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Dhinesh Kumar M, Karthikeyan M, Kaniraja G, Muthukumar K, Muneeswaran G, Karunakaran C. Computational modelling and optimization studies of electropentamer for molecular imprinting of DJ-1. J Mol Graph Model 2024; 128:108715. [PMID: 38306790 DOI: 10.1016/j.jmgm.2024.108715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
Parkinson's disease (PD) is the most prevalent type of incurable movement disorder. Recent research findings propose that the familial PD-associated molecule DJ-1 exists in cerebrospinal fluid (CSF) and that its levels may be altered as Parkinson's disease advances. By using a molecularly imprinted polymer (MIP) as an artificial receptor, it becomes possible to create a functional MIP with predetermined selectivity for various templates, particularly for the DJ-1 biomarker associated with Parkinson's disease. It mostly depends on molecular recognition via interactions between functional monomers and template molecules. So, the computational methods for the appropriate choice of functional monomers for creating molecular imprinting electropolymers (MIEPs) with particular recognition for the detection of DJ-1, a pivotal biomarker involved in PD, are undertaken in this study. Here, molecular docking, molecular dynamics simulations (MD), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods, and quantum mechanical calculation have been applied to investigate the intermolecular interaction between DJ-1 and several functional electropentamers, viz., polypyrrole (PPy), poly(3,4-ethylenedioxythiophene) (PEDOT), poly(o-aminophenol) (POAP), and polythiophene (PTS). In this context, the electropentamers were selected to mimic the imprinted electropolymer system. We analyzed the most stable configurations of the formed complexes involving DJ-1 and electropentamers as a model system for MIEPs. Among these, PEDOT exhibited a more uniform arrangement around DJ-1, engaging in numerous van der Waals, H-bond, electrostatic, and hydrophobic interactions. Hence, it can be regarded as a preferable choice for synthesizing a MIP for DJ-1 recognition. Thus, it will aid in selecting a suitable functional monomer, which is of greater significance in the design and development of selective DJ-1/MIP sensors.
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Affiliation(s)
- Marimuthu Dhinesh Kumar
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar, 626 001, Tamil Nadu, India
| | - Murugesan Karthikeyan
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar, 626 001, Tamil Nadu, India
| | - Ganesan Kaniraja
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar, 626 001, Tamil Nadu, India
| | | | - Gurusamy Muneeswaran
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan
| | - Chandran Karunakaran
- Biomedical Research Laboratory, Department of Chemistry, Virudhunagar Hindu Nadars' Senthikumara Nadar College (Autonomous & Affiliated to Madurai Kamaraj University), Virudhunagar, 626 001, Tamil Nadu, India.
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Nicholls IA, Golker K, Olsson GD, Suriyanarayanan S, Wiklander JG. The Use of Computational Methods for the Development of Molecularly Imprinted Polymers. Polymers (Basel) 2021; 13:2841. [PMID: 34502881 PMCID: PMC8434026 DOI: 10.3390/polym13172841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022] Open
Abstract
Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.
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Affiliation(s)
- Ian A. Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden; (K.G.); (G.D.O.); (S.S.); (J.G.W.)
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Xing J, Li N, Liang Y, Zhu F. Microwave-assisted synthesis of magnetic Pb(II)-imprinted-poly(schiff base-co-MAA) for selective recognition and extraction of Pb(II) from industrial wastewater. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2021.1930033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Junde Xing
- School of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, P. R. China
| | - Na Li
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, P. R. China
| | - Yukun Liang
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, P. R. China
| | - Fang Zhu
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan, Shanxi, P. R. China
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García Y, Úsuga BA, Campos CH, Alderete JB, Jiménez VA. NanoMIPs Design for Fucose and Mannose Recognition: A Molecular Dynamics Approach. J Chem Inf Model 2021; 61:2048-2061. [PMID: 33784106 DOI: 10.1021/acs.jcim.0c01446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nanoscale molecularly imprinted polymers (nanoMIPs) are powerful molecular recognition tools with broad applications in the diagnosis, prognosis, and treatment of complex diseases. In this work, fully atomistic molecular dynamics (MD) simulations are used to assist the design of nanoMIPs with recognition capacity toward l-fucose and d-mannose as prototype disease biomarkers. MD simulations were conducted on prepolymerization mixtures containing different molar ratios of the monomers N-isopropylacrylamide (NIPAM), methacrylamide (MAM), and (4-acrylamidophenyl)(amino)methaniminium acetate (AB) and fixed molar ratios of the cross-linker ethylene glycol dimethacrylate (EGDMA) in explicit acetonitrile as the porogenic solvent. Prepolymerization mixtures containing ternary mixtures of NIPAM (50%), MAM (25%), and AB (25%) exhibit the best imprinting potential for both l-fucose and d-mannose, as they maximize (i) the stability of template-monomer plus template-cross-linker interactions, (ii) the number of functional monomers plus cross-linkers organized around the template, and (iii) the number of hydrogen bonds participating in template recognition. The studied prepolymerization mixtures exhibit an overall increased recognition capacity toward d-mannose over l-fucose, which is attributed to the higher hydrogen-bonding capacity of the former template. Our results are valuable to guide the synthesis of efficient nanoMIPs for sugar recognition and provide a computational framework extensible to any other template, monomer, or cross-linker combination, thus constituting a promising strategy for the rational design of molecularly imprinted materials.
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Affiliation(s)
- Yadiris García
- Instituto de Química de Recursos Naturales, Universidad de Talca, Avenida Lircay S/N, Talca, Chile 3460000
| | - Brandon A Úsuga
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
| | - Cristian H Campos
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción, Chile 4070371
| | - Joel B Alderete
- Instituto de Química de Recursos Naturales, Universidad de Talca, Avenida Lircay S/N, Talca, Chile 3460000
| | - Verónica A Jiménez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile 4300866
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Olsson GD, Wiklander JG, Nicholls IA. Using Molecular Dynamics in the Study of Molecularly Imprinted Polymers. Methods Mol Biol 2021; 2359:241-268. [PMID: 34410675 DOI: 10.1007/978-1-0716-1629-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Molecular dynamics (MD) simulations of prepolymerization mixtures can provide detailed insights concerning the molecular-level mechanisms underlying the performance of molecularly imprinted polymers (MIPs) and can be used for the in silico screening of candidate polymer systems. Here, we describe the use of MD simulations of all-atom, all-component MIP prepolymerization mixtures and procedures for the evaluation of the simulation data using the Amber simulation software suite.
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Affiliation(s)
- Gustaf D Olsson
- Bioorganic & Biophysical Chemistry Laboratory, Department of Chemistry & Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Jesper G Wiklander
- Bioorganic & Biophysical Chemistry Laboratory, Department of Chemistry & Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden
| | - Ian A Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Department of Chemistry & Biomedical Sciences, Centre for Biomaterials Chemistry, Linnaeus University, Kalmar, Sweden.
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Shinde S, Incel A, Mansour M, Olsson GD, Nicholls IA, Esen C, Urraca J, Sellergren B. Urea-Based Imprinted Polymer Hosts with Switchable Anion Preference. J Am Chem Soc 2020; 142:11404-11416. [PMID: 32425049 PMCID: PMC7467678 DOI: 10.1021/jacs.0c00707] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The
design of artificial oxyanion receptors with switchable ion
preference is a challenging goal in host–guest chemistry. We
here report on molecularly imprinted polymers (MIPs) with an external
phospho-sulpho switch driven by small molecule modifiers. The polymers
were prepared by hydrogen bond-mediated imprinting of the mono- or
dianions of phenyl phosphonic acid (PPA), phenyl sulfonic acid (PSA),
and benzoic acid (BA) using N-3,5-bis-(trifluoromethyl)-phenyl-Ń-4-vinylphenyl urea (1) as the functional
host monomer. The interaction mode between the functional monomer
and the monoanions was elucidated by 1H NMR titrations
and 1H–1H NMR NOESY supported by molecular
dynamic simulation, which confirmed the presence of high-order complexes.
PPA imprinted polymers bound PPA with an equilibrium constant Keq = 1.8 × 105 M–1 in acetonitrile (0.1% 1,2,2,6,6-pentamethylpiperidine) and inorganic
HPO42– and SO42– with Keq = 2.9 × 103 M–1 and 4.5 × 103 M–1, respectively, in aqueous buffer. Moreover, the chromatographic
retentivity of phosphonate versus sulfonate was shown to be completely
switched on this polymer when changing from a basic to an acidic modifier.
Mechanistic insights into this system were obtained from kinetic investigations
and DSC-, MALDI-TOF-MS-, 1H NMR-studies of linear polymers
prepared in the presence of template. The results suggest the formation
of template induced 1–1 diad repeats in the polymer main chain
shedding unique light on the relative contributions of configurational
and conformational imprinting.
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Affiliation(s)
- Sudhirkumar Shinde
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden.,Faculty of Chemistry, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Anil Incel
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden
| | - Mona Mansour
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden
| | - Gustaf D Olsson
- Bioorganic & Biophysical Chemistry Laboratory, Linneaus University Center for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Ian A Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Linneaus University Center for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, 39182 Kalmar, Sweden
| | - Cem Esen
- Faculty of Chemistry, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Javier Urraca
- Faculty of Chemistry, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Börje Sellergren
- Department of Biomedical Sciences, Faculty of Health and Society, Malmö University, 20506 Malmö, Sweden.,Faculty of Chemistry, Technical University of Dortmund, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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Sullivan MV, Dennison SR, Archontis G, Reddy SM, Hayes JM. Toward Rational Design of Selective Molecularly Imprinted Polymers (MIPs) for Proteins: Computational and Experimental Studies of Acrylamide Based Polymers for Myoglobin. J Phys Chem B 2019; 123:5432-5443. [DOI: 10.1021/acs.jpcb.9b03091] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark V. Sullivan
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Sarah R. Dennison
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | | | - Subrayal M. Reddy
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Joseph M. Hayes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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Golker K, Olsson GD, Nicholls IA. The influence of a methyl substituent on molecularly imprinted polymer morphology and recognition – Acrylic acid versus methacrylic acid. Eur Polym J 2017. [DOI: 10.1016/j.eurpolymj.2017.04.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Boroznjak R, Reut J, Tretjakov A, Lomaka A, Öpik A, Syritski V. A computational approach to study functional monomer-protein molecular interactions to optimize protein molecular imprinting. J Mol Recognit 2017; 30. [PMID: 28444792 DOI: 10.1002/jmr.2635] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/06/2017] [Accepted: 03/17/2017] [Indexed: 12/19/2022]
Abstract
Molecular imprinting has become a promising approach for synthesis of polymeric materials having binding sites with a predetermined selectivity for a given analyte, the so-called molecularly imprinted polymers (MIPs), which can be used as artificial receptors in various application fields. Realization of binding sites in a MIP involves the formation of prepolymerization complexes between a template molecule and monomers, their subsequent polymerization, and the removal of the template. It is believed that the strength of the monomer-template interactions in the prepolymerization mixture influences directly on the quality of the binding sites in a MIP and consequently on its performance. In this study, a computational approach allowing the rational selection of an appropriate monomer for building a MIP capable of selectively rebinding macromolecular analytes has been developed. Molecular docking combined with quantum chemical calculations was used for modeling and comparing molecular interactions among a model macromolecular template, immunoglobulin G (IgG), and 1 of 3 electropolymerizable functional monomers: m-phenylenediamine (mPD), dopamine, and 3,4-ethylenedioxythiophene, as well as to predict the probable arrangement of multiple monomers around the protein. It was revealed that mPD was arranged more uniformly around IgG participating in multiple H-bond interactions with its polar residues and, therefore, could be considered as more advantageous for synthesis of a MIP for IgG recognition (IgG-MIP). These theoretical predictions were verified by the experimental results and found to be in good agreement showing higher binding affinity of the mPD-based IgG-MIP toward IgG as compared with the IgG-MIPs generated from the other 2 monomers.
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Affiliation(s)
- R Boroznjak
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, Estonia
| | - J Reut
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, Estonia
| | - A Tretjakov
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, Estonia
| | - A Lomaka
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - A Öpik
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, Estonia
| | - V Syritski
- Department of Materials and Environmental Technology, Tallinn University of Technology, Tallinn, Estonia
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Ashley J, Shukor Y, Tothill IE. The use of differential scanning fluorimetry in the rational design of plastic antibodies for protein targets. Analyst 2016; 141:6463-6470. [DOI: 10.1039/c6an01155a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Predicted interactions between acrylic monomers and proteins, and melting profiles using DSF in the rational design of MIP-NPs for proteins.
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Affiliation(s)
- Jon Ashley
- Cranfield University
- College Road
- Cranfield
- UK
| | - Yunus Shukor
- Dept. of Biochemistry
- Faculty of Biotechnology and Biomolecular Sciences
- Universiti Putra Malaysia
- Selangor
- Malaysia
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