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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: 0] [Impact Index Per Article: 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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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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Zink S, Moura FA, Autreto PADS, Galvão DS, Mizaikoff B. Virtually imprinted polymers (VIPs): understanding molecularly templated materialsviamolecular dynamics simulations. Phys Chem Chem Phys 2018; 20:13145-13152. [DOI: 10.1039/c7cp08284c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Theoretical model of molecularly imprinted polymers based on molecular dynamics simulations.
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Affiliation(s)
- S. Zink
- Institute of Analytical and Bioanalytical Chemistry
- Ulm University
- 89081 Ulm
- Germany
| | - F. A. Moura
- Gleb Wataghin Physics Institute
- State University of Campinas UNICAMP
- 13083-970 Campinas
- Brazil
| | | | - D. S. Galvão
- Gleb Wataghin Physics Institute
- State University of Campinas UNICAMP
- 13083-970 Campinas
- Brazil
| | - B. Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry
- Ulm University
- 89081 Ulm
- Germany
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Yankelov R, Yungerman I, Srebnik S. The selectivity of protein-imprinted gels and its relation to protein properties: A computer simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/27/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Rami Yankelov
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa Israel 32000
| | - Irena Yungerman
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa Israel 32000
| | - Simcha Srebnik
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa Israel 32000
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Curk T, Dobnikar J, Frenkel D. Rational design of molecularly imprinted polymers. SOFT MATTER 2016; 12:35-44. [PMID: 26452006 DOI: 10.1039/c5sm02144h] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Molecular imprinting is the process whereby a polymer matrix is cross-linked in the presence of molecules with surface sites that can bind selectively to certain ligands on the polymer. The cross-linking process endows the polymer matrix with a chemical 'memory', such that the target molecules can subsequently be recognized by the matrix. We present a simple model that accounts for the key features of this molecular recognition. Using a combination of analytical calculations and Monte Carlo simulations, we show that the model can account for the binding of rigid particles to an imprinted polymer matrix with valence-limited interactions. We show how the binding multivalency and the polymer material properties affect the efficiency and selectivity of molecular imprinting. Our calculations allow us to formulate design criteria for optimal molecular imprinting.
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Affiliation(s)
- Tine Curk
- International Research Center for Soft Matter, Beijing University of Chemical Technology, Beijing, China. and Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Jure Dobnikar
- International Research Center for Soft Matter, Beijing University of Chemical Technology, Beijing, China.
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, UK
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Whitcombe MJ, Kirsch N, Nicholls IA. Molecular imprinting science and technology: a survey of the literature for the years 2004-2011. J Mol Recognit 2014; 27:297-401. [PMID: 24700625 DOI: 10.1002/jmr.2347] [Citation(s) in RCA: 275] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/28/2013] [Accepted: 12/01/2013] [Indexed: 12/11/2022]
Abstract
Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed.
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Levi L, Srebnik S. Simulation of Protein-Imprinted Polymers. 3. Imprinting Selectivity. J Phys Chem B 2011; 115:14469-74. [DOI: 10.1021/jp206940j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Liora Levi
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel 32000
| | - Simcha Srebnik
- Department of Chemical Engineering, Technion — Israel Institute of Technology, Haifa, Israel 32000
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Levi L, Raim V, Srebnik S. A brief review of coarse-grained and other computational studies of molecularly imprinted polymers. J Mol Recognit 2011; 24:883-91. [DOI: 10.1002/jmr.1135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Liora Levi
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa; Israel; 32000
| | - Vladimir Raim
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa; Israel; 32000
| | - Simcha Srebnik
- Department of Chemical Engineering; Technion - Israel Institute of Technology; Haifa; Israel; 32000
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Dourado EMA, Herdes C, van Tassel PR, Sarkisov L. Molecular recognition effects in atomistic models of imprinted polymers. Int J Mol Sci 2011; 12:4781-804. [PMID: 21954325 PMCID: PMC3179132 DOI: 10.3390/ijms12084781] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 07/08/2011] [Accepted: 07/25/2011] [Indexed: 12/02/2022] Open
Abstract
In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects.
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Affiliation(s)
- Eduardo M. A. Dourado
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, Edinburgh, Midlothian EH9 3JL, UK; E-Mail:
| | - Carmelo Herdes
- Centro de Química de Évora, Universidade de Évora, Rua Romão Romalho 59, 7000 Évora, Portugal; E-Mail:
| | - Paul R. van Tassel
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520-8286, USA; E-Mail:
| | - Lev Sarkisov
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, Edinburgh, Midlothian EH9 3JL, UK; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-131-650-4862
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Mojica ERE, Autschbach J, Bright FV, Aga DS. Synthesis and evaluation of tetracycline imprinted xerogels: Comparison of experiment and computational modeling. Anal Chim Acta 2011; 684:63-71. [DOI: 10.1016/j.aca.2010.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 10/18/2022]
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Levi L, Srebnik S. Simulation of Protein-Imprinted Polymers. 2. Imprinting Efficiency. J Phys Chem B 2010; 114:16744-51. [DOI: 10.1021/jp108762t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Liora Levi
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, 32000 Israel
| | - Simcha Srebnik
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, 32000 Israel
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Levi L, Srebnik S. Simulation of Protein-Imprinted Polymers. 1. Imprinted Pore Properties. J Phys Chem B 2009; 114:107-14. [DOI: 10.1021/jp9087767] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Liora Levi
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel 32000
| | - Simcha Srebnik
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel 32000
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