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Ceddia G, Pinoli P, Ceri S, Masseroli M. Matrix Factorization-based Technique for Drug Repurposing Predictions. IEEE J Biomed Health Inform 2020; 24:3162-3172. [PMID: 32365039 DOI: 10.1109/jbhi.2020.2991763] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Classical drug design methodologies are hugely costly and time-consuming, with approximately 85% of the new proposed molecules failing in the first three phases of the FDA drug approval process. Thus, strategies to find alternative indications for already approved drugs that leverage computational methods are of crucial relevance. We previously demonstrated the efficacy of the Non-negative Matrix Tri-Factorization, a method that allows exploiting both data integration and machine learning, to infer novel indications for approved drugs. In this work, we present an innovative enhancement of the NMTF method that consists of a shortest-path evaluation of drug-protein pairs using the protein-to-protein interaction network. This approach allows inferring novel protein targets that were never considered as drug targets before, increasing the information fed to the NMTF method. Indeed, this novel advance enables the investigation of drug-centric predictions, simultaneously identifying therapeutic classes, protein targets and diseases associated with a particular drug. To test our methodology, we applied the NMTF and shortest-path enhancement methods to an outdated collection of data and compared the predictions against the most updated version, obtaining very good performance, with an Average Precision Score of 0.82. The data enhancement strategy allowed increasing the number of putative protein targets from 3,691 to 15,295, while the predictive performance of the method is slightly increased. Finally, we also validated our top-scored predictions according to the literature, finding relevant confirmation of predicted interactions between drugs and protein targets, as well as of predicted annotations between drugs and both therapeutic classes and diseases.
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Mitchelson FJ. The pharmacology of McN-A-343. Pharmacol Ther 2012; 135:216-45. [DOI: 10.1016/j.pharmthera.2012.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 05/07/2012] [Indexed: 01/01/2023]
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Abstract
Muscarinic agonists act mainly via muscarinic M₃ cholinoceptors to cause contraction of the iris sphincter, ciliary muscle and trabecular meshwork as well as increase outflow facility of aqueous humour. In the iris dilator, the effect of muscarinic agonists is species dependent but is predominantly relaxation via muscarinic M₃ receptors. In the conjunctiva, muscarinic agonists stimulate goblet cell secretion which contributes to the protective tear film. Muscarinic M₂ and M₃ receptors appear mainly involved. In the lens muscarinic agonists act via muscarinic M₁ receptors to produce depolarization and increase [Ca(2+)](i). All five subtypes of muscarinic receptor are present in the retina. In the developing retina, acetylcholine appears to limit purinergic stimulation of retinal development and decrease cell proliferation. In the adult retina acetylcholine and other muscarinic agonists may have complex effects, for example, enhancing light-evoked neuronal firing in transient ON retinal ganglion cells and inhibiting firing in OFF retinal ganglion cells. In the lacrimal gland, muscarinic agonists activate M₃ receptors on secretory globular acinar cells to stimulate tear secretion and also cause contraction of myoepithelial cells. In Sjögren's syndrome, antibodies to the muscarinic M₃ receptor disrupt normal gland function leading to xerophthalmia although the mechanism of action of the antibody is still not clear. Atropine and pirenzepine are useful in limiting the development of myopia in children probably by an action on muscarinic receptors in the sclera, although many other muscarinic receptor antagonists are not effective.
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Affiliation(s)
- Frederick Mitchelson
- Department of Pharmacology, University of Melbourne, Melbourne, VIC 3010, Australia.
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George N, Shiny PJ, Miriam J, Nancy CA, Dhanasekar KR, Peedicayil J. Inhibitory effect of anticholinergics on the contraction of isolated caprine urinary bladder detrusor muscle. ACTA ACUST UNITED AC 2010; 30:173-7. [DOI: 10.1111/j.1474-8673.2009.00447.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Storr M, Geisler F, Neuhuber WL, Schusdziarra V, Allescher HD. Endomorphin-1 and -2, endogenous ligands for the mu-opioid receptor, inhibit striated and smooth muscle contraction in the rat oesophagus. Neurogastroenterol Motil 2000; 12:441-8. [PMID: 11012944 DOI: 10.1046/j.1365-2982.2000.00220.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently, morphological evidence for an interaction of autonomic nerve fibres and extrinsic motor innervation of the rat oesophagus has emerged. The aim of the present study was to investigate the possible influence of endogenous and exogenous opioids on rat oesophageal smooth and striated muscle function in vitro. The entire oesophagus (excluding the lower oesophageal sphincter) with both Nervi (Nn) vagi, including the Nn recurrentes, was dissected and placed in an organ bath (100 mL, 37 degrees) with oxygenated Krebs-Ringer buffer. Contractile activity was measured in a longitudinal direction with a force transducer. Both Nn vagi were placed on a bipolar platinum electrode 2 cm distant from the oesophagus. Vagal stimulation (VS), applied for 1 s (40 V, 0.5 ms, 20 Hz) resulted in a biphasic contractile response that was completely blocked by 10(-6) M tetrodotoxin. The first part consisted of a tetanic striated muscle contraction, as it was abolished by tubocurarine (10(-5) M, n=5) but unaffected by atropine (10(-6) M, n=3) or hexamethonium (10(-4) M, n=4). In contrast, the second part was completely inhibited by hexamethonium (10(-4) M) and atropine (10(-6)M), whereas tubocurarine (10(-5) M) showed no influence, indicating a stimulation of preganglionic nerve fibres supplying oesophageal smooth muscle (muscularis mucosae) via relays in myenteric ganglia. In order to characterize opioid influence on the oesophageal striated and smooth muscle contractility, the following experiments were carried out. 10(-6) M endomorphin-1 and -2, endogenous mu-opioid-receptor agonists, reduced the contractile response of the striated (EM-2, -25.1+/-5.3%; n=16), and the smooth muscle (EM-2, -81.9+/-3.3%; n=11). Both effects were reversible by the opioid receptor antagonist naloxone (10(-6) M) and therefore, mediated via opioid receptors. Neither SNC-80, an agonist on the delta-opioid-receptor, U-69593, an agonist on the kappa-opioid-receptor, nor nociceptin, an agonist at the ORL1 (opioid receptor-like) receptor, had a significant effect on the striated muscle contraction. In contrast to SNC-80, U-69593 and nociceptin inhibited smooth muscle contraction but this relaxation could not be antagonized by naloxone. None of the opioid receptor antagonists used had an effect on basal tonus or muscle contraction following VS. Our data provide evidence for an autonomic modulation of vagal motor innervation of the striated and smooth oesophageal muscle. Endomorphin-1 and -2, both selective mu-opioid receptor agonists, cause an inhibition of striated and smooth muscle response which is reversible by naloxone, an opioid receptor antagonist. The location of the mu-opioid receptor still has to be established.
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Affiliation(s)
- M Storr
- GAP, Department of Internal Medicine II, Technical University Munich, FRG
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Coupar IM, Liu L. A simple method for measuring the effects of drugs on intestinal longitudinal and circular muscle. J Pharmacol Toxicol Methods 1996; 36:147-54. [PMID: 8959580 DOI: 10.1016/s1056-8719(96)00110-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A tissue preparation is described which makes it possible to examine the effect of drugs on the nerves that control both longitudinal and circular muscles of the small intestine. The preparation consists of a segment of rat ileum set up to measure the tension developed in the longitudinal muscle and intraluminal pressure developed by the circular muscle in response to transmural electrical stimulation. The method showed that both muscles differed in their patterns of responses to transmural stimulation from the threshold of 2.5-60 Hz. All responses were tetrodotoxin-sensitive, the fast longitudinal muscle contraction and the intraluminal pressure response being caused by both pre- and postganglionic cholinergic nerves. The responses differed in their sensitivities to the alpha 2-adrenoceptor agonists clonidine and UK 14,304, whereby the cholinergic responses of the circular but not longitudinal muscle were inhibited by the agonists. Comparison of results with the guinea-pig ileum set up in the same way revealed a marked species variation in responses, in that the intraluminal pressure response of the guinea-pig ileum was not sensitive to alpha 2-adrenoceptor agonists. This clear species difference makes it possible to use the circular muscle of the rat ileum, as measured indirectly via intraluminal pressure, to assess compounds for activity at alpha 2-adrenoceptors over a wide range of frequencies.
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Affiliation(s)
- I M Coupar
- Department of Pharmaceutical Biology and Pharmacology, Victorian College of Pharmacy, Monash University, Parkville, Australia
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Kerr KP, Stevenson JE, Mitchelson F. Simultaneous comparison of nicotinic receptor antagonists on three nicotinic acetylcholine receptors. J Pharm Pharmacol 1995; 47:1002-6. [PMID: 8932684 DOI: 10.1111/j.2042-7158.1995.tb03286.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The relative potencies of several nicotinic cholinoceptor antagonists in producing tetanic fade and reduction of striated muscle contraction were investigated in the isolated guinea-pig oesophagus as well as the guinea-pig and rat phrenic nerve-diaphragm preparations. Contractile smooth muscle responses to vagal stimulation, which involves ganglionic activation, were also measured simultaneously with striated muscle responses in the oesophagus. The relative potency for inhibiting the response of oesophageal smooth muscle to vagal stimulation (20 Hz) was trimetaphan > mecamylamine > hexamethonium > tubocurarine > pancuronium. For oesophageal striated muscle, production of tetanic fade at 100 Hz and reduction in peak tetanic tension at 20 or 100 Hz showed a similar relative potency; pancuronium > tubocurarine > mecamylamine > trimetaphan > hexamethonium and similar results were obtained in the guinea-pig diaphragm for the antagonists investigated (pancuronium, tubocurarine and mecamylamine). In the rat phrenic nerve-diaphragm preparation, production of tetanic fade at 50 Hz and reduction in twitch or tetanic tension all showed the relative potency; tubocurarine > pancuronium > mecamylamine > trimetaphan > hexamethonium. These findings indicate differences in the nicotinic cholinoceptor subtypes involved in vagal ganglionic responses and those in tetanic fade.
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Affiliation(s)
- K P Kerr
- Victorian College of Pharmacy, Monash University, School of Pharmacology, Parkville, Victoria, Australia
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Kerr KP, Mitchelson F, Coupar IM. Vagal nerve stimulation of the guinea-pig oesophagus. ACTA PHYSIOLOGICA SCANDINAVICA 1995; 154:213-20. [PMID: 7572217 DOI: 10.1111/j.1748-1716.1995.tb09903.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Vagal nerve stimulation of the isolated guinea-pig oesophagus resulted in a triphasic contractile response which was abolished by tetrodotoxin. The mechanisms for each of the three responses were investigated. The first response was abolished by the neuromuscular blocking drug, tubocurarine, and was unaffected by atropine. The second response to vagal nerve stimulation was abolished by the ganglion blocking drug, hexamethonium, and by tubocurarine at a higher concentration than that required to block the first response. The second response was also abolished by atropine and was enhanced by physostigmine. It was concluded that this response was due to preganglionic stimulation of smooth muscle. omega-Conotoxin GVIA selectively inhibited the third response. This response was resistant to the neuromuscular and ganglion blocking drugs yet was abolished by atropine and was enhanced by physostigmine. This implicates the involvement of cholinergic neurones activated independently of nicotinic ganglionic receptors. The third response was also selectively abolished by capsaicin and enhanced by thiorphan. Contractile responses resulting from exogenous substance P were abolished by atropine and tetrodotoxin and enhanced by physostigmine. These findings suggest that the third response may be mediated by the action of a substance P-like neuropeptide released from sensory nerve endings which subsequently activate cholinergic neurones.
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Affiliation(s)
- K P Kerr
- School of Pharmacology, Victorian College of Pharmacy, Monash University, Australia
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Choo LK, Mitchelson F. Selective inhibition of responses to carbachol and McN-A-343 in the rabbit vas deferens. Clin Exp Pharmacol Physiol 1990; 17:601-11. [PMID: 1703935 DOI: 10.1111/j.1440-1681.1990.tb01361.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
1. The effect of several selective muscarine receptor antagonists were evaluated on the responses of carbachol (CCh) and McN-A-343 (McN) during sympathetic nerve stimulation in the rabbit vas deferens. 2. The muscarine M1 receptor antagonist pirenzepine exhibited similar apparent pKB values for antagonism of the prejunctional inhibitory response of either CCh (pKB, 8.2) or McN (pKB, 8.5) on sympathetic nerve stimulation. 3. The muscarine M2 receptor antagonists, pancuronium and the bisalkyl ammonium compound 'C7/3-phth' were selective inhibitors of the postjunctional facilitatory response produced by CCh on sympathetic nerve stimulation. They were also 17- and three-fold, respectively, less potent against the inhibitory responses of McN on sympathetic nerve stimulation. The apparent pKB value of pancuronium on the inhibitory response produced by CCh did not differ significantly (P greater than 0.05) from that using McN. A similar finding was made for C7/3-phth. 4. Selective blockade of the inhibitory response to CCh with pirenzepine (0.03 or 0.5 mumol/L) did not significantly (P greater than 0.05) modify the apparent pKB value for pancuronium on the facilitatory response of CCh. 5. Selective blockade of the facilitatory response to CCh with a low concentration of pancuronium (0.5 mumol/L) did not significantly (P greater than 0.05) modify the apparent pKB value for pancuronium (30 mumol/L) on the inhibitory response of CCh. 6. It is suggested that CCh and McN activate the same prejunctional M1 muscarine receptor and that pancuronium is the most selective of the muscarine M2 receptor antagonists presently tested in this preparation for distinguishing between muscarine M1 and M2 receptors.
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Affiliation(s)
- L K Choo
- School of Pharmacology, Victorian College of Pharmacy, Parkville, Australia
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Eglen RM, Michel AD, Cornett CM, Kunysz EA, Whiting RL. The interaction of hexamethonium with muscarinic receptor subtypes in vitro. Br J Pharmacol 1989; 98:499-506. [PMID: 2819331 PMCID: PMC1854706 DOI: 10.1111/j.1476-5381.1989.tb12623.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
1. The action of hexamethonium has been studied at a range of muscarinic receptors in vitro by use of both functional and radioligand binding studies. 2. In functional studies, hexamethonium exhibited little or no significant (P less than 0.05) antagonism of contractile responses to carbachol at muscarinic receptors in the guinea-pig ileum, oesophageal muscularis mucosae, urinary bladder and trachea. However, antagonism was observed at muscarinic receptors in the guinea-pig left atria mediating negative inotropic responses and the calculated pKB value was 3.80. Hexamethonium also antagonized contractile responses to carbachol in the canine saphenous vein. The pKB value at these receptors was 3.75. 3. In the presence of 3.2 mM hexamethonium, the pA2 value for methoctramine at atrial muscarinic receptors was reduced by approximately 10 fold (control pA2 value was 7.81 +/- 0.05; pA2 value in hexamethonium was 6.73 +/- 0.04). In contrast at tracheal muscarinic receptors, the pA2 values for methoctramine were unaffected in the presence of 3.2 mM hexamethonium (control pA2 = 5.58 +/- 0.07; pA2 value in hexamethonium was 5.63 +/- 0.12). All values quoted are mean +/- s.e. mean, n = 8. 4. In competition radioligand binding studies, hexamethonium exhibited a higher affinity for cardiac M2 receptors (pKi = 3.68) than for cerebrocortical M1 receptors (pKi = 3.28) or for submaxillary gland M3 receptors (pKi = 2.61). At M2 receptors hexamethonium at concentrations of 0.1-10 mM, increased the half life of the dissociation rate of [3H]-N-methylscopolamine 1.6-4.3 fold. This was observed at M3 receptors only at 10 mM, when the half life was increased 1.7 fold. 5. We conclude that hexamethonium, in addition to its well characterized nicotinic antagonist properties, can act as a weak muscarinic antagonist and differentiates between cardiac M2 receptors and glandular/smooth muscle M3 receptors. However, hexamethonium differentiates less clearly between M1 and M2 receptors. The selectivity between M2 and M3 receptors observed in the present study with hexamethonium is comparable to other M2 selective antagonists such as AF-DX 116 and himbacine. 6. Caution should be exercised with regard to the inclusion of hexamethonium in functionsal studies of M2 muscarinic receptor subtypes at concentrations of 0.1 mm and above.
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Affiliation(s)
- R M Eglen
- Institute of Pharmacology, Syntex Research, Palo Alto, CA 94303
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Eglen RM, Montgomery WW, Dainty IA, Dubuque LK, Whiting RL. The interaction of methoctramine and himbacine at atrial, smooth muscle and endothelial muscarinic receptors in vitro. Br J Pharmacol 1988; 95:1031-8. [PMID: 3219478 PMCID: PMC1854290 DOI: 10.1111/j.1476-5381.1988.tb11736.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
1. The action of methoctramine and himbacine at muscarinic receptors has been studied using guinea-pig isolated trachea, oesophageal muscularis mucosae, paced left atria, and rat aortic preparations. 2. Methoctramine (1 x 10(-6)-3.2 x 10(-4) M), but not himbacine, elicited positive inotropic responses. These responses were enhanced by pretreating the animals with reserpine. The responses in reserpine-treated animals were not antagonized by phentolamine (1 x 10(-6) M) but were antagonized by propranolol (1 x 10(-6) M). 3. Methoctramine, but not himbacine, exhibited allosteric inhibitory effects at cardiac muscarinic receptors, resulting in a curvilinear Schild plot. Deviations from competitive antagonism were also observed in combination dose-ratio experiments using atropine and methoctramine. At 1 x 10(-6) M, the pKB value for methoctramine was 7.88 +/- 0.15 (mean +/- s.e.mean, n = 5). The pA2 value for himbacine at cardiac muscarinic receptors was 8.52 +/- 0.06 (n = 3). 4. At tracheal and oesophageal muscularis mucosal smooth muscle receptors, the Schild plots for both antagonists were linear. The pA2 values for methoctramine at receptors in these two preparations were similar (6.08 +/- 0.05 and 6.03 +/- 0.09 respectively, n = 4) and were approximately 60 fold less than those values observed at atrial receptors. Himbacine, also exhibited similar values at muscarinic receptors in the trachea and oesophageal muscularis mucosae (7.61 +/- 0.05 and 7.57 +/- 0.04 respectively, n = 4). 5. Muscarinic receptors mediating relaxation of the rat aortic endothelium exhibited pA2 values for methoctramine (5.87 +/- 0.12, n = 6) which were similar to those observed in the smooth muscle, but not the atria. The pA2 values for himbacine at endothelial muscarinic receptors were approximately 0.5 pA2 units lower than those observed at muscarinic receptors in smooth muscle (6.92 + 0.80, n = 6). In addition, the Schild slopes for methoctramine and himbacine at these receptors were significantly (P < 0.05) less than unity. 6. Methoctramine, and to a lesser extent himbacine, are potent and selective antagonists for cardiac muscarinic receptors. However, caution should be used in interpretation of the data with methoctramine in view of the inhibitory allosteric properties and direct inotropic actions of this compound.
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Affiliation(s)
- R M Eglen
- Institute of Pharmacology, Syntex Research, Palo Alto, CA 94304
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Affiliation(s)
- F Mitchelson
- School of Pharmacology, Victorian College of Pharmacy, Melbourne, Australia
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