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Leedale J, Sharkey KJ, Colley HE, Norton ÁM, Peeney D, Mason CL, Sathish JG, Murdoch C, Sharma P, Webb SD. A Combined In Vitro/In Silico Approach to Identifying Off-Target Receptor Toxicity. iScience 2018; 4:84-96. [PMID: 30240756 PMCID: PMC6147237 DOI: 10.1016/j.isci.2018.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 04/19/2018] [Accepted: 05/15/2018] [Indexed: 12/20/2022] Open
Abstract
Many xenobiotics can bind to off-target receptors and cause toxicity via the dysregulation of downstream transcription factors. Identification of subsequent off-target toxicity in these chemicals has often required extensive chemical testing in animal models. An alternative, integrated in vitro/in silico approach for predicting toxic off-target functional responses is presented to refine in vitro receptor identification and reduce the burden on in vivo testing. As part of the methodology, mathematical modeling is used to mechanistically describe processes that regulate transcriptional activity following receptor-ligand binding informed by transcription factor signaling assays. Critical reactions in the signaling cascade are identified to highlight potential perturbation points in the biochemical network that can guide and optimize additional in vitro testing. A physiologically based pharmacokinetic model provides information on the timing and localization of different levels of receptor activation informing whole-body toxic potential resulting from off-target binding.
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Affiliation(s)
- Joseph Leedale
- EPSRC Liverpool Centre for Mathematics in Healthcare, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK.
| | - Kieran J Sharkey
- EPSRC Liverpool Centre for Mathematics in Healthcare, Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
| | - Helen E Colley
- School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK
| | - Áine M Norton
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, UK
| | - David Peeney
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, UK
| | - Chantelle L Mason
- Department of Applied Mathematics, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Jean G Sathish
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, UK; Immuno and Molecular Toxicology, Drug Safety Evaluation, Bristol-Myers Squibb, 1 Squibb Drive, New Brunswick, NJ 08903, USA
| | - Craig Murdoch
- School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK
| | - Parveen Sharma
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, UK.
| | - Steven D Webb
- Department of Applied Mathematics, Liverpool John Moores University, Liverpool L3 3AF, UK
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Salentinig S, Tangso KJ, Hawley A, Boyd BJ. pH-driven colloidal transformations based on the vasoactive drug nicergoline. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:14776-81. [PMID: 25409414 DOI: 10.1021/la503824z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The structure of colloidal self-assembled drug delivery systems can be influenced by intermolecular interactions between drug and amphiphilic molecules, and is important to understand in the context of designing improved delivery systems. Controlling these structures can enable controlled or targeted release systems for poorly water-soluble drugs. Here we present the interaction of the hydrophobic vasoactive drug nicergoline with the internal structure of nanostructured emulsion particles based on the monoglyceride-water system. Addition of this drug leads to modification of the internal bicontinuous cubic structure to generate highly pH-responsive systems. The colloidal structures were characterized with small-angle X-ray scattering and visualized using cryogenic transmission electron microscopy. Reversible transformations to inverse micelles at high pH, vesicles at low pH, and the modification of the spacing of the bicontinuous cubic structure at intermediate pH were observed, and enabled the in situ determination of an apparent pKa for the drug in this system--a difficult task using solution-based approaches. The characterization of this phase behavior is also highly interesting for the design of pH-responsive controlled release systems for poorly water-soluble drug molecules.
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Affiliation(s)
- Stefan Salentinig
- Drug Delivery, Disposition and Dynamics, and §ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, VIC 3052, Australia
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Meloun M, Ferenčíková Z, Javůrek M. Reliability of dissociation constants and resolution capability of SQUAD(84) and SPECFIT/32 in the regression of multiwavelength spectrophotometric pH-titration data. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 86:305-314. [PMID: 22078078 DOI: 10.1016/j.saa.2011.10.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/23/2011] [Accepted: 10/17/2011] [Indexed: 05/31/2023]
Abstract
The resolving power of multicomponent spectral analysis and the computation reliability of the stability constants and molar absorptivities determined for five variously protonated anions of physostigmine salicylate by the SQUAD(84) and SPECFIT/32 programs has been examined with the use of simulated and experimental spectra containing overlapping spectral bands. The reliability of the dissociation constants of drug was proven with goodness-of-fit tests and by examining the influence of pre-selected noise level s(inst)(A) in synthetic spectra regarding the precision s(pK) and also accuracy of the estimated dissociation constants. Precision was examined as the linear regression model s(pK)=β(0)+β(1)s(inst)(A). In all cases the intercept β(0) was statistically insignificant. When an instrumental error s(inst)(A) is small and less than 0.5 mAU, the parameters' estimates are nearly the same as the bias ΔpK=pK(a,calc)-pK(a,true) is quite negligible. In all four dissociation constants the bias seems to be quite small even though for pK(a4) it is a little bit higher, i.e., +0.05 for s(inst)(A) about 1.0 mAU. In the interval of s(inst)(A) from 0.1 to 1.0 mAU all four dissociation constants pK(i) are accurate enough. Of the various regression diagnostics considered, the goodness-of-fit is the most efficient criterion of whether the parameters found adequately represent the data. The magnitude of instrumental error s(inst)(A) only slightly affects the shape of a Cattel's scree graph s(k)(A)=f(k) to determine the true number of light-absorbing species in the equilibrium mixture.
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Affiliation(s)
- Milan Meloun
- Department of Analytical Chemistry, University of Pardubice, CZ 532 10 Pardubice, Czech Republic.
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The thermodynamic dissociation constants of methotrexate by the nonlinear regression and factor analysis of multiwavelength spectrophotometric pH-titration data. OPEN CHEM 2010. [DOI: 10.2478/s11532-010-0023-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe mixed dissociation constants of methotrexate — chemically (2S)-2-[(4-{[(2,4-diamino-7,8-dihydropteridin-6-yl)methyl] (methyl)amino}phenyl)formamido]pentanedioic acid (the cas number 59-05-2) at various ionic strengths I of range 0.01–0.4, and at temperatures of 25°C and 37°C, were determined with the use of two different multiwavelength and multivariate treatments of spectral data, SPECFIT32 and SQUAD(84) nonlinear regression analyses and INDICES factor analysis according to a general rule of first, determining the number of components, and then calculating the spectral responses and concentrations of the components. Concurrently, the experimental determination of the thermodynamic dissociation constants was in agreement with its computational prediction of the PALLAS programme based on knowledge of the chemical structures of the drug. The factor analysis in the INDICES programme predicts the correct number of light-absorbing components when the data quality is high and the instrumental error is known. Three thermodynamic dissociation constants were estimated by nonlinear regression of {pK a , I} data: for methotrexate pK a1T= 2.895(13), pK a2T= 4.410(14), pK a3T= 5.726(15) at 25°C and pK a1T= 3.089(15), pK a2T= 4.392(12), pK a3T= 5.585(11) at 37°C, where the figure in brackets is the standard deviation in last significant digits. The reliability of the dissociation constants of the drug were proven by conducting goodness-of-fit tests of the multiwavelength spectrophotometric pH-titration data.
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Jerez G, Kaufman G, Prystai M, Schenkeveld S, Donkor KK. Determination of thermodynamic pKavalues of benzimidazole and benzimidazole derivatives by capillary electrophoresis. J Sep Sci 2009; 32:1087-95. [DOI: 10.1002/jssc.200800482] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Multivariate kinetic hard-modelling of spectroscopic data: A comparison of the esterification of butanol by acetic anhydride on different scales and with different instruments. Chem Eng Sci 2008. [DOI: 10.1016/j.ces.2008.01.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Meloun M, Bordovská S, Galla L. The thermodynamic dissociation constants of four non-steroidal anti-inflammatory drugs by the least-squares nonlinear regression of multiwavelength spectrophotometric pH-titration data. J Pharm Biomed Anal 2007; 45:552-64. [PMID: 17825517 DOI: 10.1016/j.jpba.2007.07.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 07/23/2007] [Accepted: 07/29/2007] [Indexed: 02/05/2023]
Abstract
The mixed dissociation constants of four non-steroidal anti-inflammatory drugs (NSAIDs) ibuprofen, diclofenac sodium, flurbiprofen and ketoprofen at various ionic strengths I of range 0.003-0.155, and at temperatures of 25 degrees C and 37 degrees C, were determined with the use of two different multiwavelength and multivariate treatments of spectral data, SPECFIT/32 and SQUAD(84) nonlinear regression analyses and INDICES factor analysis. The factor analysis in the INDICES program predicts the correct number of components, and even the presence of minor ones, when the data quality is high and the instrumental error is known. The thermodynamic dissociation constant pK(a)(T) was estimated by nonlinear regression of (pK(a), I) data at 25 degrees C and 37 degrees C. Goodness-of-fit tests for various regression diagnostics enabled the reliability of the parameter estimates found to be proven. PALLAS, MARVIN, SPARC, ACD/pK(a) and Pharma Algorithms predict pK(a) being based on the structural formulae of drug compounds in agreement with the experimental value. The best agreement seems to be between the ACD/pK(a) program and experimentally found values and with SPARC. PALLAS and MARVIN predicted pK(a,pred) values with larger bias errors in comparison with the experimental value for all four drugs.
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Affiliation(s)
- Milan Meloun
- Department of Analytical Chemistry, University of Pardubice, CZ 532 10 Pardubice, Czech Republic.
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Meloun M, Bordovská S, Vrána A. The thermodynamic dissociation constants of the anticancer drugs camptothecine, 7-ethyl-10-hydroxycamptothecine, 10-hydroxycamptothecine and 7-ethylcamptothecine by the least-squares nonlinear regression of multiwavelength spectrophotometric pH-titration data. Anal Chim Acta 2007; 584:419-32. [DOI: 10.1016/j.aca.2006.11.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 11/16/2006] [Accepted: 11/17/2006] [Indexed: 10/23/2022]
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Meloun M, Bordovská S, Syrový T. A novel computational strategy for the pKa estimation of drugs by non-linear regression of multiwavelength spectrophotometric pH-titration data exhibiting small spectral changes. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1235] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Meloun M, Bordovská S, Syrový T, Vrána A. Tutorial on a chemical model building by least-squares non-linear regression of multiwavelength spectrophotometric pH-titration data. Anal Chim Acta 2006; 580:107-21. [PMID: 17723762 DOI: 10.1016/j.aca.2006.07.043] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 07/04/2006] [Accepted: 07/20/2006] [Indexed: 11/22/2022]
Abstract
Although the modern instrumentation enables for the increased amount of data to be delivered in shorter time, computer-assisted spectra analysis is limited by the intelligence and by the programmed logic tool applications. Proposed tutorial covers all the main steps of the data processing which involve the chemical model building, from calculating the concentration profiles and, using spectra regression, fitting the protonation constants of the chemical model to multiwavelength and multivariate data measured. Suggested diagnostics are examined to see whether the chemical model hypothesis can be accepted, as an incorrect model with false stoichiometric indices may lead to slow convergence, cyclization or divergence of the regression process minimization. Diagnostics concern the physical meaning of unknown parameters beta(qr) and epsilon(qr), physical sense of associated species concentrations, parametric correlation coefficients, goodness-of-fit tests, error analyses and spectra deconvolution, and the correct number of light-absorbing species determination. All of the benefits of spectrophotometric data analysis are demonstrated on the protonation constants of the ionizable anticancer drug 7-ethyl-10-hydroxycamptothecine, using data double checked with the SQUAD(84) and SPECFIT/32 regression programs and with factor analysis of the INDICES program. The experimental determination of protonation constants with their computational prediction based on a knowledge of chemical structures of the drug was through the combined MARVIN and PALLAS programs. If the proposed model adequately represents the data, the residuals should form a random pattern with a normal distribution N(0, s2), with the residual mean equal to zero, and the standard deviation of residuals being near to experimental noise. Examination of residual plots may be assisted by a graphical analysis of residuals, and systematic departures from randomness indicate that the model and parameter estimates are not satisfactory.
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Affiliation(s)
- Milan Meloun
- Department of Analytical Chemistry, University of Pardubice, 532 10 Pardubice, Czech Republic.
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