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1.
Biomolecules ; 12(11)2022 Nov 11.
Article in English | MEDLINE | ID: covidwho-2109923

ABSTRACT

BACKGROUND: SARS-CoV-2 has undergone mutations, yielding clinically relevant variants. HYPOTHESIS: We hypothesized that in SARS-CoV-2, two highly conserved Orf3a and E channels directly related to the virus replication were a target for the detection and inhibition of the viral replication, independent of the variant, using FDA-approved ion channel modulators. METHODS: A combination of a fluorescence potassium ion assay with channel modulators was developed to detect SARS-CoV-2 Orf3a/E channel activity. Two FDA-approved drugs, amantadine (an antiviral) and amitriptyline (an antidepressant), which are ion channel blockers, were tested as to whether they inhibited Orf3a/E channel activity in isolated virus variants and in nasal swab samples from COVID-19 patients. The variants were confirmed by PCR sequencing. RESULTS: In isolated SARS-CoV-2 Alpha, Beta, and Delta variants, the channel activity of Orf3a/E was detected and inhibited by emodin and gliclazide (IC50 = 0.42 mM). In the Delta swab samples, amitriptyline and amantadine inhibited the channel activity of viral proteins, with IC50 values of 0.73 mM and 1.11 mM, respectively. In the Omicron swab samples, amitriptyline inhibited the channel activity, with an IC50 of 0.76 mM. CONCLUSIONS: We developed an efficient method to screen FDA-approved ion channel modulators that could be repurposed to detect and inhibit SARS-CoV-2 viral replication, independent of variants.


Subject(s)
COVID-19 , Ion Channels , SARS-CoV-2 , Humans , Amantadine/pharmacology , Amitriptyline/pharmacology , COVID-19/drug therapy , Ion Channels/antagonists & inhibitors , SARS-CoV-2/drug effects , Drug Evaluation, Preclinical , Drug Repositioning
2.
Stem Cell Reports ; 17(9): 1959-1975, 2022 09 13.
Article in English | MEDLINE | ID: covidwho-2000717

ABSTRACT

In vitro tissue models hold great promise for modeling diseases and drug responses. Here, we used emulsion microfluidics to form micro-organospheres (MOSs), which are droplet-encapsulated miniature three-dimensional (3D) tissue models that can be established rapidly from patient tissues or cells. MOSs retain key biological features and responses to chemo-, targeted, and radiation therapies compared with organoids. The small size and large surface-to-volume ratio of MOSs enable various applications including quantitative assessment of nutrient dependence, pathogen-host interaction for anti-viral drug screening, and a rapid potency assay for chimeric antigen receptor (CAR)-T therapy. An automated MOS imaging pipeline combined with machine learning overcomes plating variation, distinguishes tumorspheres from stroma, differentiates cytostatic versus cytotoxic drug effects, and captures resistant clones and heterogeneity in drug response. This pipeline is capable of robust assessments of drug response at individual-tumorsphere resolution and provides a rapid and high-throughput therapeutic profiling platform for precision medicine.


Subject(s)
Antineoplastic Agents , Organoids , Antineoplastic Agents/pharmacology , Drug Evaluation, Preclinical/methods , Humans , Microfluidics , Precision Medicine
3.
Pharmacol Rev ; 74(1): 141-206, 2022 01.
Article in English | MEDLINE | ID: covidwho-1978532

ABSTRACT

The number of successful drug development projects has been stagnant for decades despite major breakthroughs in chemistry, molecular biology, and genetics. Unreliable target identification and poor translatability of preclinical models have been identified as major causes of failure. To improve predictions of clinical efficacy and safety, interest has shifted to three-dimensional culture methods in which human cells can retain many physiologically and functionally relevant phenotypes for extended periods of time. Here, we review the state of the art of available organotypic culture techniques and critically review emerging models of human tissues with key importance for pharmacokinetics, pharmacodynamics, and toxicity. In addition, developments in bioprinting and microfluidic multiorgan cultures to emulate systemic drug disposition are summarized. We close by highlighting important trends regarding the fabrication of organotypic culture platforms and the choice of platform material to limit drug absorption and polymer leaching while supporting the phenotypic maintenance of cultured cells and allowing for scalable device fabrication. We conclude that organotypic and microphysiological human tissue models constitute promising systems to promote drug discovery and development by facilitating drug target identification and improving the preclinical evaluation of drug toxicity and pharmacokinetics. There is, however, a critical need for further validation, benchmarking, and consolidation efforts ideally conducted in intersectoral multicenter settings to accelerate acceptance of these novel models as reliable tools for translational pharmacology and toxicology. SIGNIFICANCE STATEMENT: Organotypic and microphysiological culture of human cells has emerged as a promising tool for preclinical drug discovery and development that might be able to narrow the translation gap. This review discusses recent technological and methodological advancements and the use of these systems for hit discovery and the evaluation of toxicity, clearance, and absorption of lead compounds.


Subject(s)
Drug Discovery , Drug-Related Side Effects and Adverse Reactions , Drug Development , Drug Evaluation, Preclinical , Humans , Multicenter Studies as Topic
4.
J Pharmacol Toxicol Methods ; 117: 107206, 2022.
Article in English | MEDLINE | ID: covidwho-1967213

ABSTRACT

The 2021 Annual Safety Pharmacology (SP) Society (SPS) meeting was held virtually October 4-8, 2021 due to the continuing COVID-19 global pandemic. This themed issue of J Pharmacol Toxicol Methods comprises articles arising from the meeting. As in previous years the manuscripts reflect various areas of innovation in SP including a perspective on aging and its impact on drug attrition during safety assessments, an integrated assessment of respiratory, cardiovascular and animal activity of in vivo nonclinical studies, development of a dynamic QT-rate correction method in primates, evaluation of the "comprehensive in vitro proarrhythmia assay" (CiPA) ion channel protocol to the automated patch clamp, and best practices regarding the conduct of hERG electrophysiology studies and an analysis of secondary pharmacology assays by the FDA. The meeting also generated 85 abstracts (reproduced in the current volume of J Pharmacol Toxicol Methods). It appears that the validation of methods remains a challenge in SP. Nevertheless, the continued efforts to mine approaches to detection of proarrhythmia liability remains a baffling obsession given the ability of Industry to completely prevent drugs entering into clinical study only to be found to have proarrhythmic properties, with no reports of such for at least ten years. Perhaps it is time to move on from CiPA and find genuine problems to solve?


Subject(s)
COVID-19 , Drug-Related Side Effects and Adverse Reactions , Animals , Drug Evaluation, Preclinical/methods , Indoles , Ion Channels , Propionates
5.
Comput Biol Chem ; 98: 107694, 2022 Jun.
Article in English | MEDLINE | ID: covidwho-1944667

ABSTRACT

The COVID-19 has a worldwide spread, which has prompted concerted efforts to find successful drug treatments. Drug design focused on finding antiviral therapeutic agents from plant-derived compounds which may disrupt the attachment of SARS-CoV-2 to host cells is with a pivotal need and role in the last year. Herein, we provide an approach based on drug design methods combined with machine learning approaches to classify and discover inhibitors for COVID-19 from natural products. The spike receptor-binding domain (RBD) was docked with database of 125 ligands. The docking protocol based on several steps was performed within Autodock Vina to identify the high-affinity binding mode and to reveal more insights into interaction between the phytochemicals and the RBD domain. A protein-ligand interaction analyzer has been developed. The drug-likeness properties of explored inhibitors are analyzed in the frame of exploratory data analyses. The developed computational protocol yielded a comprehensive pipeline for predicting the inhibitors to prevent the entry RBD region.


Subject(s)
Antiviral Agents , COVID-19 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Biological Products/chemistry , Biological Products/pharmacology , COVID-19/drug therapy , Drug Evaluation, Preclinical , Humans , Ligands , Molecular Docking Simulation , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/metabolism
6.
Viruses ; 14(6)2022 05 24.
Article in English | MEDLINE | ID: covidwho-1911606

ABSTRACT

The COVID-19 pandemic began in 2019, but it is still active. The development of an effective vaccine reduced the number of deaths; however, a treatment is still needed. Here, we aimed to inhibit viral entry to the host cell by inhibiting spike (S) protein cleavage by several proteases. We developed a computational pipeline to repurpose FDA-approved drugs to inhibit protease activity and thus prevent S protein cleavage. We tested some of our drug candidates and demonstrated a decrease in protease activity. We believe our pipeline will be beneficial in identifying a drug regimen for COVID-19 patients.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/pharmacology , Drug Evaluation, Preclinical , Drug Repositioning , Humans , Molecular Docking Simulation , Peptide Hydrolases , Spike Glycoprotein, Coronavirus/metabolism , Virus Internalization
7.
Biotechnol Bioeng ; 119(10): 2669-2688, 2022 10.
Article in English | MEDLINE | ID: covidwho-1905798

ABSTRACT

In the current pandemic, scenario the world is facing a huge shortage of effective drugs and other prophylactic medicine to treat patients which created havoc in several countries with poor resources. With limited demand and supply of effective drugs, researchers rushed to repurpose the existing approved drugs for the treatment of COVID-19. The process of drug screening and testing is very costly and requires several steps for validation and treatment efficacy evaluation ranging from in-vitro to in-vivo setups. After these steps, a clinical trial is mandatory for the evaluation of treatment efficacy and side effects in humans. These processes enhance the overall cost and sometimes the lead molecule show adverse effects in humans and the trial ends up in the final stages. Recently with the advent of three-dimensional (3D) organoid culture which mimics the human tissue exactly the process of drug screening and testing can be done in a faster and cost-effective manner. Further 3D organoids prepared from stems cells taken from individuals can be beneficial for personalized drug therapy which could save millions of lives. This review discussed approaches and techniques for the synthesis of 3D-printed human organoids for drug screening. The key findings of the usage of organoids for personalized medicine for the treatment of COVID-19 have been discussed. In the end, the key challenges for the wide applicability of human organoids for drug screening with prospects of future orientation have been included.


Subject(s)
COVID-19 , Organoids , COVID-19/drug therapy , Drug Evaluation, Preclinical/methods , Humans , Pandemics , Printing, Three-Dimensional
8.
Biomed Pharmacother ; 151: 113104, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1850705

ABSTRACT

The Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2) has continuously evolved, resulting in the emergence of several variants of concern (VOCs). To study mechanisms of viral entry and potentially identify specific inhibitors, we pseudotyped lentiviral vectors with different SARS-CoV-2 VOC spike variants (D614G, Alpha, Beta, Delta, Omicron/BA.1), responsible for receptor binding and membrane fusion. These SARS-CoV-2 lentiviral pseudoviruses were applied to screen 774 FDA-approved drugs. For the assay we decided to use CaCo2 cells, since they equally allow cell entry through both the direct membrane fusion pathway mediated by TMPRSS2 and the endocytosis pathway mediated by cathepsin-L. The active molecules which showed stronger differences in their potency to inhibit certain SARS-CoV-2 VOCs included antagonists of G-protein coupled receptors, like phenothiazine-derived antipsychotic compounds such as Chlorpromazine, with highest activity against the Omicron pseudovirus. In general, our data showed that the various VOCs differ in their preferences for cell entry, and we were able to identify synergistic combinations of inhibitors. Notably, Omicron singled out by relying primarily on the endocytosis pathway while Delta preferred cell entry via membrane fusion. In conclusion, our data provide new insights into different entry preferences of SARS-CoV-2 VOCs, which might help to identify new drug targets.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/drug therapy , Caco-2 Cells , Drug Evaluation, Preclinical , Humans , Spike Glycoprotein, Coronavirus/metabolism
9.
Methods Mol Biol ; 2452: 379-391, 2022.
Article in English | MEDLINE | ID: covidwho-1844277

ABSTRACT

Identification of an effective antiviral for the treatment of COVID-19 is considered one of the holy grails in the bid to end the pandemic. However, the novelty of SARS-CoV-2, along with the little knowledge available about its infection characteristics at the beginning of this pandemic, challenges the scientific world on how one may be able to promptly identify promising drug candidates from a myriad of compound libraries. Here, we describe a cytopathic effect (CPE)-based drug screening assay for SARS-CoV-2 which allows for rapid assessment of drug compound libraries through pre- or posttreatment drug screening procedures and evaluation using a light microscope. By comparing the virus-induced CPE of the drug-treated cells against the vehicle and drug controls, potent drug candidates can be quickly identified for further downstream studies.


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Drug Evaluation, Preclinical , Humans , Pandemics
10.
Eur J Med Chem ; 228: 114030, 2022 Jan 15.
Article in English | MEDLINE | ID: covidwho-1768048

ABSTRACT

The epidemic coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread worldwide and efficacious therapeutics are urgently needed. 3-Chymotrypsin-like cysteine protease (3CLpro) is an indispensable protein in viral replication and represents an attractive drug target for fighting COVID-19. Herein, we report the discovery of 9,10-dihydrophenanthrene derivatives as non-peptidomimetic and non-covalent inhibitors of the SARS-CoV-2 3CLpro. The structure-activity relationships of 9,10-dihydrophenanthrenes as SARS-CoV-2 3CLpro inhibitors have carefully been investigated and discussed in this study. Among all tested 9,10-dihydrophenanthrene derivatives, C1 and C2 display the most potent SARS-CoV-2 3CLpro inhibition activity, with IC50 values of 1.55 ± 0.21 µM and 1.81 ± 0.17 µM, respectively. Further enzyme kinetics assays show that these two compounds dose-dependently inhibit SARS-CoV-2 3CLprovia a mixed-inhibition manner. Molecular docking simulations reveal the binding modes of C1 in the dimer interface and substrate-binding pocket of the target. In addition, C1 shows outstanding metabolic stability in the gastrointestinal tract, human plasma, and human liver microsome, suggesting that this agent has the potential to be developed as an orally administrated SARS-CoV-2 3CLpro inhibitor.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/drug therapy , Coronavirus 3C Proteases/antagonists & inhibitors , Drug Discovery/methods , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Dose-Response Relationship, Drug , Drug Evaluation, Preclinical , Gastrointestinal Tract/metabolism , Humans , Kinetics , Microsomes, Liver/metabolism , Molecular Docking Simulation , Protein Binding , Structure-Activity Relationship , Viral Nonstructural Proteins/antagonists & inhibitors
11.
Int J Mol Sci ; 23(6)2022 Mar 17.
Article in English | MEDLINE | ID: covidwho-1760650

ABSTRACT

The recent covid crisis has provided important lessons for academia and industry regarding digital reorganization. Among the fascinating lessons from these times is the huge potential of data analytics and artificial intelligence. The crisis exponentially accelerated the adoption of analytics and artificial intelligence, and this momentum is predicted to continue into the 2020s and beyond. Drug development is a costly and time-consuming business, and only a minority of approved drugs generate returns exceeding the research and development costs. As a result, there is a huge drive to make drug discovery cheaper and faster. With modern algorithms and hardware, it is not too surprising that the new technologies of artificial intelligence and other computational simulation tools can help drug developers. In only two years of covid research, many novel molecules have been designed/identified using artificial intelligence methods with astonishing results in terms of time and effectiveness. This paper reviews the most significant research on artificial intelligence in de novo drug design for COVID-19 pharmaceutical research.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Artificial Intelligence , COVID-19/drug therapy , COVID-19/virology , Drug Design , SARS-CoV-2/drug effects , Antiviral Agents/therapeutic use , Drug Discovery/methods , Drug Evaluation, Preclinical , High-Throughput Nucleotide Sequencing , Humans , Ligands , SARS-CoV-2/physiology , Small Molecule Libraries , Structure-Activity Relationship
12.
Sci Rep ; 11(1): 22796, 2021 11 23.
Article in English | MEDLINE | ID: covidwho-1758351

ABSTRACT

The current severe situation of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been reversed and posed great threats to global health. Therefore, there is an urgent need to find out effective antiviral drugs. The 3-chymotrypsin-like protease (3CLpro) in SARS-CoV-2 serve as a promising anti-virus target due to its essential role in the regulation of virus reproduction. Here, we report an improved integrated approach to identify effective 3CLpro inhibitors from effective Chinese herbal formulas. With this approach, we identified the 5 natural products (NPs) including narcissoside, kaempferol-3-O-gentiobioside, rutin, vicenin-2 and isoschaftoside as potential anti-SARS-CoV-2 candidates. Subsequent molecular dynamics simulation additionally revealed that these molecules can be tightly bound to 3CLpro and confirmed effectiveness against COVID-19. Moreover, kaempferol-3-o-gentiobioside, vicenin-2 and isoschaftoside were first reported to have SARS-CoV-2 3CLpro inhibitory activity. In summary, this optimized integrated strategy for drug screening can be utilized in the discovery of antiviral drugs to achieve rapid acquisition of drugs with specific effects on antiviral targets.


Subject(s)
Antiviral Agents/analysis , Drug Evaluation, Preclinical/methods , SARS-CoV-2/drug effects , Biological Products/analysis , Biological Products/pharmacology , COVID-19/drug therapy , COVID-19/metabolism , Computational Biology/methods , Coronavirus 3C Proteases/drug effects , Coronavirus 3C Proteases/metabolism , Drug Discovery/methods , Flavonols/metabolism , Flavonols/pharmacology , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity
13.
Proc Natl Acad Sci U S A ; 119(8)2022 02 22.
Article in English | MEDLINE | ID: covidwho-1758461

ABSTRACT

Viral causes of pneumonia pose constant threats to global public health, but there are no specific treatments currently available for the condition. Antivirals are ineffective when administered late after the onset of symptoms. Pneumonia is caused by an exaggerated inflammatory cytokine response to infection, but tissue necrosis and damage caused by virus also contribute to lung pathology. We hypothesized that viral pneumonia can be treated effectively if both virus and inflammation are simultaneously targeted. Combined treatment with the antiviral drug cidofovir and etanercept, which targets tumor necrosis factor (TNF), down-regulated nuclear factor kappa B-signaling and effectively reduced morbidity and mortality during respiratory ectromelia virus (ECTV) infection in mice even when treatment was initiated after onset of clinical signs. Treatment with cidofovir alone reduced viral load, but animals died from severe lung pathology. Treatment with etanercept had no effect on viral load but diminished levels of inflammatory cytokines and chemokines including TNF, IL-6, IL-1ß, IL-12p40, TGF-ß, and CCL5 and dampened activation of the STAT3 cytokine-signaling pathway, which transduces signals from multiple cytokines implicated in lung pathology. Consequently, combined treatment with a STAT3 inhibitor and cidofovir was effective in improving clinical disease and lung pathology in ECTV-infected mice. Thus, the simultaneous targeting of virus and a specific inflammatory cytokine or cytokine-signaling pathway is effective in the treatment of pneumonia. This approach might be applicable to pneumonia caused by emerging and re-emerging viruses, like seasonal and pandemic influenza A virus strains and severe acute respiratory syndrome coronavirus 2.


Subject(s)
Anti-Inflammatory Agents, Non-Steroidal/administration & dosage , Antiviral Agents/therapeutic use , Cidofovir/therapeutic use , Etanercept/administration & dosage , Pneumonia, Viral/drug therapy , Animals , Antiviral Agents/pharmacology , Cell Line , Chlorocebus aethiops , Cidofovir/pharmacology , Cytokines/metabolism , Drug Evaluation, Preclinical , Drug Therapy, Combination , Ectromelia virus/drug effects , Female , Lung/drug effects , Lung/metabolism , Mice, Inbred C57BL , NF-kappa B/metabolism , Pneumonia, Viral/metabolism , STAT3 Transcription Factor/metabolism , Signal Transduction/drug effects , Tumor Necrosis Factor-alpha/antagonists & inhibitors , Viral Load/drug effects
14.
Future Med Chem ; 14(6): 393-405, 2022 03.
Article in English | MEDLINE | ID: covidwho-1715941

ABSTRACT

Background: Since December 2019, SARS-CoV-2 has continued to spread rapidly around the world. The effective drugs may provide a long-term strategy to combat this virus. The main protease (Mpro) and papain-like protease (PLpro) are two important targets for the inhibition of SARS-CoV-2 virus replication and proliferation. Materials & methods: In this study, deep reinforcement learning, covalent docking and molecular dynamics simulations were used to identify novel compounds that have the potential to inhibit both Mpro and PLpro. Results & conclusion: Three compounds were identified that can effectively occupy the Mpro protein cavity with the PLpro protein cavity and form high-frequency contacts with key amino acid residues (Mpro: His41, Cys145, Glu166; PLpro: Cys111). These three compounds can be further investigated as potential lead compounds for SARS-CoV-2 inhibitors.


Subject(s)
Antiviral Agents/pharmacology , Deep Learning , Drug Evaluation, Preclinical , SARS-CoV-2/drug effects , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology
15.
Molecules ; 27(4)2022 Feb 09.
Article in English | MEDLINE | ID: covidwho-1715566

ABSTRACT

Betulinic acid (BA) and its derivatives exhibit a variety of biological activities, especially their anti-HIV-1 activity, but generally have only modest inhibitory potency against influenza virus. The entry of influenza virus into host cells can be competitively inhibited by multivalent derivatives targeting hemagglutinin. In this study, a series of hexa-, hepta- and octavalent BA derivatives based on α-, ß- and γ-cyclodextrin scaffolds, respectively, with varying lengths of flexible oligo(ethylene glycol) linkers was designed and synthesized using a microwave-assisted copper-catalyzed 1,3-dipolar cycloaddition reaction. The generated BA-cyclodextrin conjugates were tested for their in vitro activity against influenza A/WSN/33 (H1N1) virus and cytotoxicity. Among the tested compounds, 58, 80 and 82 showed slight cytotoxicity to Madin-Darby canine kidney cells with viabilities ranging from 64 to 68% at a high concentration of 100 µM. Four conjugates 51 and 69-71 showed significant inhibitory effects on influenza infection with half maximal inhibitory concentration values of 5.20, 9.82, 7.48 and 7.59 µM, respectively. The structure-activity relationships of multivalent BA-cyclodextrin conjugates were discussed, highlighting that multivalent BA derivatives may be potential antiviral agents against influenza infection.


Subject(s)
Antiviral Agents , Cyclodextrins/chemistry , Influenza A Virus, H1N1 Subtype/metabolism , Orthomyxoviridae Infections/drug therapy , Pentacyclic Triterpenes/chemistry , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Dogs , Drug Evaluation, Preclinical , Madin Darby Canine Kidney Cells , Orthomyxoviridae Infections/metabolism , Structure-Activity Relationship
16.
Nihon Yakurigaku Zasshi ; 157(2): 111-114, 2022.
Article in Japanese | MEDLINE | ID: covidwho-1714694

ABSTRACT

The expansion of COVID-19 in the world has not ended yet, and the situation in Japan is still unpredictable. Under these circumstances, the development of SARS-CoV-2 treatments such as vaccines and medicines is still underway. We have been conducting research on the drug screening for SARS-CoV-2 using the supercomputer "Fugaku". Specifically, we searched for and identified therapeutic drug candidates that showed high affinity to the target protein (main protease) related to the multiplication of SARS-CoV-2 from among about 2,000 existing drugs by performing molecular dynamics calculations using Fugaku. This is the first attempt in the world to screen drugs on a scale of several thousand using molecular dynamics calculations, and it is a case where we were able to take on the challenge because Fugaku is ranked No. 1 in the world. In this chapter, we will show the impact of the supercomputer "Fugaku" on drug discovery using our search for therapeutic agents for SARS-CoV-2 as an example.


Subject(s)
COVID-19 , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Drug Evaluation, Preclinical , Drug Repositioning , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protease Inhibitors/pharmacology , Protease Inhibitors/therapeutic use , SARS-CoV-2
17.
Commun Biol ; 5(1): 169, 2022 02 25.
Article in English | MEDLINE | ID: covidwho-1713217

ABSTRACT

SARS-CoV-2 proteases Mpro and PLpro are promising targets for antiviral drug development. In this study, we present an antiviral screening strategy involving a novel in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations for rapid identification of protease inhibitors with low cytotoxicity. We identified eight compounds with anti-SARS-CoV-2 activity from a library of 64 repurposed drugs and modeled at protease active sites by in silico docking. We demonstrate that Sitagliptin and Daclatasvir inhibit PLpro, and MG-101, Lycorine HCl, and Nelfinavir mesylate inhibit Mpro of SARS-CoV-2. The X-ray crystal structure of Mpro in complex with MG-101 shows a covalent bond formation between the inhibitor and the active site Cys145 residue indicating its mechanism of inhibition is by blocking the substrate binding at the active site. Thus, we provide methods for rapid and effective screening and development of inhibitors for blocking virus polyprotein processing as SARS-CoV-2 antivirals. Additionally, we show that the combined inhibition of Mpro and PLpro is more effective in inhibiting SARS-CoV-2 and the delta variant.


Subject(s)
Coronavirus 3C Proteases/antagonists & inhibitors , Coronavirus Papain-Like Proteases/antagonists & inhibitors , Drug Evaluation, Preclinical/methods , SARS-CoV-2/enzymology , Viral Protease Inhibitors/analysis , COVID-19/drug therapy , Drug Repositioning , HEK293 Cells , Humans , Molecular Docking Simulation , Molecular Targeted Therapy
18.
Comput Math Methods Med ; 2022: 9604456, 2022.
Article in English | MEDLINE | ID: covidwho-1704361

ABSTRACT

OBJECTIVE: To investigate the potential pharmacological value of extracts from honeysuckle on patients with mild coronavirus disease 2019 (COVID-19) infection. METHODS: The active components and targets of honeysuckle were screened by Traditional Chinese Medicine Database and Analysis Platform (TCMSP). SwissADME and pkCSM databases predict pharmacokinetics of ingredients. The Gene Expression Omnibus (GEO) database collected transcriptome data for mild COVID-19. Data quality control, differentially expressed gene (DEG) identification, enrichment analysis, and correlation analysis were implemented by R toolkit. CIBERSORT evaluated the infiltration of 22 immune cells. RESULTS: The seven active ingredients of honeysuckle had good oral absorption and medicinal properties. Both the active ingredient targets of honeysuckle and differentially expressed genes of mild COVID-19 were significantly enriched in immune signaling pathways. There were five overlapping immunosignature genes, among which RELA and MAP3K7 expressions were statistically significant (P < 0.05). Finally, immune cell infiltration and correlation analysis showed that RELA, MAP3K7, and natural killer (NK) cell are with highly positive correlation and highly negatively correlated with hematopoietic stem cells. CONCLUSION: Our analysis suggested that honeysuckle extract had a safe and effective protective effect against mild COVID-19 by regulating a complex molecular network. The main mechanism was related to the proportion of infiltration between NK cells and hematopoietic stem cells.


Subject(s)
COVID-19/drug therapy , Drugs, Chinese Herbal/therapeutic use , Lonicera , Phytotherapy , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacokinetics , Antiviral Agents/therapeutic use , COVID-19/genetics , COVID-19/immunology , Computational Biology , Databases, Pharmaceutical/statistics & numerical data , Drug Evaluation, Preclinical , Drugs, Chinese Herbal/chemistry , Drugs, Chinese Herbal/pharmacokinetics , Gene Expression/drug effects , Gene Ontology , Gene Regulatory Networks/drug effects , Gene Regulatory Networks/immunology , Hematopoietic Stem Cells/drug effects , Hematopoietic Stem Cells/immunology , Humans , Killer Cells, Natural/drug effects , Killer Cells, Natural/immunology , Lonicera/chemistry , Medicine, Chinese Traditional , Pandemics , SARS-CoV-2/drug effects
20.
J Am Chem Soc ; 144(7): 2905-2920, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1683927

ABSTRACT

Drugs targeting SARS-CoV-2 could have saved millions of lives during the COVID-19 pandemic, and it is now crucial to develop inhibitors of coronavirus replication in preparation for future outbreaks. We explored two virtual screening strategies to find inhibitors of the SARS-CoV-2 main protease in ultralarge chemical libraries. First, structure-based docking was used to screen a diverse library of 235 million virtual compounds against the active site. One hundred top-ranked compounds were tested in binding and enzymatic assays. Second, a fragment discovered by crystallographic screening was optimized guided by docking of millions of elaborated molecules and experimental testing of 93 compounds. Three inhibitors were identified in the first library screen, and five of the selected fragment elaborations showed inhibitory effects. Crystal structures of target-inhibitor complexes confirmed docking predictions and guided hit-to-lead optimization, resulting in a noncovalent main protease inhibitor with nanomolar affinity, a promising in vitro pharmacokinetic profile, and broad-spectrum antiviral effect in infected cells.


Subject(s)
Antiviral Agents/pharmacology , Coronavirus 3C Proteases/metabolism , Cysteine Proteinase Inhibitors/pharmacology , SARS-CoV-2/drug effects , Small Molecule Libraries/pharmacology , Animals , Antiviral Agents/metabolism , Antiviral Agents/pharmacokinetics , Catalytic Domain , Chlorocebus aethiops , Coronavirus 3C Proteases/chemistry , Cysteine Proteinase Inhibitors/metabolism , Cysteine Proteinase Inhibitors/pharmacokinetics , Drug Evaluation, Preclinical , Humans , Microbial Sensitivity Tests , Microsomes, Liver/metabolism , Molecular Docking Simulation , Protein Binding , SARS-CoV-2/enzymology , Small Molecule Libraries/metabolism , Small Molecule Libraries/pharmacokinetics , Vero Cells
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