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1.
Expert Rev Hematol ; 14(9): 819-830, 2021 09.
Article in English | MEDLINE | ID: covidwho-1349725

ABSTRACT

INTRODUCTION: Ibrutinib is a highly effective drug for patients with chronic lymphocytic leukemia (CLL), and is well tolerated even by older patients and those unfit to receive conventional immuno-chemotherapy. AREAS COVERED: The occurrence of adverse events was revealed as a major cause of ibrutinib failure in the real-world. Ibrutinib-induced lymphocytosis carries the risk of an untimely interruption of therapy because it may be misinterpreted as disease progression. In addition, drug interactions can worsen ibrutinib-associated toxicities by increasing the plasma concentration of ibrutinib. In this review, we present a case of major hemorrhage and atrial fibrillation (AF) during ibrutinib use and summarize the adverse events associated with ibrutinib. Furthermore, the practical management of ibrutinib-associated toxicities was covered with reference to a drug interaction mechanism. EXPERT OPINION: Clinicians should examine the prescribed drugs prior to ibrutinib initiation and carefully monitor toxicities while taking ibrutinib. A reduced dose of ibrutinib with the concurrent use of CYP3A inhibitors such as antifungal agents could be an attractive strategy to reduce toxicities and may confer financial benefits. Reducing unexpected toxicities is as significant as achieving treatment response in the era of life-long therapy with ibrutinib in patients with CLL.


Subject(s)
Adenine/analogs & derivatives , Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy , Piperidines/therapeutic use , Protein Kinase Inhibitors/therapeutic use , Adenine/adverse effects , Adenine/pharmacology , Adenine/therapeutic use , Aged , COVID-19/complications , Disease Management , Drug Interactions , Drug-Related Side Effects and Adverse Reactions/etiology , Drug-Related Side Effects and Adverse Reactions/therapy , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/complications , Male , Piperidines/adverse effects , Piperidines/pharmacology , Protein Kinase Inhibitors/adverse effects , Protein Kinase Inhibitors/pharmacology
2.
Int Immunopharmacol ; 99: 108012, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1330894

ABSTRACT

ALK targeting with tyrosine kinase inhibitors (TKIs) is a highly potent treatment option for the therapy of ALK positive non-small cell lung cancer (NSCLC). However, pharmacokinetics of TKIs leads to clinically significant drug interactions, and the interfering co-medication may hamper the anti-cancer therapeutic management. Here, we present for the first time a drug interaction profile of ALK-TKIs, crizotinib and alectinib, and immunosuppressive agent cyclosporine A in kidney transplant recipients diagnosed with ALK+ lung cancer. Based on therapeutic drug monitoring of cyclosporin A plasma level, the dose of cyclosporine A has been adjusted to achieve a safe and effective therapeutic level in terms of both cancer treatment and kidney transplant condition. Particularly, 15 years upon the kidney transplantation, the stage IV lung cancer patient was treated with the 1st-line chemotherapy, the 2nd-line ALK-TKI crizotinib followed by ALK-TKI alectinib. The successful therapy with ALK-TKIs has been continuing for more than 36 months, including the period when the patient was treated for COVID-19 bilateral pneumonia. Hence, the therapy of ALK+ NSCLC with ALK-TKIs in organ transplant recipients treated with cyclosporine A may be feasible and effective.


Subject(s)
Anaplastic Lymphoma Kinase/antagonists & inhibitors , Carbazoles/pharmacology , Carcinoma, Non-Small-Cell Lung/drug therapy , Crizotinib/pharmacology , Lung Neoplasms/drug therapy , Piperidines/pharmacology , Protein-Tyrosine Kinases/antagonists & inhibitors , Carcinoma, Non-Small-Cell Lung/pathology , Carcinoma, Non-Small-Cell Lung/secondary , Drug Interactions , Humans , Kidney Transplantation , Lung Neoplasms/pathology , Male , Middle Aged , Protein Kinase Inhibitors/pharmacology
3.
Bioorg Chem ; 115: 105196, 2021 10.
Article in English | MEDLINE | ID: covidwho-1322004

ABSTRACT

So far, there is still no specific drug against COVID-19. Taking compound 1 with anti-EBOV activity as the lead, fifty-four 12N-substituted aloperine derivatives were synthesized and evaluated for the anti-SARS-CoV-2 activities using pseudotyped virus model. Among them, 8a exhibited the most potential effects against both pseudotyped and authentic SARS-CoV-2, as well as SARS-CoV and MERS-CoV, indicating a broad-spectrum anti-coronavirus profile. The mechanism study disclosed that 8a might block a late stage of viral entry, mainly via inhibiting host cathepsin B activity rather than directly targeting cathepsin B protein. Also, 8a could significantly reduce the release of multiple inflammatory cytokines in a time- and dose-dependent manner, such as IL-6, IL-1ß, IL-8 and MCP-1, the major contributors to cytokine storm. Therefore, 8a is a promising agent with the advantages of broad-spectrum anti-coronavirus and anti-cytokine effects, thus worthy of further investigation.


Subject(s)
Antiviral Agents/pharmacology , Piperidines/pharmacology , Quinolizidines/pharmacology , SARS-CoV-2/drug effects , Virus Internalization/drug effects , Animals , Antiviral Agents/chemical synthesis , Antiviral Agents/pharmacokinetics , Antiviral Agents/toxicity , Cathepsin B/antagonists & inhibitors , Chlorocebus aethiops , Cytokines/metabolism , HEK293 Cells , Humans , Male , Mice , Microbial Sensitivity Tests , Molecular Structure , Piperidines/chemical synthesis , Piperidines/pharmacokinetics , Piperidines/toxicity , Quinolizidines/chemical synthesis , Quinolizidines/pharmacokinetics , Quinolizidines/toxicity , Rats, Sprague-Dawley , Structure-Activity Relationship , Vero Cells
4.
Curr Opin Chem Biol ; 65: 74-84, 2021 12.
Article in English | MEDLINE | ID: covidwho-1312961

ABSTRACT

Drug repurposing aims to find new uses for already existing and approved drugs. We now provide a brief overview of recent developments in drug repurposing using machine learning alongside other computational approaches for comparison. We also highlight several applications for cancer using kinase inhibitors, Alzheimer's disease as well as COVID-19.


Subject(s)
Alzheimer Disease/drug therapy , COVID-19/drug therapy , Drug Repositioning/trends , Machine Learning , Neoplasms/drug therapy , Antineoplastic Agents/therapeutic use , Antiviral Agents/therapeutic use , Clemastine/pharmacology , Computational Biology/methods , Dipyridamole/pharmacology , Humans , Hydroxychloroquine/pharmacology , Lenalidomide/pharmacology , Neuroprotective Agents/therapeutic use , Piperazines/pharmacology , Piperidines/pharmacology , Protein Kinase Inhibitors/pharmacology
5.
Nat Commun ; 12(1): 3907, 2021 06 23.
Article in English | MEDLINE | ID: covidwho-1281720

ABSTRACT

SARS-CoV-2 (2019-nCoV) is the pathogenic coronavirus responsible for the global pandemic of COVID-19 disease. The Spike (S) protein of SARS-CoV-2 attaches to host lung epithelial cells through the cell surface receptor ACE2, a process dependent on host proteases including TMPRSS2. Here, we identify small molecules that reduce surface expression of TMPRSS2 using a library of 2,560 FDA-approved or current clinical trial compounds. We identify homoharringtonine and halofuginone as the most attractive agents, reducing endogenous TMPRSS2 expression at sub-micromolar concentrations. These effects appear to be mediated by a drug-induced alteration in TMPRSS2 protein stability. We further demonstrate that halofuginone modulates TMPRSS2 levels through proteasomal-mediated degradation that involves the E3 ubiquitin ligase component DDB1- and CUL4-associated factor 1 (DCAF1). Finally, cells exposed to homoharringtonine and halofuginone, at concentrations of drug known to be achievable in human plasma, demonstrate marked resistance to SARS-CoV-2 infection in both live and pseudoviral in vitro models. Given the safety and pharmacokinetic data already available for the compounds identified in our screen, these results should help expedite the rational design of human clinical trials designed to combat active COVID-19 infection.


Subject(s)
COVID-19/drug therapy , Homoharringtonine/pharmacology , Piperidines/pharmacology , Quinazolinones/pharmacology , SARS-CoV-2/drug effects , SARS-CoV-2/physiology , Serine Endopeptidases/metabolism , Virus Internalization/drug effects , Angiotensin-Converting Enzyme 2/metabolism , Animals , COVID-19/metabolism , COVID-19/pathology , COVID-19/virology , Cells, Cultured , Chlorocebus aethiops , High-Throughput Screening Assays/methods , Humans , Lung/drug effects , Lung/metabolism , Lung/pathology , Lung/virology , Mice , Protein Synthesis Inhibitors/pharmacology , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/metabolism
6.
Eur J Immunol ; 51(9): 2330-2340, 2021 09.
Article in English | MEDLINE | ID: covidwho-1261763

ABSTRACT

The molecular mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was characterized to identify novel therapies. The impact of tofacitinib, IL-6R Ab, or TNFi therapy was determined on Spike protein or LPS/IFN-γ-induced signaling, inflammation, and metabolic reprogramming in MΦs and/or rheumatoid arthritis (RA) fibroblast-like synoviocyte (FLS). ACE2 frequency was markedly expanded in MΦs compared to T cells and RA FLS. Tofacitinib suppresses Spike protein potentiated STAT1 signaling, whereas this function was unchanged by TNFi. Tofacitinib impairs IL-6/IFN/LPS-induced STAT1 and STAT3 phosphorylation in RA MΦs and FLS. Interestingly, tofacitinib had a broader inhibitory effect on the monokines, glycolytic regulators, or oxidative metabolites compared to IL-6R Ab and TNFi in Spike-protein-activated MΦs. In contrast, all three therapies disrupted IFN-α and IFN-ß secretion in response to Spike protein; nonetheless, the IFN-γ was only curtailed by tofacitinib or IL-6R Ab. While tofacitinib counteracted MΦ metabolic rewiring instigated by Spike protein, it was inconsequential on the glycolysis expansion mediated via HK2 and/or LDHA in the activated RA MΦ and FLS. Nevertheless, the potentiated inflammatory response and the diminished oxidative phosphorylation modulated by Spike protein and/or LPS/IFN-γ stimulation in MΦs or RA FLS were reversed by tofacitinib. In conclusion, tofacitinib suppresses MΦ inflammation and immunometabolism triggered by Spike protein and may provide a promising strategy for COVID-19 patients.


Subject(s)
COVID-19/drug therapy , Macrophages/drug effects , Piperidines/pharmacology , Pyrimidines/pharmacology , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/metabolism , Arthritis, Rheumatoid/metabolism , COVID-19/metabolism , Cells, Cultured , Fibroblasts/drug effects , Fibroblasts/metabolism , Humans , Interleukin-6/metabolism , Macrophages/metabolism , Receptors, Interleukin-6/metabolism , STAT1 Transcription Factor/metabolism , STAT3 Transcription Factor/metabolism , Signal Transduction/drug effects , Tumor Necrosis Factor-alpha/metabolism
7.
Front Immunol ; 12: 635018, 2021.
Article in English | MEDLINE | ID: covidwho-1211810

ABSTRACT

Objective: Bacterial and viral infectious triggers are linked to spondyloarthritis (SpA) including psoriatic arthritis (PsA) development, likely via dendritic cell activation. We investigated spinal entheseal plasmacytoid dendritic cells (pDCs) toll-like receptor (TLR)-7 and 9 activation and therapeutic modulation, including JAK inhibition. We also investigated if COVID-19 infection, a potent TLR-7 stimulator triggered PsA flares. Methods: Normal entheseal pDCs were characterized and stimulated with imiquimod and CpG oligodeoxynucleotides (ODN) to evaluate TNF and IFNα production. NanoString gene expression assay of total pDCs RNA was performed pre- and post- ODN stimulation. Pharmacological inhibition of induced IFNα protein was performed with Tofacitinib and PDE4 inhibition. The impact of SARS-CoV2 viral infection on PsA flares was evaluated. Results: CD45+HLA-DR+CD123+CD303+CD11c- entheseal pDCs were more numerous than blood pDCs (1.9 ± 0.8% vs 0.2 ± 0.07% of CD45+ cells, p=0.008) and showed inducible IFNα and TNF protein following ODN/imiquimod stimulation and were the sole entheseal IFNα producers. NanoString data identified 11 significantly upregulated differentially expressed genes (DEGs) including TNF in stimulated pDCs. Canonical pathway analysis revealed activation of dendritic cell maturation, NF-κB signaling, toll-like receptor signaling and JAK/STAT signaling pathways following ODN stimulation. Both tofacitinib and PDE4i strongly attenuated ODN induced IFNα. DAPSA scores elevations occurred in 18 PsA cases with SARS-CoV2 infection (9.7 ± 4 pre-infection and 35.3 ± 7.5 during infection). Conclusion: Entheseal pDCs link microbes to TNF/IFNα production. SARS-CoV-2 infection is associated with PsA Flares and JAK inhibition suppressed activated entheseal plasmacytoid dendritic Type-1 interferon responses as pointers towards a novel mechanism of PsA and SpA-related arthropathy.


Subject(s)
Arthritis, Psoriatic/complications , COVID-19/complications , Dendritic Cells/metabolism , Interferon-alpha/metabolism , Janus Kinases/antagonists & inhibitors , Adjuvants, Immunologic/pharmacology , Adult , Aged , COVID-19/genetics , COVID-19/metabolism , Computational Biology , Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism , Dendritic Cells/drug effects , Female , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , Humans , Imiquimod/pharmacology , Janus Kinases/metabolism , Male , Middle Aged , NF-kappa B/metabolism , Oligonucleotides/pharmacology , Phosphodiesterase 4 Inhibitors/pharmacology , Piperidines/pharmacology , Protein Kinase Inhibitors/pharmacology , Pyrimidines/pharmacology , Signal Transduction/drug effects , Signal Transduction/genetics , Toll-Like Receptor 7/metabolism , Toll-Like Receptor 9/metabolism , Transcriptome , Tumor Necrosis Factor-alpha/metabolism
8.
PLoS Pathog ; 17(2): e1009371, 2021 02.
Article in English | MEDLINE | ID: covidwho-1138592

ABSTRACT

Morbilliviruses, such as measles virus (MeV) and canine distemper virus (CDV), are highly infectious members of the paramyxovirus family. MeV is responsible for major morbidity and mortality in non-vaccinated populations. ERDRP-0519, a pan-morbillivirus small molecule inhibitor for the treatment of measles, targets the morbillivirus RNA-dependent RNA-polymerase (RdRP) complex and displayed unparalleled oral efficacy against lethal infection of ferrets with CDV, an established surrogate model for human measles. Resistance profiling identified the L subunit of the RdRP, which harbors all enzymatic activity of the polymerase complex, as the molecular target of inhibition. Here, we examined binding characteristics, physical docking site, and the molecular mechanism of action of ERDRP-0519 through label-free biolayer interferometry, photoaffinity cross-linking, and in vitro RdRP assays using purified MeV RdRP complexes and synthetic templates. Results demonstrate that unlike all other mononegavirus small molecule inhibitors identified to date, ERDRP-0519 inhibits all phosphodiester bond formation in both de novo initiation of RNA synthesis at the promoter and RNA elongation by a committed polymerase complex. Photocrosslinking and resistance profiling-informed ligand docking revealed that this unprecedented mechanism of action of ERDRP-0519 is due to simultaneous engagement of the L protein polyribonucleotidyl transferase (PRNTase)-like domain and the flexible intrusion loop by the compound, pharmacologically locking the polymerase in pre-initiation conformation. This study informs selection of ERDRP-0519 as clinical candidate for measles therapy and identifies a previously unrecognized druggable site in mononegavirus L polymerase proteins that can silence all synthesis of viral RNA.


Subject(s)
Antiviral Agents/pharmacology , Enzyme Inhibitors/pharmacology , Measles virus/drug effects , Measles/drug therapy , Morpholines/pharmacology , Piperidines/pharmacology , Pyrazoles/pharmacology , RNA, Viral/biosynthesis , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Small Molecule Libraries/pharmacology , Animals , Chlorocebus aethiops , Measles/metabolism , Measles/virology , Measles virus/enzymology , Mutation , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , Vero Cells
9.
Mol Cancer Res ; 19(4): 549-554, 2021 04.
Article in English | MEDLINE | ID: covidwho-1058113

ABSTRACT

The outbreak of the novel coronavirus disease 2019 (COVID-19) has emerged as one of the biggest global health threats worldwide. As of October 2020, more than 44 million confirmed cases and more than 1,160,000 deaths have been reported globally, and the toll is likely to be much higher before the pandemic is over. There are currently little therapeutic options available and new potential targets are intensively investigated. Recently, Bruton tyrosine kinase (BTK) has emerged as an interesting candidate. Elevated levels of BTK activity have been reported in blood monocytes from patients with severe COVID-19, compared with those from healthy volunteers. Importantly, various studies confirmed empirically that administration of BTK inhibitors (acalabrutinib and ibrutinib) decreased the duration of mechanical ventilation and mortality rate for hospitalized patients with severe COVID-19. Herein, we review the current information regarding the role of BTK in severe acute respiratory syndrome coronavirus 2 infections and the suitability of its inhibitors as drugs to treat COVID-19. The use of BTK inhibitors in the management of COVID-19 shows promise in reducing the severity of the immune response to the infection and thus mortality. However, BTK inhibition may be contributing in other ways to inhibit the effects of the virus and this will need to be carefully studied.


Subject(s)
Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors , Antiviral Agents/pharmacology , COVID-19/drug therapy , Adenine/analogs & derivatives , Adenine/pharmacology , Agammaglobulinaemia Tyrosine Kinase/metabolism , Antiviral Agents/adverse effects , Benzamides/pharmacology , COVID-19/complications , COVID-19/enzymology , Humans , Lung/drug effects , Lung/virology , Molecular Targeted Therapy , Neoplasms/drug therapy , Neoplasms/virology , Piperidines/pharmacology , Protein Kinase Inhibitors/adverse effects , Protein Kinase Inhibitors/pharmacology , Pyrazines/pharmacology , Thrombosis/drug therapy , Thrombosis/virology
10.
Sci Rep ; 11(1): 2512, 2021 01 28.
Article in English | MEDLINE | ID: covidwho-1054059

ABSTRACT

Whenever some phenomenon can be represented as a graph or a network it seems pertinent to explore how much the mathematical properties of that network impact the phenomenon. In this study we explore the same philosophy in the context of immunology. Our objective was to assess the correlation of "size" (number of edges and minimum vertex cover) of the JAK/STAT network with treatment effect in rheumatoid arthritis (RA), phenotype of viral infection and effect of immunosuppressive agents on a system infected with the coronavirus. We extracted the JAK/STAT pathway from Kyoto Encyclopedia of Genes and Genomes (KEGG, hsa04630). The effects of the following drugs, and their combinations, commonly used in RA were tested: methotrexate, prednisolone, rituximab, tocilizumab, tofacitinib and baricitinib. Following viral systems were also tested for their ability to evade the JAK/STAT pathway: Measles, Influenza A, West Nile virus, Japanese B virus, Yellow Fever virus, respiratory syncytial virus, Kaposi's sarcoma virus, Hepatitis B and C virus, cytomegalovirus, Hendra and Nipah virus and Coronavirus. Good correlation of edges and minimum vertex cover with clinical efficacy were observed (for edge, rho = - 0.815, R2 = 0.676, p = 0.007, for vertex cover rho = - 0.793, R2 = 0.635, p = 0.011). In the viral systems both edges and vertex cover were associated with acuteness of viral infections. In the JAK/STAT system already infected with coronavirus, maximum reduction in size was achieved with baricitinib. To conclude, algebraic and combinatorial invariant of a network may explain its biological behaviour. At least theoretically, baricitinib may be an attractive target for treatment of coronavirus infection.


Subject(s)
Arthritis, Rheumatoid/metabolism , Janus Kinases/metabolism , STAT Transcription Factors/metabolism , Virus Diseases/drug therapy , Virus Diseases/metabolism , Antibodies, Monoclonal, Humanized/pharmacology , Arthritis, Rheumatoid/genetics , Azetidines/pharmacology , Gene Regulatory Networks , Humans , Janus Kinases/genetics , Methotrexate/pharmacology , Models, Statistical , Piperidines/pharmacology , Prednisolone/pharmacology , Purines/pharmacology , Pyrazoles/pharmacology , Pyrimidines/pharmacology , Rituximab/pharmacology , STAT Transcription Factors/genetics , Signal Transduction/drug effects , Sulfonamides/pharmacology
11.
J Med Chem ; 64(2): 1170-1179, 2021 01 28.
Article in English | MEDLINE | ID: covidwho-1019736

ABSTRACT

Ifenprodil (1) is a potent GluN2B-selective N-methyl-d-aspartate (NMDA) receptor antagonist that is used as a cerebral vasodilator and has been examined in clinical trials for the treatment of drug addiction, idiopathic pulmonary fibrosis, and COVID-19. To correlate biological data with configuration, all four ifenprodil stereoisomers were prepared by diastereoselective reduction and subsequent separation of enantiomers by chiral HPLC. The absolute configuration of ifenprodil stereoisomers was determined by X-ray crystal structure analysis of (1R,2S)-1a and (1S,2S)-1d. GluN2B affinity, ion channel inhibitory activity, and selectivity over α, σ, and 5-HT receptors were evaluated. (1R,2R)-Ifenprodil ((1R,2R)-1c) showed the highest affinity toward GluN2B-NMDA receptors (Ki = 5.8 nM) and high inhibition of ion flux in two-electrode voltage clamp experiments (IC50 = 223 nM). Whereas the configuration did not influence considerably the GluN2B-NMDA receptor binding, (1R)-configuration is crucial for elevated inhibitory activity. (1R,2R)-Configured ifenprodil (1R,2R)-1c exhibited high selectivity for GluN2B-NMDA receptors over adrenergic, serotonergic, and σ1 receptors.


Subject(s)
Antifibrinolytic Agents/chemistry , Antifibrinolytic Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Piperidines/chemical synthesis , Piperidines/pharmacology , Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors , Antifibrinolytic Agents/chemical synthesis , Antiviral Agents/chemical synthesis , COVID-19/drug therapy , COVID-19/metabolism , Crystallography, X-Ray , Dose-Response Relationship, Drug , Humans , Idiopathic Pulmonary Fibrosis/drug therapy , Idiopathic Pulmonary Fibrosis/metabolism , Models, Molecular , Molecular Structure , Piperidines/chemistry , Receptors, N-Methyl-D-Aspartate/metabolism , Stereoisomerism , Structure-Activity Relationship
12.
Eur J Pharmacol ; 892: 173779, 2021 Feb 05.
Article in English | MEDLINE | ID: covidwho-959761

ABSTRACT

The rapid outbreak of the COVID-19 also known as SARS-CoV2 has been declared pandemic with serious global concern. As there is no effective therapeutic against COVID-19, there is an urgent need for explicit treatment against it. The focused objective of the current study is to propose promising drug candidates against the newly identified potential therapeutic target (endonuclease, NSP15) of SARS-CoV2. NSP15 is an attractive druggable target due to its critical role in SARS-CoV2 replication and virulence in addition to interference with the host immune system. Here in the present study, we integrated the high throughput computational screening and dynamic simulation approach to identify the most promising candidate lead compound against NSP15.5-fluoro-2-oxo-1H-pyrazine-3-carboxamide (favipiravir), (3R,4R, 5R)-3,4-Bis(benzyloxy)-5-((benzyloxy) methyl) dihydrofuran-2(3H)-one) remedesivir, 1,3-thiazol-5-ylmethyl N-[(2S,3S, 5S)-3-hydroxy-5-[[(2 S)-3-methyl-2-[[methyl-[(2-propan-2-yl-1,3-thiazol-4-yl)methyl]carbamoyl]amino]butanoyl]amino]-1,6-diphenylhexan-2-yl]carbamate (ritonavir), ethyl (3R,4R, 5S)-4-acetamido-5-amino-3-pentan-3-yloxycyclohexene-1-carboxylate (oseltamivir), and (2 S)-N-[(2S,4S, 5S)-5-[[2-(2,6-dimethylphenoxy)acetyl]amino]-4-hydroxy-1,6-diphenylhexan-2-yl]-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide (lopinavir) were chosen as a training set to generate the pharmacophore model. A dataset of ~140,000 compounds library was screened against the designed pharmacophore model and 10 unique compounds were selected that passed successfully through geometry constraints, Lipinski Rule of 5, and ADME/Tox filters along with a strong binding affinity for NSP15 binding cavity. The best fit compound was selected for dynamic simulation to have detailed structural features critical for binding with the NSP15 protein. Given our detailed integrative computational analysis, a Small molecule (3,3-Dimethyl-N-[4-(1-piperidinylcarbonyl) phenyl] butanamide) with drug-like properties and high binding affinity with the NSP15 is proposed as a most promising potential drug against COVID-19. The current computational integrative approach may complement high-throughput screening and the shortlisted small molecule may contribute to selective targeting of NSP15 to stop the replication of SARS-CoV2.


Subject(s)
Antiviral Agents/pharmacology , Benzamides/pharmacology , COVID-19/metabolism , Endoribonucleases/metabolism , Piperidines/pharmacology , SARS-CoV-2 , Viral Nonstructural Proteins/metabolism , Antiviral Agents/pharmacokinetics , Antiviral Agents/toxicity , Benzamides/pharmacokinetics , Drug Design , Endoribonucleases/chemistry , High-Throughput Screening Assays , Molecular Docking Simulation , Molecular Dynamics Simulation , Piperidines/pharmacokinetics , Viral Nonstructural Proteins/chemistry
13.
Elife ; 92020 11 23.
Article in English | MEDLINE | ID: covidwho-940328

ABSTRACT

Bruton's tyrosine kinase (BTK) is targeted in the treatment of B-cell disorders including leukemias and lymphomas. Currently approved BTK inhibitors, including Ibrutinib, a first-in-class covalent inhibitor of BTK, bind directly to the kinase active site. While effective at blocking the catalytic activity of BTK, consequences of drug binding on the global conformation of full-length BTK are unknown. Here, we uncover a range of conformational effects in full-length BTK induced by a panel of active site inhibitors, including large-scale shifts in the conformational equilibria of the regulatory domains. Additionally, we find that a remote Ibrutinib resistance mutation, T316A in the BTK SH2 domain, drives spurious BTK activity by destabilizing the compact autoinhibitory conformation of full-length BTK, shifting the conformational ensemble away from the autoinhibited form. Future development of BTK inhibitors will need to consider long-range allosteric consequences of inhibitor binding, including the emerging application of these BTK inhibitors in treating COVID-19.


Treatments for blood cancers, such as leukemia and lymphoma, rely heavily on chemotherapy, using drugs that target a vulnerable aspect of the cancer cells. B-cells, a type of white blood cell that produces antibodies, require a protein called Bruton's tyrosine kinase, or BTK for short, to survive. The drug ibrutinib (Imbruvica) is used to treat B-cell cancers by blocking BTK. The BTK protein consists of several regions. One of them, known as the kinase domain, is responsible for its activity as an enzyme (which allows it to modify other proteins by adding a 'tag' known as a phosphate group). The other regions of BTK, known as regulatory modules, control this activity. In BTK's inactive form, the regulatory modules attach to the kinase domain, blocking the regulatory modules from interacting with other proteins. When BTK is activated, it changes its conformation so the regulatory regions detach and become available for interactions with other proteins, at the same time exposing the active kinase domain. Ibrutinib and other BTK drugs in development bind to the kinase domain to block its activity. However, it is not known how this binding affects the regulatory modules. Previous efforts to study how drugs bind to BTK have used a version of the protein that only had the kinase domain, instead of the full-length protein. Now, Joseph et al. have studied full-length BTK and how it binds to five different drugs. The results reveal that ibrutinib and another drug called dasatinib both indirectly disrupt the normal position of the regulatory domains pushing BTK toward a conformation that resembles the activated state. By contrast, the three other compounds studied do not affect the inactive structure. Joseph et al. also examined a mutation in BTK that confers resistance against ibrutinib. This mutation increases the activity of BTK by disrupting the inactive structure, leading to B cells surviving better. Understanding how drug resistance mechanisms can work will lead to better drug treatment strategies for cancer. BTK is also a target in other diseases such as allergies or asthma and even COVID-19. If interactions between partner proteins and the regulatory domain are important in these diseases, then they may be better treated with drugs that maintain the regulatory modules in their inactive state. This research will help to design drugs that are better able to control BTK activity.


Subject(s)
Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors , Catalytic Domain , Protein Conformation/drug effects , Protein Kinase Inhibitors/pharmacology , Adenine/analogs & derivatives , Adenine/chemistry , Adenine/metabolism , Adenine/pharmacology , Agammaglobulinaemia Tyrosine Kinase/chemistry , Agammaglobulinaemia Tyrosine Kinase/genetics , COVID-19/metabolism , COVID-19/prevention & control , COVID-19/virology , Dasatinib/chemistry , Dasatinib/metabolism , Dasatinib/pharmacology , Humans , Leukemia, Lymphocytic, Chronic, B-Cell/genetics , Leukemia, Lymphocytic, Chronic, B-Cell/prevention & control , Models, Molecular , Molecular Structure , Mutation , Piperidines/chemistry , Piperidines/metabolism , Piperidines/pharmacology , Protein Kinase Inhibitors/chemistry , Protein Kinase Inhibitors/metabolism , SARS-CoV-2/physiology , src Homology Domains/genetics
14.
Drug Res (Stuttg) ; 71(4): 213-218, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-922287

ABSTRACT

The continued spread of 2019-nCoV has prompted widespread concern around the world. WHO formally named COVID-19 and International Committee on Taxonomy called it Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Due to this viral attack, the whole world is in lockdown. Presently, there is no effective way to control it, except social distancing and hygienic activity. World class scientists and researchers are trying to make vaccine and discover the medicine against the control and cure to this deadly viral disease. Our aim to presenting this article is kick-off deadly viral disease i.e COVID-19 by an easy way with minimum intervention and effort. Different ayurvedic therapeutic agents (Curcuma Longa L, Green tea and Piper nigrum) inhabit entry of virus in host cell, transmission of pathogen and improve the immunity. Curcumin and piperine (1-piperoylpiperidine) interact to each other and form a π-π intermolecular complex which enhance the bioavailability of curcumin by inhibition of glucuronidation of curcumin in liver. Both the molecules curcumin and catechin get bound directly to receptors binding domain of S-protein and ACE-2 receptors of host cell, due to which these molecules inhibit the entry of virus in host cell i. e. animal survives from being infected.


Subject(s)
Angiotensin-Converting Enzyme 2/antagonists & inhibitors , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , COVID-19/drug therapy , SARS-CoV-2/drug effects , Alkaloids/pharmacology , Animals , Benzodioxoles/pharmacology , COVID-19/virology , Curcumin/pharmacology , Curcumin/therapeutic use , Humans , Piperidines/pharmacology , Polyunsaturated Alkamides/pharmacology , Spike Glycoprotein, Coronavirus/metabolism , Virus Internalization/drug effects
15.
Front Immunol ; 11: 2094, 2020.
Article in English | MEDLINE | ID: covidwho-789288

ABSTRACT

The spread of the novel human respiratory coronavirus (SARS-CoV-2) is a global public health emergency. There is no known successful treatment as of this time, and there is a need for medical options to mitigate this current epidemic. SARS-CoV-2 uses the angiotensin-converting enzyme 2 (ACE2) receptor and is primarily trophic for the lower and upper respiratory tract. A number of current studies on COVID-19 have demonstrated the substantial increase in pro-inflammatory factors in the lungs during infection. The virus is also documented in the central nervous system and, particularly in the brainstem, which plays a key role in respiratory and cardiovascular function. Currently, there are few antiviral approaches, and several alternative drugs are under investigation. Two of these are Idelalisib and Ebastine, already proposed as preventive strategies in airways and allergic diseases. The interesting and evolving potential of phosphoinositide 3-kinase δ (PI3Kδ) inhibitors, together with Ebastine, lies in their ability to suppress the release of pro-inflammatory cytokines, such as IL-1ß, IL-8, IL-6, and TNF-α, by T cells. This may represent an optional therapeutic choice for COVID-19 to reduce inflammatory reactions and mortality, enabling patients to recover faster. This concise communication aims to provide new potential therapeutic targets capable of mitigating and alleviating SARS-CoV-2 pandemic infection.


Subject(s)
Betacoronavirus , Class I Phosphatidylinositol 3-Kinases/antagonists & inhibitors , Coronavirus Infections/drug therapy , Drug Repositioning/methods , Molecular Targeted Therapy/methods , Pneumonia, Viral/drug therapy , Angiotensin-Converting Enzyme 2 , Angiotensin-Converting Enzyme Inhibitors/therapeutic use , Anti-Inflammatory Agents/therapeutic use , Antirheumatic Agents/therapeutic use , Antiviral Agents/therapeutic use , Butyrophenones/pharmacology , Butyrophenones/therapeutic use , COVID-19 , Class I Phosphatidylinositol 3-Kinases/metabolism , Coronavirus Infections/virology , Humans , Inflammation/drug therapy , Inflammation/immunology , Interleukin-6/antagonists & inhibitors , Interleukin-6/blood , Pandemics , Peptidyl-Dipeptidase A/metabolism , Piperidines/pharmacology , Piperidines/therapeutic use , Pneumonia, Viral/virology , Purines/pharmacology , Purines/therapeutic use , Quinazolinones/pharmacology , Quinazolinones/therapeutic use , SARS-CoV-2
16.
Nucleic Acids Res ; 48(17): 9694-9709, 2020 09 25.
Article in English | MEDLINE | ID: covidwho-745778

ABSTRACT

DNA breaks recruit and activate PARP1/2, which deposit poly-ADP-ribose (PAR) to recruit XRCC1-Ligase3 and other repair factors to promote DNA repair. Clinical PARP inhibitors (PARPi) extend the lifetime of damage-induced PARP1/2 foci, referred to as 'trapping'. To understand the molecular nature of 'trapping' in cells, we employed quantitative live-cell imaging and fluorescence recovery after photo-bleaching. Unexpectedly, we found that PARP1 exchanges rapidly at DNA damage sites even in the presence of clinical PARPi, suggesting the persistent foci are not caused by physical stalling. Loss of Xrcc1, a major downstream effector of PAR, also caused persistent PARP1 foci without affecting PARP1 exchange. Thus, we propose that the persistent PARP1 foci are formed by different PARP1 molecules that are continuously recruited to and exchanging at DNA lesions due to attenuated XRCC1-LIG3 recruitment and delayed DNA repair. Moreover, mutation analyses of the NAD+ interacting residues of PARP1 showed that PARP1 can be physically trapped at DNA damage sites, and identified H862 as a potential regulator for PARP1 exchange. PARP1-H862D, but not PARylation-deficient PARP1-E988K, formed stable PARP1 foci upon activation. Together, these findings uncovered the nature of persistent PARP1 foci and identified NAD+ interacting residues involved in the PARP1 exchange.


Subject(s)
DNA Damage , DNA Repair/drug effects , Poly (ADP-Ribose) Polymerase-1/genetics , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Binding Sites , Catalytic Domain , Cell Line, Tumor , DNA Repair/physiology , Fluorescence Resonance Energy Transfer , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Humans , Indazoles/pharmacology , Kinetics , Molecular Imaging , NAD/metabolism , Piperidines/pharmacology , Poly(ADP-ribose) Polymerases/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , X-ray Repair Cross Complementing Protein 1/genetics , X-ray Repair Cross Complementing Protein 1/metabolism
17.
Eur J Cancer ; 138: 109-112, 2020 10.
Article in English | MEDLINE | ID: covidwho-739806
18.
J Phys Chem Lett ; 11(19): 8008-8016, 2020 Oct 01.
Article in English | MEDLINE | ID: covidwho-728962

ABSTRACT

The pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has quickly spread globally, infecting millions and killing hundreds of thousands of people. Herein, to identify potential antiviral agents, 97 natural amide-like compounds known as alkamides and piperamides were tested against SARS-CoV-2 main protease (Mpro) and RNA-dependent RNA polymerase (RdRp), and the human angiotensin-converting enzyme 2 (ACE2) using molecular docking and molecular dynamics simulations. The docking results showed that alkamides and dimeric piperamides from Piper species have a high binding affinity and potential antiviral activity against SARS-CoV-2. The absorption, distribution, metabolism, and excretion (ADME) profile and Lipinski's rule of five showed that dimeric piperamides have druglikeness potential. The molecular dynamics results showed that pipercyclobutanamide B forms a complex with Mpro at a similar level of stability than N3-I. Our overall results indicate that alkamides and piperamides, and specifically pipercyclobutanamide B, should be further studied as compounds with SARS-CoV-2 antiviral properties.


Subject(s)
Amides/pharmacology , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Benzodioxoles/pharmacology , Benzodioxoles/therapeutic use , Coronavirus Infections/drug therapy , Piper/chemistry , Piperidines/pharmacology , Piperidines/therapeutic use , Pneumonia, Viral/drug therapy , Amides/chemistry , Amides/therapeutic use , Angiotensin-Converting Enzyme 2 , Antiviral Agents/pharmacokinetics , Benzodioxoles/pharmacokinetics , Betacoronavirus/drug effects , COVID-19 , Coronavirus 3C Proteases , Cysteine Endopeptidases , Humans , Models, Molecular , Molecular Docking Simulation , Molecular Dynamics Simulation , Pandemics , Peptidyl-Dipeptidase A/drug effects , Piperidines/pharmacokinetics , SARS-CoV-2 , Viral Nonstructural Proteins/antagonists & inhibitors
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