article in English | MEDLINE | ID: covidwho-2038719

ABSTRACT

BACKGROUND: No consensus has been reached on an optimal blood lactate evaluation system although several approaches have been reported in the literature in recent years. A group-based trajectory modeling (GBTM) method could better stratify patients with acute respiratory distress syndrome (ARDS) complicated with sepsis in the intensive care unit (ICU). PATIENTS AND METHODS: 760 patients from the comprehensive ICU of Tianjin Medical University General Hospital with ARDS complicated with sepsis were eligible for analysis. Serial serum lactate levels were measured within 48 h of admission. In addition to the GBTM lactate groups, the initial lactate, peak lactate level, the area under the curve of serial lactate (lactate AUC), and lactate clearance were also considered for comparison. The short- and long-term outcomes were the 30- and 90-day mortality, respectively. RESULTS: Three lactate groups were identified based on GBTM, with group 3 exhibiting the worse short- [hazard ratio (HR) for 30-day mortality: 2.96, 95% confidence interval (CI) 1.79-4.87, P < 0.001] and long term (HR for 90-day mortality: 3.49, 95% CI 2.06-5.89, P < 0.001) outcomes followed by group 2 (HR for 30-day mortality: 2.05, 95% CI 1.48-2.84, P < 0.001 and HR for 90-day mortality: 1.99, 95% CI 1.48-2.67, P < 0.001). GBTM lactate groups exhibited significantly improved diagnostic performance of initial lactate + SOFA scores/APACHE II scores models. Based on the multivariable fractional polynomial interaction (MFPI) approach, GBTM lactate groups could better differentiate high-risk patients than the initial lactate groups in short- and long-term outcomes. CONCLUSIONS: To the best of our knowledge, this is the first report that GBTM-based serial blood lactate evaluations significantly improve the diagnostic capacity of traditional critical care evaluation systems and bring many advantages over previously documented lactate evaluation systems.


Subject(s)
Respiratory Distress Syndrome , Sepsis , APACHE , Humans , Lactic Acid , Respiratory Distress Syndrome/diagnosis , Risk Assessment , Sepsis/complications , Sepsis/diagnosis
3.
Sci Rep ; 12(1): 14230, 2022 08 20.
Article in English | MEDLINE | ID: covidwho-2000936

ABSTRACT

Essential oils and aromatic extracts (oleoresins, absolutes, concretes, resinoids) are often used as food flavorings and constituents of fragrance compositions. The flavor and fragrance industry observed significant growth in the sales of some natural materials during the COVID-19 outbreak. Some companies worldwide are making false claims regarding the effectiveness of their essential oils or blends (or indirectly point toward this conclusion) against coronaviruses, even though the available data on the activity of plant materials against highly pathogenic human coronaviruses are very scarce. Our exploratory study aimed to develop pioneering knowledge and provide the first experimental results on the inhibitory properties of hundreds of flavor and fragrance materials against SARS-CoV-2 main and papain-like proteases and the antiviral potential of the most active protease inhibitors. As essential oils are volatile products, they could provide an interesting therapeutic strategy for subsidiary inhalation in the long term.


Subject(s)
COVID-19 , Oils, Volatile , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Humans , Oils, Volatile/pharmacology , Protease Inhibitors , SARS-CoV-2
4.
Pharmaceuticals (Basel) ; 15(8)2022 Aug 03.
Article in English | MEDLINE | ID: covidwho-1969411

ABSTRACT

The development of novel agents to combat COVID-19 is of high importance. SARS-CoV-2 main protease (Mpro) is a highly attractive target for the development of novel antivirals and a variety of inhibitors have already been developed. Accumulating evidence on the pathobiology of COVID-19 has shown that lipids and lipid metabolizing enzymes are critically involved in the severity of the infection. The purpose of the present study was to identify an inhibitor able to simultaneously inhibit both SARS-CoV-2 Mpro and phospholipase A2 (PLA2), an enzyme which plays a significant role in inflammatory diseases. Evaluating several PLA2 inhibitors, we demonstrate that the previously known potent inhibitor of Group IIA secretory PLA2, GK241, may also weakly inhibit SARS-CoV-2 Mpro. Molecular mechanics docking and molecular dynamics calculations shed light on the interactions between GK241 and SARS-CoV-2 Mpro. 2-Oxoamide GK241 may represent a lead molecular structure for the development of dual PLA2 and SARS-CoV-2 Mpro inhibitors.

5.
Molecules ; 27(13)2022 Jul 04.
Article in English | MEDLINE | ID: covidwho-1917637

ABSTRACT

The main protease (Mpro) of the betacoronavirus SARS-CoV-2 is an attractive target for the development of treatments for COVID-19. Structure-based design is a successful approach to discovering new inhibitors of the Mpro. Starting from crystal structures of the Mpro in complexes with the Hepatitis C virus NS3/4A protease inhibitors boceprevir and telaprevir, we optimized the potency of the alpha-ketoamide boceprevir against the Mpro by replacing its P1 cyclobutyl moiety by a γ-lactam as a glutamine surrogate. The resulting compound, MG-78, exhibited an IC50 of 13 nM versus the recombinant Mpro, and similar potency was observed for its P1' N-methyl derivative MG-131. Crystal structures confirmed the validity of our design concept. In addition to SARS-CoV-2 Mpro inhibition, we also explored the activity of MG-78 against the Mpro of the alphacoronavirus HCoV NL63 and against enterovirus 3C proteases. The activities were good (0.33 µM, HCoV-NL63 Mpro), moderate (1.45 µM, Coxsackievirus 3Cpro), and relatively poor (6.7 µM, enterovirus A71 3Cpro), respectively. The structural basis for the differences in activities was revealed by X-ray crystallo-graphy. We conclude that the modified boceprevir scaffold is suitable for obtaining high-potency inhibitors of the coronavirus Mpros but further optimization would be needed to target enterovirus 3Cpros efficiently.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases , Cysteine Endopeptidases/chemistry , Humans , Proline/analogs & derivatives , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins
6.
Chinese Preventive Medicine ; 22(4):246-249, 2021.
Article in Chinese | CAB Abstracts | ID: covidwho-1761323

ABSTRACT

Objective: To understand the epidemiological characteristics of a cluster of COVID-19 caused by an imported case in late December 2020, and to provide reference for the prevention and control of COVID-19.

7.
Molecules ; 27(3)2022 Feb 04.
Article in English | MEDLINE | ID: covidwho-1686900

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has led to a pandemic, that continues to be a huge public health burden. Despite the availability of vaccines, there is still a need for small-molecule antiviral drugs. In an effort to identify novel and drug-like hit matter that can be used for subsequent hit-to-lead optimization campaigns, we conducted a high-throughput screening of a 160 K compound library against SARS-CoV-2, yielding a 1-heteroaryl-2-alkoxyphenyl analog as a promising hit. Antiviral profiling revealed this compound was active against various beta-coronaviruses and preliminary mode-of-action experiments demonstrated that it interfered with viral entry. A systematic structure-activity relationship (SAR) study demonstrated that a 3- or 4-pyridyl moiety on the oxadiazole moiety is optimal, whereas the oxadiazole can be replaced by various other heteroaromatic cycles. In addition, the alkoxy group tolerates some structural diversity.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Heterocyclic Compounds/pharmacology , SARS-CoV-2/drug effects , Virus Replication/drug effects , Animals , Chlorocebus aethiops , High-Throughput Screening Assays , Microbial Sensitivity Tests , Structure-Activity Relationship , Vero Cells
8.
Nat Neurosci ; 24(11): 1522-1533, 2021 11.
Article in English | MEDLINE | ID: covidwho-1500484

ABSTRACT

Coronavirus disease 2019 (COVID-19) can damage cerebral small vessels and cause neurological symptoms. Here we describe structural changes in cerebral small vessels of patients with COVID-19 and elucidate potential mechanisms underlying the vascular pathology. In brains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals and animal models, we found an increased number of empty basement membrane tubes, so-called string vessels representing remnants of lost capillaries. We obtained evidence that brain endothelial cells are infected and that the main protease of SARS-CoV-2 (Mpro) cleaves NEMO, the essential modulator of nuclear factor-κB. By ablating NEMO, Mpro induces the death of human brain endothelial cells and the occurrence of string vessels in mice. Deletion of receptor-interacting protein kinase (RIPK) 3, a mediator of regulated cell death, blocks the vessel rarefaction and disruption of the blood-brain barrier due to NEMO ablation. Importantly, a pharmacological inhibitor of RIPK signaling prevented the Mpro-induced microvascular pathology. Our data suggest RIPK as a potential therapeutic target to treat the neuropathology of COVID-19.


Subject(s)
Blood-Brain Barrier/metabolism , Brain/metabolism , Coronavirus 3C Proteases/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , Microvessels/metabolism , SARS-CoV-2/metabolism , Animals , Blood-Brain Barrier/pathology , Brain/pathology , Chlorocebus aethiops , Coronavirus 3C Proteases/genetics , Cricetinae , Female , Humans , Intracellular Signaling Peptides and Proteins/genetics , Male , Mesocricetus , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, Transgenic , Microvessels/pathology , SARS-CoV-2/genetics , Vero Cells
9.
Sustainability ; 13(8):4141, 2021.
Article in English | ProQuest Central | ID: covidwho-1362546

ABSTRACT

Alleviating human sufferings during and in the aftermath of disasters is one of the most important goals in humanitarian relief logistics. The lack of relief commodities, especially life-saving items, is a life-threatening loss to victims and must be considered when making emergency supply allocation and transportation decisions, even in the pre-disaster prepositioning phase. This paper proposes a scenario-based stochastic program that integrates the decisions of prepositioning facility locations, quantities of stocked emergency supplies, and service allocations in each scenario in the same modeling framework. The estimation of victims’ losses for waiting for emergency supplies is measured in the typical deprivation cost function and treated as one of the main bases of decision making, besides traditional transportation costs, in determining the service allocation strategies in each scenario. Specifically, a case study with data from the hurricane threat in the Gulf Coast area of the US was conducted to demonstrate the application of this model and the significance of considering victims’ welfare loss in humanitarian relief logistics. Some interesting managerial insights were also drawn from a series of numerical experiments and sensitivity analyses.

10.
Research of Environmental Sciences ; 33(7):1632-1639, 2020.
Article in Chinese | GIM | ID: covidwho-1196352

ABSTRACT

Chlorine disinfectants were widely used during the coronavirus disease(COVID-19). Water quality and human health might be affected by chlorine residues. Residual chlorine and its guideline value was not set in the quality standards of drinking water sources in China. The lack of result evaluation and standards of field rapid analysis methods were also problems to be solved.In order to provide a reference for monitoring and evaluation of residual chlorine in water in public health events, the domestic and international guideline values, laboratory analysis standards and field rapid analysis methods for residual chlorine in drinking water were summarized. The results showed that:(1) The guideline values of residual chlorine in the distribution systems(0.1-2.0 mg/L) and at the point of delivery(0.1-1.8 mg/L), and the maximum concentration of residual chlorine in drinking water(4-5 mg/L) were set by other countries, regions and WHO.(2) Colorimetric and titrimetric methods were considered as standards or recommended analytical methods for laboratories because of their rapid response,stability, high accuracy and high precision. High performance liquid chromatography(HPLC) could also be applied for trace analysis of residual chlorine due to its low detection limit and high sensitivity.(3) Most field rapid analysis and on-line monitoring methods were colorimetric and electrochemical methods, but there was no uniform standard method. The research showed that the maximum concentration of residual chlorine in drinking water in foreign countries, regions or organizations was 5 mg/L. The recommended minimum concentrations for residual chlorine to point of delivery were 0.5 mg/L in high-risk circumstances.It was suggested to carry out the standardization research on the field monitoring methods of water.

12.
Chinese Journal of Biologicals ; 33(12):1409-1413, 2020.
Article in Chinese | GIM | ID: covidwho-1073828

ABSTRACT

Objective: To systematically analyze the 670 convalescent plasma (CP) samples from patients with coronavirus disease 2019 (COVID-19).

13.
J Diabetes ; 13(3): 243-252, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-933955

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is currently posing significant threats to public health worldwide. It is notable that a substantial proportion of patients with sever COVID-19 have coexisting diabetic conditions, indicating the progression and outcome of COVID-19 may relate to diabetes. However, it is still unclear whether diabetic treatment principles can be used for the treatment of COVID-19. METHODS: We conducted a computational approach to screen all commonly used clinical oral hypoglycemic drugs to identify the potential inhibitors for the main protease (Mpro ) of SARS-CoV-2, which is one of the key drug targets for anti-COVID-19 drug discovery. RESULTS: Six antidiabetic drugs with docking scores higher than 8.0 (cutoff value), including repaglinide, canagliflozin, glipizide, gliquidone, glimepiride, and linagliptin, were predicted as the promising inhibitors of Mpro . Interestingly, repaglinide, one of the six antidiabetic drugs with the highest docking score for Mpro , was similar to a previously predicted active molecule nelfinavir, which is a potential anti-HIV and anti-COVID-19 drug. Moreover, we found repaglinide shared similar docking pose and pharmacophores with a reported ligand (N3 inhibitor) and nelfinavir, demonstrating that repaglinide would interact with Mpro in a similar way. CONCLUSION: These results indicated that these six antidiabetic drugs may have an extra effect on the treatment of COVID-19, although further studies are necessary to confirm these findings.


Subject(s)
COVID-19/drug therapy , Hypoglycemic Agents/pharmacology , Viral Matrix Proteins/antagonists & inhibitors , A549 Cells , Antiviral Agents/pharmacology , Binding Sites , Drug Discovery , Humans , Models, Molecular , Molecular Docking Simulation , Molecular Dynamics Simulation , Nelfinavir/pharmacology , Protease Inhibitors/pharmacology
14.
Nat Chem Biol ; 17(2): 222-228, 2021 02.
Article in English | MEDLINE | ID: covidwho-899948

ABSTRACT

In December 2019, the first cases of infection with a novel coronavirus, SARS-CoV-2, were diagnosed. Currently, there is no effective antiviral treatment for COVID-19. To address this emerging problem, we focused on the SARS-CoV-2 main protease that constitutes one of the most attractive antiviral drug targets. We have synthesized a combinatorial library of fluorogenic substrates with glutamine in the P1 position. We used it to determine the substrate preferences of the SARS-CoV and SARS-CoV-2 main proteases. On the basis of these findings, we designed and synthesized a potent SARS-CoV-2 inhibitor (Ac-Abu-DTyr-Leu-Gln-VS, half-maximal effective concentration of 3.7 µM) and two activity-based probes, for one of which we determined the crystal structure of its complex with the SARS-CoV-2 Mpro. We visualized active SARS-CoV-2 Mpro in nasopharyngeal epithelial cells of patients suffering from COVID-19 infection. The results of our work provide a structural framework for the design of inhibitors as antiviral agents and/or diagnostic tests.


Subject(s)
Antiviral Agents/chemistry , COVID-19/diagnostic imaging , Coronavirus 3C Proteases/antagonists & inhibitors , Epithelial Cells/virology , Protease Inhibitors/chemistry , SARS-CoV-2/drug effects , Antiviral Agents/pharmacology , COVID-19/pathology , COVID-19/virology , Catalytic Domain , Combinatorial Chemistry Techniques , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/genetics , Coronavirus 3C Proteases/metabolism , Crystallography, X-Ray , Drug Design , Epithelial Cells/ultrastructure , Fluorescent Dyes/chemistry , Gene Expression , Glutamine/chemistry , Humans , Models, Molecular , Nasopharynx/virology , Protease Inhibitors/pharmacology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , SARS Virus/drug effects , SARS Virus/enzymology , SARS-CoV-2/enzymology , Substrate Specificity
15.
Int J Chron Obstruct Pulmon Dis ; 15: 2487-2494, 2020.
Article in English | MEDLINE | ID: covidwho-874299

ABSTRACT

Background: Social distancing and restriction measures during the COVID-19 epidemic may have impacts on medication availability and healthcare utilization for COPD patients, and thereby affect standard disease management. We aimed to investigate the change of respiratory symptoms, pharmacological treatment and healthcare utilization of COPD patients during the epidemic in Beijing, China. Methods: We conducted a single-center, cross-sectional survey performed at Peking University Third Hospital and recruited patients with COPD who were interviewed by phone call. Clinical data, including respiratory symptoms, pharmacological treatment, management and healthcare access before and during the COVID-19 epidemic from January 25 to April 25, 2020, were collected. Results: A total of 153 patients were enrolled for analysis. Before the epidemic, 81.7% (125/153) had long-term maintenance medication and ICS/LABA (60.8%) and LAMA (57.5%) were most commonly used. During the epidemic, 75.2% (115/153) maintained their pharmacological treatment and 6.5% (10/153) had to reduce or stop taking medications, with a slight decrease of patients taking ICS/LABA (53.6%) and LAMA (56.9%). Most of the patients [76.5% (117/153)] had a low symptom burden, with a CAT score <10 during the epidemic. Of 153 patients, 45 (29.4%) patients reported worsening of respiratory symptoms but only 15.6% (7/45) sought medical care in hospitals, while the remaining expressed concerns about cross-infection in the hospital (55.5%, 25/45) or had mild symptoms which were managed by themselves (28.8%, 13/45). Conclusion: During the COVID-19 epidemic in Beijing, most of our COPD patients maintained their long-term pharmacological treatment and had mild-to-moderate symptoms. Approximately, 30.0% of the patients experienced worsening of respiratory symptoms, but most of them did not seek medical care in the hospital due to concerns about cross-infection.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Health Services Accessibility , Patient Acceptance of Health Care , Pneumonia, Viral/epidemiology , Pulmonary Disease, Chronic Obstructive/therapy , Aged , Aged, 80 and over , Beijing , COVID-19 , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Pandemics , Pulmonary Disease, Chronic Obstructive/complications , SARS-CoV-2 , Self-Management
16.
Chin Med ; 15: 102, 2020.
Article in English | MEDLINE | ID: covidwho-797649

ABSTRACT

Scutellaria baicalensis Georgi. (SB) is a common heat-clearing medicine in traditional Chinese medicine (TCM). It has been used for thousands of years in China and its neighboring countries. Clinically, it is mostly used to treat diseases such as cold and cough. SB has different harvesting periods and processed products for different clinical symptoms. Botanical researches proved that SB included in the Chinese Pharmacopoeia (1st, 2020) was consistent with the medicinal SB described in ancient books. Modern phytochemical analysis had found that SB contains hundreds of active ingredients, of which flavonoids are its major components. These chemical components are the material basis for SB to exert pharmacological effects. Pharmacological studies had shown that SB has a wide range of pharmacological activities such as antiinflammatory, antibacterial, antiviral, anticancer, liver protection, etc. The active ingredients of SB were mostly distributed in liver and kidney, and couldn't be absorbed into brain via oral absorption. SB's toxicity was mostly manifested in liver fibrosis and allergic reactions, mainly caused by baicalin. The non-medicinal application prospects of SB were broad, such as antibacterial plastics, UV-resistant silk, animal feed, etc. In response to the Coronavirus Disease In 2019 (COVID-19), based on the network pharmacology research, SB's active ingredients may have potential therapeutic effects, such as baicalin and baicalein. Therefore, the exact therapeutic effects are still need to be determined in clinical trials. SB has been reviewed in the past 2 years, but the content of these articles were not comprehensive and accurate. In view of the above, we made a comprehensive overview of the research progress of SB, and expect to provide ideas for the follow-up study of SB.

18.
J Med Chem ; 63(9): 4562-4578, 2020 05 14.
Article in English | MEDLINE | ID: covidwho-613484

ABSTRACT

The main protease of coronaviruses and the 3C protease of enteroviruses share a similar active-site architecture and a unique requirement for glutamine in the P1 position of the substrate. Because of their unique specificity and essential role in viral polyprotein processing, these proteases are suitable targets for the development of antiviral drugs. In order to obtain near-equipotent, broad-spectrum antivirals against alphacoronaviruses, betacoronaviruses, and enteroviruses, we pursued a structure-based design of peptidomimetic α-ketoamides as inhibitors of main and 3C proteases. Six crystal structures of protease-inhibitor complexes were determined as part of this study. Compounds synthesized were tested against the recombinant proteases as well as in viral replicons and virus-infected cell cultures; most of them were not cell-toxic. Optimization of the P2 substituent of the α-ketoamides proved crucial for achieving near-equipotency against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl), display low-micromolar EC50 values against enteroviruses, alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7 cells, 11r exhibits three-digit picomolar activity against the Middle East Respiratory Syndrome coronavirus.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus/drug effects , Enterovirus/drug effects , Lactams/pharmacology , Peptidomimetics/pharmacology , Virus Replication/drug effects , 3C Viral Proteases , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/metabolism , Binding Sites , Cell Line, Tumor , Chlorocebus aethiops , Coronavirus/enzymology , Coronavirus 3C Proteases , Crystallography, X-Ray , Cysteine Endopeptidases/chemistry , Cysteine Endopeptidases/metabolism , Drug Design , Enterovirus/enzymology , Humans , Lactams/chemical synthesis , Lactams/metabolism , Peptidomimetics/chemical synthesis , Peptidomimetics/metabolism , Protease Inhibitors/chemical synthesis , Protease Inhibitors/metabolism , Protease Inhibitors/pharmacology , Protein Binding , Vero Cells , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/metabolism , Viral Proteins/antagonists & inhibitors , Viral Proteins/chemistry , Viral Proteins/metabolism
19.
Science ; 368(6489): 409-412, 2020 04 24.
Article in English | MEDLINE | ID: covidwho-164984

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a global health emergency. An attractive drug target among coronaviruses is the main protease (Mpro, also called 3CLpro) because of its essential role in processing the polyproteins that are translated from the viral RNA. We report the x-ray structures of the unliganded SARS-CoV-2 Mpro and its complex with an α-ketoamide inhibitor. This was derived from a previously designed inhibitor but with the P3-P2 amide bond incorporated into a pyridone ring to enhance the half-life of the compound in plasma. On the basis of the unliganded structure, we developed the lead compound into a potent inhibitor of the SARS-CoV-2 Mpro The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route.


Subject(s)
Amides/chemistry , Amides/pharmacology , Betacoronavirus/drug effects , Betacoronavirus/enzymology , Cysteine Endopeptidases/chemistry , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/chemistry , Amides/metabolism , Animals , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacokinetics , Antiviral Agents/pharmacology , Binding Sites , Cell Line, Tumor , Coronavirus 3C Proteases , Crystallography, X-Ray , Cysteine Endopeptidases/metabolism , Drug Design , Half-Life , Humans , Lung/metabolism , Mice , Models, Molecular , Protease Inhibitors/metabolism , Protease Inhibitors/pharmacokinetics , Protein Domains , Protein Multimerization , Pyridones/chemistry , SARS-CoV-2 , Viral Nonstructural Proteins/metabolism , Virus Replication/drug effects
20.
J Integr Med ; 18(3): 229-241, 2020 05.
Article in English | MEDLINE | ID: covidwho-97719

ABSTRACT

OBJECTIVE: Lung-toxin Dispelling Formula No. 1, referred to as Respiratory Detox Shot (RDS), was developed based on a classical prescription of traditional Chinese medicine (TCM) and the theoretical understanding of herbal properties within TCM. Therapeutic benefits of using RDS for both disease control and prevention, in the effort to contain the coronavirus disease 2019 (COVID-19), have been shown. However, the biochemically active constituents of RDS and their mechanisms of action are still unclear. The goal of the present study is to clarify the material foundation and action mechanism of RDS. METHODS: To conduct an analysis of RDS, an integrative analytical platform was constructed, including target prediction, protein-protein interaction (PPI) network, and cluster analysis; further, the hub genes involved in the disease-related pathways were identified, and the their corresponding compounds were used for in vitro validation of molecular docking predictions. The presence of these validated compounds was also measured in samples of the RDS formula to quantify the abundance of the biochemically active constituents. In our network pharmacological study, a total of 26 bioinformatic programs and databases were used, and six networks, covering the entire Zang-fu viscera, were constructed to comprehensively analyze the intricate connections among the compounds-targets-disease pathways-meridians of RDS. RESULTS: For all 1071 known chemical constituents of the nine ingredients in RDS, identified from established TCM databases, 157 passed drug-likeness screening and led to 339 predicted targets in the constituent-target network. Forty-two hub genes with core regulatory effects were extracted from the PPI network, and 134 compounds and 29 crucial disease pathways were implicated in the target-constituent-disease network. Twelve disease pathways attributed to the Lung-Large Intestine meridians, with six and five attributed to the Kidney-Urinary Bladder and Stomach-Spleen meridians, respectively. One-hundred and eighteen candidate constituents showed a high binding affinity with SARS-coronavirus-2 3-chymotrypsin-like protease (3CLpro), as indicated by molecular docking using computational pattern recognition. The in vitro activity of 22 chemical constituents of RDS was validated using the 3CLpro inhibition assay. Finally, using liquid chromatography mass spectrometry in data-independent analysis mode, the presence of seven out of these 22 constituents was confirmed and validated in an aqueous decoction of RDS, using reference standards in both non-targeted and targeted approaches. CONCLUSION: RDS acts primarily in the Lung-Large Intestine, Kidney-Urinary Bladder and Stomach-Spleen meridians, with other Zang-fu viscera strategically covered by all nine ingredients. In the context of TCM meridian theory, the multiple components and targets of RDS contribute to RDS's dual effects of health-strengthening and pathogen-eliminating. This results in general therapeutic effects for early COVID-19 control and prevention.


Subject(s)
Antiviral Agents/chemistry , Betacoronavirus/chemistry , Coronavirus Infections/drug therapy , Drugs, Chinese Herbal/chemistry , Medicine, Chinese Traditional , Molecular Docking Simulation , Pneumonia, Viral/drug therapy , Antiviral Agents/therapeutic use , Betacoronavirus/enzymology , COVID-19 , Coronavirus 3C Proteases , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Cysteine Endopeptidases/chemistry , Drugs, Chinese Herbal/therapeutic use , Humans , Mass Spectrometry , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , Protein Interaction Maps , SARS-CoV-2 , Viral Nonstructural Proteins/chemistry
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