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Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays. Methods 2021; 195:57-71. [PMID: 33453392 PMCID: PMC7807167 DOI: 10.1016/j.ymeth.2021.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/10/2021] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2'-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = 5903). The screening was performed against viral targets using three sequential docking modes (i.e., HTVS, SP, and XP). Virtual screening identified ∼290 potential inhibitors based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. The resulting top eight hits were tested for their SARS-CoV-2 anti-viral activity in-vitro. Among these, a known inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), was found to be a potent inhibitor of SARS-CoV-2. Further, target validation through enzymatic assays confirmed 3CLpro to be the target. This is the first study that has showcased BIM IX as a COVID-19 inhibitor thereby validating our pipeline.
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Haick JM, Brueggemann LI, Cribbs LL, Denning MF, Schwartz J, Byron KL. PKC-dependent regulation of Kv7.5 channels by the bronchoconstrictor histamine in human airway smooth muscle cells. Am J Physiol Lung Cell Mol Physiol 2017; 312:L822-L834. [PMID: 28283479 DOI: 10.1152/ajplung.00567.2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/23/2017] [Accepted: 03/07/2017] [Indexed: 12/13/2022] Open
Abstract
Kv7 potassium channels have recently been found to be expressed and functionally important for relaxation of airway smooth muscle. Previous research suggests that native Kv7 currents are inhibited following treatment of freshly isolated airway smooth muscle cells with bronchoconstrictor agonists, and in intact airways inhibition of Kv7 channels is sufficient to induce bronchiolar constriction. However, the mechanism by which Kv7 currents are inhibited by bronchoconstrictor agonists has yet to be elucidated. In the present study, native Kv7 currents in cultured human trachealis smooth muscle cells (HTSMCs) were observed to be inhibited upon treatment with histamine; inhibition of Kv7 currents was associated with membrane depolarization and an increase in cytosolic Ca2+ ([Ca2+]cyt). The latter response was inhibited by verapamil, a blocker of L-type voltage-sensitive Ca2+ channels (VSCCs). Protein kinase C (PKC) has been implicated as a mediator of bronchoconstrictor actions, although the targets of PKC are not clearly established. We found that histamine treatment significantly and dose-dependently suppressed currents through overexpressed wild-type human Kv7.5 (hKv7.5) channels in cultured HTSMCs, and this effect was inhibited by the PKC inhibitor Ro-31-8220 (3 µM). The PKC-dependent suppression of hKv7.5 currents corresponded with a PKC-dependent increase in hKv7.5 channel phosphorylation. Knocking down or inhibiting PKCα, or mutating hKv7.5 serine 441 to alanine, abolished the inhibitory effects of histamine on hKv7.5 currents. These findings provide the first evidence linking PKC activation to suppression of Kv7 currents, membrane depolarization, and Ca2+ influx via L-type VSCCs as a mechanism for histamine-induced bronchoconstriction.
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Affiliation(s)
- Jennifer M Haick
- Department of Molecular Pharmacology and Therapeutics, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Lioubov I Brueggemann
- Department of Molecular Pharmacology and Therapeutics, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Leanne L Cribbs
- Department of Cell & Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Mitchell F Denning
- Department of Pathology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and
| | - Jeffrey Schwartz
- Department of Thoracic and Cardiovascular Surgery, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Kenneth L Byron
- Department of Molecular Pharmacology and Therapeutics, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois;
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Elmedal B, Mulvany MJ, Simonsen U. Dual impact of a nitric oxide donor, GEA 3175, in human pulmonary smooth muscle. Eur J Pharmacol 2005; 516:78-84. [PMID: 15899479 DOI: 10.1016/j.ejphar.2005.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 04/05/2005] [Accepted: 04/11/2005] [Indexed: 11/25/2022]
Abstract
Nitric oxide (NO) donors could constitute an alternative to inhaled NO as treatment in some patients with pulmonary hypertension. Therefore, the present study investigated the relaxation mechanisms of a novel NO donor, 3-(3-chloro-2-methylphenyl)-5-[[4-methylphenyl)sulphonyl]amino]-)hydroxide (GEA 3175) in segments of human pulmonary arteries and bronchioles, which were mounted in microvascular myographs. GEA 3175 induced concentration-dependent relaxations and was more potent in pulmonary arteries than in bronchioles. A blocker of soluble guanylyl cyclase, 1H-[1,2,4]oxadiazolo[4,3,-a]quinoxalin-1-one (ODQ), and iberiotoxin, a blocker of large-conductance calcium-activated K channels, both reduced relaxations induced by GEA 3175 in pulmonary arteries and bronchioles. Combining of ODQ and iberiotoxin did not produce additional inhibition. GEA 3175 relaxation is mediated through guanylyl cyclase-dependent mechanisms followed by activation of large-conductance calcium-activated K(+) channels. The dilatation of both pulmonary small arteries and airways by GEA 3175 seems advantageous, if it is considered administered as inhalation therapy for pulmonary hypertension.
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Affiliation(s)
- Britt Elmedal
- Department of Pharmacology, University of Aarhus, 8000 Aarhus C, Denmark
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Moir LM, Leung SY, Eynott PR, McVicker CG, Ward JPT, Chung KF, Hirst SJ. Repeated allergen inhalation induces phenotypic modulation of smooth muscle in bronchioles of sensitized rats. Am J Physiol Lung Cell Mol Physiol 2003; 284:L148-59. [PMID: 12388362 DOI: 10.1152/ajplung.00105.2002] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Repeated ovalbumin (OA) or saline exposure of sensitized Brown Norway rats was examined on agonist reactivity, airway smooth muscle (ASM) content, and contractile protein expression in small bronchioles at 24 h, 7 days, and 35 days after challenge. OA increased ASM content (P < 0.05 vs. saline) at 24 h, which resolved by 7 days. Maximum developed tension (T(max)) to carbachol, KCl, and 4-beta-phorbol 12,13-dibutyrate was increased (P < 0.05) by OA in bronchioles at 24 h but was abrogated after correction for ASM. Differences in T(max) were not present at 7 days. In contrast, at 35 days, T(max) was increased (P < 0.05) after correction for ASM. Smooth muscle (sm)-alpha-actin, sm-myosin heavy chain (MHC) isoform 1, calponin, smoothelin-A, and sm-myosin light chain kinase expression were reduced (P < 0.05) by OA at 24 h in bronchioles but not in trachealis. Consistent with contraction findings, no difference in expression of these proteins was detected at 7 days. At 35 days, however, with the exception of sm-alpha-actin, their abundance was again reduced (P < 0.05) by OA. Nonmuscle MHC and beta-actin were unchanged throughout by OA. These findings indicate persistent changes in contractile protein content, consistent with ASM phenotypic modulation in vivo, which occur in response to repeated OA inhalation. Thus, OA exposure induces structural changes in bronchiole ASM content and in agonist responsiveness ex vivo that resemble remodeling in asthma.
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Affiliation(s)
- Lyn M Moir
- Department of Asthma, Allergy and Respiratory Science, The Guy's, King's and St. Thomas' School of Medicine, King's College London, London SE1 9RT, UK
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Snetkov VA, Hapgood KJ, McVicker CG, Lee TH, Ward JP. Mechanisms of leukotriene D4-induced constriction in human small bronchioles. Br J Pharmacol 2001; 133:243-52. [PMID: 11350860 PMCID: PMC1572783 DOI: 10.1038/sj.bjp.0704076] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We examined the mechanisms underlying leukotriene D4- (LTD4) induced constriction of human small (300 - 500 micron i.d.) bronchioles, and the effect of LTD4 on ion currents and Ca2+ transients in smooth muscle cells (SMC) isolated from these bronchioles. LTD4 caused a concentration-dependent bronchoconstriction with an EC50=0.58+/-0.05 nM (n=7) which was not easily reversible upon washout. This bronchoconstriction was entirely dependent on extracellular Ca2+. Blockade of L-type Ca2+ channels with nifedipine (10 microM) reduced LTD4 response by 39+/-2% (n=8), whilst La3+, Gd3+ and SK&F 96,365 abolished LTD4-induced bronchoconstriction completely and reversibly, suggesting the majority of Ca2+ entry was via non-selective cation channels. Antagonists of PI-PLC (U73,122 and ET-18-OCH3), PLD (propranolol) and PKC (cheleretrine and Ro31-8220) were without any effect on LTD4-induced bronchoconstriction, whilst the PC-PLC inhibitor D609 caused complete relaxation. Inhibition of protein tyrosine kinase with tyrphostin A23 (100 microM) caused about 50% relaxation, although the inactive analogue tyrphostin A1 was without effect. In freshly isolated SMC from human small bronchioles LTD4 caused a slow increase of intracellular Ca2+ concentration, with a consequent rise of the activity of large conductance Ca2+-dependent K+ channels and the amplitude of depolarization-induced outward whole-cell current. Again, no effect of LTD4 could be observed in the absence of extracellular Ca2+. We conclude that LTD4 causes constriction of these small bronchioles primarily by activating Ca2+ entry via non-voltage gated channels, possibly by a PC-PLC mediated pathway.
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Affiliation(s)
- V A Snetkov
- Department of Respiratory Medicine and Allergy, Guy's, King's and St Thomas' School of Medicine, King's College London, Guy's Campus, London SE1 9RT.
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Webb BLJ, Hirst SJ, Giembycz MA. Protein kinase C isoenzymes: a review of their structure, regulation and role in regulating airways smooth muscle tone and mitogenesis. Br J Pharmacol 2000; 130:1433-52. [PMID: 10928943 PMCID: PMC1572212 DOI: 10.1038/sj.bjp.0703452] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2000] [Revised: 04/06/2000] [Accepted: 05/03/2000] [Indexed: 12/14/2022] Open
Affiliation(s)
- Benjamin L J Webb
- Protein Phosphorylation Laboratory, Imperial Cancer Research Fund, 44 Lincoln' Inn Fields, London, WC2A 3PX
| | - Stuart J Hirst
- Department of Respiratory Medicine & Allergy, King' College London, 5th Floor Thomas Guy House, GKT School of Medicine, Guy' Campus, London, SE1 9RT
| | - Mark A Giembycz
- Thoracic Medicine, Imperial College School of Medicine at the National Heart and Lung Institute, Dovehouse Street, London, SW3 6LY
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Van de Voorde J, Joos G. Regionally different influence of contractile agonists on isolated rat airway segments. RESPIRATION PHYSIOLOGY 1998; 112:185-94. [PMID: 9716302 DOI: 10.1016/s0034-5687(98)00031-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rats are increasingly used to study airway inflammation and bronchial responsiveness. Relative little is known on the contribution of small airways in this animal model. We therefore compared the responsiveness to various inflammatory agents of isolated trachea, main bronchi (using classic organ bath) and isolated bronchioles (using small myograph) from Wistar and Fisher 344 rats. The largest contraction was elicited on all preparations by carbachol. Histamine elicited a (small) contraction only on bronchioles. The contractions elicited by serotonin, bradykinin, and the thromboxane A2-mimetic U-46619 were always relatively larger in bronchioles than in trachea and main bronchi. The sensitivities to carbachol and serotonin were smaller in bronchioles. The tachykinins substance P and neurokinin A elicited no substantial contraction on bronchioles or main bronchi. Trachea of Fisher 344 but not of Wistar rats showed a small contraction. No other differences were found between preparations from Wistar and Fisher 344 rats. It is concluded that rat trachea, main bronchi and small bronchioles show regional and strain-dependent variations in their responsiveness to contractile agents.
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Affiliation(s)
- J Van de Voorde
- Department of Physiology and Human Pathophysiology, University of Gent, Belgium.
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Webb BL, Lindsay MA, Barnes PJ, Giembycz MA. Protein kinase C isoenzymes in airway smooth muscle. Biochem J 1997; 324 ( Pt 1):167-75. [PMID: 9164853 PMCID: PMC1218413 DOI: 10.1042/bj3240167] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The protein kinase C (PKC) isoenzymes expressed by bovine tracheal smooth muscle (BTSM) were identified at the protein and mRNA levels. Western immunoblot analyses reliably identified PKCalpha, PKCbetaI and PKCbetaII. In some experiments immunoreactive bands corresponding to PKCdelta, PKCepsilon and PKCTheta were also labelled, whereas the gamma, eta and zeta isoforms of PKC were never detected. Reverse transcriptase PCR of RNA extracted from BTSM using oligonucleotide primer pairs designed to recognize unique sequences in the PKC genes for which protein was absent or not reproducibly identified by immunoblotting, amplified cDNA fragments that corresponded to the predicted sizes of PKCdelta, PKCepsilon and PKCzeta, which was confirmed by Southern blotting. Anion-exchange chromatography of the soluble fraction of BTSM following homogenization in Ca2+-free buffer resolved two major peaks of activity. Using epsilon-peptide as the substrate, the first peak of activity was dependent upon Ca2+ and 4beta-PDBu (PDBu=phorbol 12, 13-dibutyrate), and represented a mixture of PKCs alpha, betaI and betaII. In contrast, the second peak of activity, which eluted at much higher ionic strength, also appeared to comprise a combination of conventional PKCs that were arbitrarily denoted PKCalpha', PKCbetaI' and PKCbetaII'. However, these novel enzymes were cofactor-independent and did not bind [3H]PDBu, but were equally sensitive to the PKC inhibitor GF 109203X compared with bona fide conventional PKCs, and migrated on SDS/polyacrylamide gels as 81 kDa polypeptides. Taken together, these data suggest that PKCs alpha', betaI' and betaII' represent modified, but not proteolysed, forms of their respective native enzymes that retain antibody immunoreactivity and sensitivity to PKC inhibitors, but have lost their sensitivity to Ca2+ and PDBu when epsilon-peptide is used as the substrate.
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Affiliation(s)
- B L Webb
- Thoracic Medicine, Imperial College School of Medicine at the National Heart and Lung Institute, Dovehouse Street, London SW3 6LY, U.K
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Dumont EC, Lambert C, Lamontagne D. Modification of aortic contractility in the cardiomyopathic hamster. Br J Pharmacol 1996; 118:1141-6. [PMID: 8818336 PMCID: PMC1909589 DOI: 10.1111/j.1476-5381.1996.tb15516.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
1. The functional arterial response in the cardiomyopathic hamster compared with inbred control, was investigated in thoracic aortae. For this purpose, vessels were cut into 6-mm rings and mounted in 20-ml organ baths. 2. In a first experimental series, the function of the endothelium was evaluated. Dose-response curves to acetylcholine (0.1 nM-10 microM) on phenylephrine (0.3 microM)-preconstricted rings of cardiomyopathic hamsters and inbred age-matched controls were comparable (log[EC50] of -7.08 +/- 0.12 and -7.18 +/- 0.12, respectively; n = 4). 3. Changes in contractility of cardiomyopathic hamster endothelium-denuded aortae were investigated. Dose-response curves to phenylephrine (1 nM-0.1 mM), angiotensin II (10 pM-0.3 microM), 5-hydroxytryptamine (5-HT) (1 nM-0.1 mM) and KCl (1 mM-0.1 M) were performed. Increased sensitivity in cardiomyopathic hamster aortae, compared to controls, was observed with phenylephrine (log[EC50] of -7.25 +/- 0.05 and -6.83 +/- 0.05, respectively, n = 6, P < 0.001) and angiotensin II (log[EC50] of -8.67 +/- 0.07 and -8.26 +/- 0.06, respectively, n = 6, P = 0.001) but not with 5-HT or KCl. A decreased maximum response in cardiomyopathic, compared to control, was observed with 5-HT (1.28 +/- 0.06 g vs 1.56 +/- 0.07 g, respectively, n = 6, P = 0.03). Comparable results were found in aortae with an intact endothelium. 4. No difference in the maximum contractile response to the G-protein activator, NaF (3, 10 and 30 mM) was observed in either group of animals. 5. Phorbol 12-myristate 13-acetate (PMA, 1-10 microM) was used to assess changes in the activity of protein kinase C (PKC). Contractility to PMA was increased in cardiomyopathic hamster aortae compared to controls (0.22 +/- 0.02 g vs 0.07 +/- 0.03 g at 3 microM, respectively, n = 6, P = 0.003). 6. Finally, cardiomyopathic hamsters aortae were found to be less sensitive when exposed to increasing concentrations of Ca2+ (10 microM-1 mM) in KCl-depolarized rings (0.58 +/- 0.04 g in cardiomyopathic vs 0.79 +/- 0.06 g in control aortae at 0.3 mM, n = 8, P = 0.03). 7. In conclusion, aortae from cardiomyopathic hamsters are more sensitive to phenylephrine and angiotensin II, but not to 5-HT, than those of controls. The increase in sensitivity does not implicate Ca2+ channels or Ca2+ itself since cardiomyopathic hamsters aortae are not more sensitive to KCl- and Ca(2+)-induced contraction. The greater effect of PMA on cardiomyopathic hamster aortae suggests that the increase in sensitivity to phenylephrine and angiotensin II involves an enhanced activity of PKC.
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Affiliation(s)
- E C Dumont
- Faculté de pharmacie, Université de Montréal, Québec, Canada
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