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Rajpal S, Mishra P, Mizaikoff B. Rational In Silico Design of Molecularly Imprinted Polymers: Current Challenges and Future Potential. Int J Mol Sci 2023; 24:ijms24076785. [PMID: 37047758 PMCID: PMC10095314 DOI: 10.3390/ijms24076785] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
The rational design of molecularly imprinted polymers has evolved along with state-of-the-art experimental imprinting strategies taking advantage of sophisticated computational tools. In silico methods enable the screening and simulation of innovative polymerization components and conditions superseding conventional formulations. The combined use of quantum mechanics, molecular mechanics, and molecular dynamics strategies allows for macromolecular modelling to study the systematic translation from the pre- to the post-polymerization stage. However, predictive design and high-performance computing to advance MIP development are neither fully explored nor practiced comprehensively on a routine basis to date. In this review, we focus on different steps along the molecular imprinting process and discuss appropriate computational methods that may assist in optimizing the associated experimental strategies. We discuss the potential, challenges, and limitations of computational approaches including ML/AI and present perspectives that may guide next-generation rational MIP design for accelerating the discovery of innovative molecularly templated materials.
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Affiliation(s)
- Soumya Rajpal
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Prashant Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Hahn-Schickard, Sedanstraße 14, 89077 Ulm, Germany
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Wu X, Shen J, Ye T, Cao H, Yuan M, Yin F, Hao L, Zhang C, Xu F. Thiourea derivatives acting as functional monomers of As(Ш) molecular imprinted polymers: A theoretical and experimental study on binding mechanisms. JOURNAL OF HAZARDOUS MATERIALS 2022; 430:128508. [PMID: 35739686 DOI: 10.1016/j.jhazmat.2022.128508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 06/15/2023]
Abstract
Thiourea derivatives are expected to be potential monomers of As(Ш) molecular imprinted polymers (MIPs) which are used to specifically recognize As(Ш). However, the specific recognition and binding mechanisms between template and monomers are unclear, which limits the practical applications of MIPs in As(Ш)detection. In this work, density functional theory (DFT) calculations, molecular dynamics (MD) simulations and experimental methods were jointly applied to explore the binding interactions between H3AsO3 and thiourea derivatives and environmental factors influences, aiming to find out the best monomer and optimal preparation conditions for H3AsO3 MIPs. Among five monomer candidates, (2, 6-difluorophenyl) thiourea (FT) was calculated to be the most potential one, while allyl thiourea (AT) was the second choice. Configurations of the most stable binding complexes were found out. The optimal solvent was found to be toluene and the bindings were more favorable at pH 7.5 in aqueous solution. Besides, EGDMA was proved as the best cross-linker with the optimal ratio of template: monomer: cross-linker= 2:3:20. Moreover, the binding interactions were identified to be hydrogen bonds, and the non-covalent nature was revealed. These findings provide references for efficient design and preparation of good-performance H3AsO3 MIPs, which can be used to detect and remove As(Ш) from environment.
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Affiliation(s)
- Xiuxiu Wu
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Jinyu Shen
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Tai Ye
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Hui Cao
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Min Yuan
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fengqin Yin
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Liling Hao
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Fei Xu
- School of Medical Instrument and Food Engineering, Shanghai Engineering Research Center for Food Rapid Detection, University of Shanghai for Science and Technology, Shanghai 200093, 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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Li ZY, Gu LL, Tong ZH, Du K, Shi JL, Kong GH. Computer simulation assisted preparation and application of myclobutanil imprinted nanoparticles. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Azizi A, Bottaro CS. A critical review of molecularly imprinted polymers for the analysis of organic pollutants in environmental water samples. J Chromatogr A 2020; 1614:460603. [DOI: 10.1016/j.chroma.2019.460603] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 01/05/2023]
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Huang YJ, Chang R, Zhu QJ. Synthesis and Characterization of a Molecularly Imprinted Polymer of Spermidine and the Exploration of Its Molecular Recognition Properties. Polymers (Basel) 2018; 10:E1389. [PMID: 30961314 PMCID: PMC6401967 DOI: 10.3390/polym10121389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/08/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
Spermidine is a functional ingredient that can extend the lifespan of many foods and indicate meat safety. However, its synthesis and enrichment is expensive and complex. To develop an effective separation material that can offer highly selective recognition of spermidine, we first applied non-covalent molecular imprinting technology using methacrylic acid as a functional monomer, azobisisobutyronitrile as an initiator, and ethylene glycol dimethacrylate as a cross-linker. The adsorption properties of the polymers were analyzed using the Scatchard equation, the Lagergren kinetic equation, and the static distribution coefficient. The optimal polymerization molar ratio of the template molecule spermidine to the functional monomer was 1:4, the maximum adsorption amount was 97.75 μmol/g, and the adsorption equilibrium time was 300 min. The selective experiment showed that the interfering substances tyramine and histamine had selectivity factor α values of 2.01 and 1.78, respectively, indicating that the prepared polymer had good spermidine recognition ability. The density function theory calculations showed that the hydrogen bond strength, steric effect, and product energy caused adsorption and separation differences among the different imprinted polymer complexes.
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Affiliation(s)
- Yu-Jie Huang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
- College of Food Safety, Guizhou Medical University, Guiyang 550025, China.
| | - Rui Chang
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
| | - Qiu-Jin Zhu
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China.
- Key Laboratory of Agricultural and Animal Products Store and Processing of Guizhou Province, Guiyang, 550025, China.
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