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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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Patai Z, Guttman A, Mikus EG. Assessment of the Airway Smooth Muscle Relaxant Effect of Drotaverine. Pharmacology 2018; 101:163-169. [PMID: 29301136 DOI: 10.1159/000485921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/29/2017] [Indexed: 11/19/2022]
Abstract
BACKGROUND Drotaverine, a type 4 cyclic nucleotide phosphodiesterase (PDE4) inhibitor, blocks the degradation of 3',5'-cyclic adenosine monophosphate. However, published receptor binding data showed that drotaverin also binds to the L-type voltage-operated calcium channel (L-VOCC). Based on these molecular mechanisms of action, a direct and indirect (by blocking the constrictor response) relaxant effect on airway smooth muscle can be predicted, which has not yet been assessed. SUMMARY Accordingly, drotaverine and reference agents were tested both on the histamine-, methacholine-, or KCl-induced contraction response and on precontracted guinea pig tracheal preparations. It was found that drotaverine not only relaxed the precontracted tracheal preparations but also decreased mediator-induced contraction. These effects of drotaverine were concentration dependent, with a significantly higher potency on the KCl-induced response, than on either the histamine or methacholine induced one. A similar result was noted for nifedipine. The PDE inhibitor, theophylline, also relaxed the precontracted preparations but was ineffective on the mediator-induced contraction in a physiologically relevant concentration range. Moreover, theophylline did not show selectivity and was the least potent relaxant among the 3 tested molecules. Key Message: These results show that drotaverine is a more potent airway smooth muscle relaxant molecule than theophylline. This enhanced potency on relaxation and inhibition of the constrictor response, at least partly, may be explained by the combined L-VOCC blocking and PDE inhibitory potential of drotaverine.
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Affiliation(s)
- Zoltán Patai
- LabMagister Training and Science Ltd., Budapest, Hungary.,Horvath Csaba Laboratory of Bioseparation Sciences, MMKK, University of Debrecen, Debrecen, Hungary
| | - András Guttman
- Horvath Csaba Laboratory of Bioseparation Sciences, MMKK, University of Debrecen, Debrecen, Hungary.,MTA-PA Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprém, Hungary
| | - Endre G Mikus
- LabMagister Training and Science Ltd., Budapest, Hungary
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Patai Z, Guttman A, Mikus EG. Potential L-Type Voltage-Operated Calcium Channel Blocking Effect of Drotaverine on Functional Models. J Pharmacol Exp Ther 2016; 359:442-451. [PMID: 27738091 DOI: 10.1124/jpet.116.237271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/12/2016] [Indexed: 11/22/2022] Open
Abstract
Drotaverine is considered an inhibitor of cyclic-3',5'-nucleotide-phophodiesterase (PDE) enzymes; however, published receptor binding data also support the potential L-type voltage- operated calcium channel (L-VOCC) blocking effect of drotaverine. Hence, in this work, we focus on the potential L-VOCC blocking effect of drotaverine by using L-VOCC-associated functional in vitro models. Accordingly, drotaverine and reference agents were tested on KCl-induced guinea pig tracheal contraction. Drotaverine, like the L-VOCC blockers nifedipine or diltiazem, inhibited the KCl-induced inward Ca2+- induced contraction in a concentration- dependent fashion. The PDE inhibitor theophylline had no effect on the KCl-evoked contractions, indicating its lack of inhibition on inward Ca2+ flow. Drotaverine was also tested on the L-VOCC-mediated resting Ca2+ refill model. In this model, the extracellular Ca2+ enters the cells to replenish the emptied intracellular Ca2+ stores. Drotaverine and L-VOCC blocker reference molecules inhibited Ca2+ replenishment of Ca2+-depleted preparations detected by agonist-induced contractions in post-Ca2+ replenishment Ca2+-free medium. Theophylline did not modify the Ca2+ store replenishment after contraction. It seems that drotaverine, but not theophylline, inhibits inward Ca2+ flux. The addition of CaCl2 to Ca2+-free medium containing the agonist induced inward Ca2+ flow and subsequent contraction of Ca2+-depleted tracheal preparations. Drotaverine, similar to the L-VOCC blockers, inhibited inward Ca2+ flow and blunted the slope of CaCl2-induced contraction in agonist containing Ca2+-free medium with Ca2+-depleted tracheal preparations. These results show that drotaverine behaves like L-VOCC blockers but, unlike PDE inhibitors using L-VOCC associated in vitro experimental models.
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Affiliation(s)
- Zoltán Patai
- LabMagister Training and Science Ltd. Budapest, Hungary (Z.P., E.G.M.), Horvath Csaba Laboratory of Bioseparation Sciences, MMKK, University of Debrecen, Debrecen, Hungary (Z.P., A.G.), MTA-PA Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary (A.G.)
| | - András Guttman
- LabMagister Training and Science Ltd. Budapest, Hungary (Z.P., E.G.M.), Horvath Csaba Laboratory of Bioseparation Sciences, MMKK, University of Debrecen, Debrecen, Hungary (Z.P., A.G.), MTA-PA Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary (A.G.)
| | - Endre G Mikus
- LabMagister Training and Science Ltd. Budapest, Hungary (Z.P., E.G.M.), Horvath Csaba Laboratory of Bioseparation Sciences, MMKK, University of Debrecen, Debrecen, Hungary (Z.P., A.G.), MTA-PA Translational Glycomics Research Group, MUKKI, University of Pannonia, Veszprem, Hungary (A.G.)
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Kurek M, Żądzińska E, Sitek A, Borowska-Strugińska B, Rosset I, Lorkiewicz W. Prenatal factors associated with the neonatal line thickness in human deciduous incisors. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2014; 66:251-63. [PMID: 25618810 DOI: 10.1016/j.jchb.2014.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 11/30/2014] [Indexed: 01/10/2023]
Abstract
The neonatal line (NNL) is used to distinguish developmental events observed in enamel which occurred before and after birth. However, there are few studies reporting relationship between the characteristics of the NNL and factors affecting prenatal conditions. The aim of the study was to determine prenatal factors that may influence the NNL thickness in human deciduous teeth. The material consisted of longitudinal ground sections of 60 modern human deciduous incisors obtained from full-term healthy children with reported birth histories and prenatal factors. All teeth were sectioned in the labio-lingual plane using diamond blade (Buechler IsoMet 1000). Final specimens were observed using scanning electron microscopy at magnifications 320×. For each tooth, linear measurements of the NNL thickness were taken on its labial surface at the three levels from the cemento-enamel junction. The difference in the neonatal line thickness between tooth types and between males and females was statistically significant. A multiple regression analyses confirmed influence of two variables on the NNL thickness standardised on tooth type and the children's sex (z-score values). These variables are the taking of an antispasmodic medicine by the mother during pregnancy and the season of the child's birth. These two variables together explain nearly 17% of the variability of the NNL. Children of mothers taking a spasmolytic medicine during pregnancy were characterised by a thinner NNL compared with children whose mothers did not take such medication. Children born in summer and spring had a thinner NNL than children born in winter. These results indicate that the prenatal environment significantly contributes to the thickness of the NNL influencing the pace of reaching the post-delivery homeostasis by the newborn's organism.
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Affiliation(s)
- M Kurek
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland.
| | - E Żądzińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - A Sitek
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - B Borowska-Strugińska
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - I Rosset
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - W Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
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Thummala VRR, Tharlapu SSJM, Rekulapalli VK, Ivaturi MR, Nittala SR. Development and Validation of a Stability-Indicating RP-HPLC Method for the Estimation of Drotaverine Impurities in API and Pharmaceutical Formulation. Sci Pharm 2014; 82:99-115. [PMID: 24634845 PMCID: PMC3951236 DOI: 10.3797/scipharm.1309-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/21/2013] [Indexed: 11/22/2022] Open
Abstract
A sensitive, stability-indicating gradient RP-HPLC method with PDA detection has been developed for the simultaneous analysis of drotaverine impurities in active pharmaceutical ingredient (API) and pharmaceutical formulations. Efficient chromatographic separation was achieved on an XTerra RP18, 150 × 4.6 mm, 5 μm column using gradient elution at 230 nm detection wavelength. The optimized mobile phase consisted of a 0.02 M potassium dihydrogen orthophosphate buffer of pH 3.0 as solvent A and acetonitrile as solvent B. The flow rate of the mobile phase was 1.0 mL min(-1) with a column temperature of 25°C. The method showed linearity over the range of 0.251-10.033 μg/mL, 0.231-9.995 μg/mL, 0.230-10.089 μg/mL, 0.334-10.011 μg/mL, and 0.324-10.050 μg/mL for impurities 1, 2, 3, 4, and drotaverine, respectively, with a correlation coefficient greater than 0.999. The relative retention times and relative response factors of impurities 1, 2, 3, 4 were 0.36, 0.90, 1.42, 1.55 and 1.04, 0.84, 1.10, 1.30, respectively. The drotaverine formulation sample was subjected to the stress conditions of acid, base, oxidative, thermal, humidity, and photolytic degradation. Drotaverine was found to degrade significantly in peroxide, base, and heat stress conditions. The degradation products were well-resolved from drotaverine and its impurities. The peak purity test results confirmed that the drotaverine peak was homogenous and pure in all stress samples and the mass balance was found to be more than 98%, thus proving the stability-indicating power of the method. The developed method was validated according to ICH guidelines with respect to specificity, linearity, limit of detection and quantification, accuracy, precision, and robustness.
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Affiliation(s)
- Veera Raghava Raju Thummala
- Analytical Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Bachupally, Hyderabad-500 072, India
| | | | - Vijay Kumar Rekulapalli
- Analytical Research and Development, Integrated Product Development, Dr. Reddy’s Laboratories Ltd., Bachupally, Hyderabad-500 072, India
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The effect of the season of birth and of selected maternal factors on linear enamel thickness in modern human deciduous incisors. Arch Oral Biol 2013; 58:951-63. [PMID: 23583018 DOI: 10.1016/j.archoralbio.2013.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/18/2013] [Accepted: 03/04/2013] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Development of human tooth enamel is a part of a foetus's development; its correctness is the outcome of genetic and maternal factors shaping its prenatal environment. Many authors reported that individuals born in different seasons experience different early developmental conditions during pregnancy. In this study, we investigated the effects of season of birth and selected maternal factors on enamel thickness of deciduous incisors. DESIGN Dental sample comprises 60 deciduous incisors. The parents who handed over their children's teeth for research fill in questionnaires containing questions about the course of pregnancy. All teeth were sectioned in the labio-linqual plane using diamond blade (Buechler IsoMet 1000). The final specimens were observed by way of scanning electron microscopy at magnifications 80× and 320×. The thickness of total enamel (TE), prenatally (PE) and postnatally (PSE) formed enamel was measured. RESULTS Children born in summer and in spring (whose first and second foetal life fall on autumn and winter) have the thinnest enamel. Season of birth, number of children in family, diseases and spasmolytic medicines using by mother during pregnancy explained almost 13% of the variability of TE. Regression analysis proved a significant influence of the season of birth and selected maternal factors on the PE thickness - these factors explained over 17% of its variability. Neither of analysed variables had influenced PSE. CONCLUSIONS Our findings suggests that the thickness of enamel of deciduous incisors depends on the season of birth and some maternal factors. The differences were observed only in the prenatally formed enamel.
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