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Johan UUM, Rahman RNZRA, Kamarudin NHA, Ali MSM. Thermodynamics of a hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9. Arch Biochem Biophys 2024; 756:109996. [PMID: 38621445 DOI: 10.1016/j.abb.2024.109996] [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: 12/04/2023] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Hyperthermostable enzymes are highly desirable biocatalysts due to their exceptional stability at extreme temperatures. Recently, a hyperthermostable carboxylesterase EstD9 from Anoxybacillus geothermalis D9 was biochemically characterized. The enzyme exhibited remarkable stability at high temperature. In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new β-sheets at 80 °C, making the core of the hydrolase fold more stable. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, which resided at the interface between the large and cap domains. To further investigate the structural adaptation in extreme conditions, the intramolecular interactions of the native structure were investigated. EstD9 revealed 18 hydrogen bond networks, 7 salt bridges, and 9 hydrophobic clusters, which is higher than the previously reported thermostable Est30. Collectively, the analysis indicates that intramolecular interactions and structural dynamics play distinct roles in preserving the overall EstD9 structure at elevated temperatures. This work is relevant to both fundamental and applied research involving protein engineering of industrial thermostable enzymes.
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Affiliation(s)
- Ummie Umaiera Mohd Johan
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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2
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Sang Y, Huang X, Li H, Hong T, Zheng M, Li Z, Jiang Z, Ni H, Li Q, Zhu Y. Improving the thermostability of Pseudoalteromonas Porphyrae κ-carrageenase by rational design and MD simulation. AMB Express 2024; 14:8. [PMID: 38245573 PMCID: PMC10799840 DOI: 10.1186/s13568-024-01661-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/22/2024] Open
Abstract
The industrial applications of the κ-carrageenases have been restricted by their poor thermostability. In this study, based on the folding free energy change (ΔΔG) and the flexibility analysis using molecular dynamics (MD) simulation for the alkaline κ-carrageenase KCgCD from Pseudoalteromonas porphyrae (WT), the mutant S190R was identified with improved thermostability. After incubation at 50 °C for 30 min, the residual activity of S190R was 63.7%, 25.7% higher than that of WT. The Tm values determined by differential scanning calorimetry were 66.2 °C and 64.4 °C for S190R and WT, respectively. The optimal temperature of S190R was 10 °C higher than that of WT. The κ-carrageenan hydrolysates produced by S190R showed higher xanthine oxidase inhibitory activity compared with the untreated κ-carrageenan. MD simulation analysis of S190R showed that the residues (V186-M194 and P196-G197) in F5 and the key residue R150 in F3 displayed the decreased flexibility, and residues of T169-N173 near the catalytic center displayed the increased flexibility. These changed flexibilities might be the reasons for the improved thermostability of mutant S190R. This study provides a useful rational design strategy of combination of ΔΔG calculation and MD simulation to improve the κ-carrageenase's thermostability for its better industrial applications.
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Affiliation(s)
- Yuyan Sang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Xiaoyi Huang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, 361008, Xiamen, China
| | - Tao Hong
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, 361021, Xiamen, China.
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, 361021, Xiamen, China.
- Research Center of Food Biotechnology of Xiamen City, 361021, Xiamen, China.
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3
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Huang Z, Ni D, Chen Z, Zhu Y, Zhang W, Mu W. Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37485919 DOI: 10.1080/10408398.2023.2238054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Enzymes can produce high-quality food with low pollution, high function, high acceptability, and medical aid. However, most enzymes, in their native form, do not meet the industrial requirements. Sequence-based and structure-based methods are the two main strategies used for enzyme modification. Molecular Dynamics (MD) simulation is a sufficiently comprehensive technology, from a molecular perspective, which has been widely used for structure information analysis and enzyme modification. In this review, we summarize the progress and development of MD simulation, particularly for software, force fields, and a standard procedure. Subsequently, we review the application of MD simulation in various food enzymes for thermostability and catalytic improvement was reviewed in depth. Finally, the limitations and prospects of MD simulation in food enzyme modification research are discussed. This review highlights the significance of MD simulation and its prospects in food enzyme modification.
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Affiliation(s)
- Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Ziwei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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4
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Misra R, Maity A, Kundu S, Bhunia M, Nanda B, Maiti NC, Pal U. Loop Dynamics and Conformational Flexibility in Dengue Serine Protease Activity: Noninvasive Perturbation by Solvent Exchange. J Chem Inf Model 2023; 63:2122-2132. [PMID: 36943246 DOI: 10.1021/acs.jcim.2c01349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Molecular mechanics play an important role in enzyme action and understanding the dynamics of loop motion is key for designing inhibitors of an enzyme, particularly targeting the allosteric sites. For the successful creation of new protease inhibitors targeting the dengue serine protease, our current investigation detailed the intricate structural dynamics of NS2B/NS3 dengue protease. This enzyme is one of the most essential enzymes in the life cycle of the dengue virus, which is responsible for the activation/processing of viral polyprotein, thus making it a potential target for drug discovery. We showed that the internal dynamics of two regions, fingers 1 and 2 (R24-G39 and L149-A164, respectively) adjacent to the active site triad of this protease, control the enzyme action. Each of these regions is composed of two antiparallel β-strands connected by β-turn/hairpin loops. The correlated bending and rocking motions in the two β-turns on either side of the active site were found to modulate the activity of the enzyme to a large extent. With increasing concentration of cosolvent dimethyl sulfoxide, correlated motions in the finger 2 region get diminished and bending of finger 1 increases, which are also reflected in the loss of enzyme activity. Decreasing temperature and mutations in neighboring nonsubstrate binding residues show similar effects on loop motion and enzyme kinetics. Therefore, in vitro noninvasive perturbation of these motions by the solvent exchange as well as cold stress in combination with in silico molecular dynamics simulations established the importance of the two β-turns in the functioning of dengue virus serotype 2 NS2B/NS3 serine protease.
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Affiliation(s)
- Rajdip Misra
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Anupam Maity
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Mrinmay Bhunia
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Banadipa Nanda
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
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5
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Rocha REO, Mariano DCB, Almeida TS, CorrêaCosta LS, Fischer PHC, Santos LH, Caffarena ER, da Silveira CH, Lamp LM, Fernandez-Quintero ML, Liedl KR, de Melo-Minardi RC, de Lima LHF. Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches. Proteins 2023; 91:218-236. [PMID: 36114781 DOI: 10.1002/prot.26424] [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: 05/26/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023]
Abstract
β-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β-glucosidase by two-point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co-evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β-glucosidases for 2G-biofuel production for industry, biotechnology, and science.
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Affiliation(s)
- Rafael Eduardo Oliveira Rocha
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago Silva Almeida
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Leon Sulfierry CorrêaCosta
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Computational Modeling Coordination (COMOD), Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Pedro Henrique Camargo Fischer
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Lucianna Helene Santos
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Leonida M Lamp
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Monica Lisa Fernandez-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Klaus Roman Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
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6
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Mukherjee D, Chakraborty G, Hasan MN, Pal U, Singh P, Rakshit T, Alsantali RI, Saha Dasgupta T, Ahmed S, Das R, Pal SK. Reversible photoswitching of spiropyran in biomolecular interfaces: A combined spectroscopy and computational study. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Biswas P, Pal U, Adhikari A, Mondal S, Ghosh R, Mukherjee D, Saha‐Dasgupta T, Choudhury SS, Das R, Pal SK. Essential Loop Dynamics Modulates Catalytic Activity in α‐Chymotrypsin. ChemistrySelect 2022. [DOI: 10.1002/slct.202104262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pritam Biswas
- Department of Microbiology St. Xavier's College, 30, Mother Teresa Sarani Kolkata 700016 India
| | - Uttam Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Aniruddha Adhikari
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Susmita Mondal
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Ria Ghosh
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Dipanjan Mukherjee
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Tanusri Saha‐Dasgupta
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | | | - Ranjan Das
- Department of Chemistry West Bengal state University, Barasat Kolkata 700126 India
| | - Samir Kumar Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
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8
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Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach. Molecules 2021; 26:molecules26216586. [PMID: 34770995 PMCID: PMC8587830 DOI: 10.3390/molecules26216586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023] Open
Abstract
The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.
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9
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Mondal S, Ghosh R, Adhikari A, Pal U, Mukherjee D, Biswas P, Darbar S, Singh S, Bose S, Saha-Dasgupta T, Pal SK. In vitro and Microbiological Assay of Functionalized Hybrid Nanomaterials To Validate Their Efficacy in Nanotheranostics: A Combined Spectroscopic and Computational Study. ChemMedChem 2021; 16:3739-3749. [PMID: 34550644 DOI: 10.1002/cmdc.202100494] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/20/2021] [Indexed: 01/05/2023]
Abstract
Functionalized nanoparticles reveal new frontiers in therapeutics and diagnostics, simultaneously referred to as theranostics. Functionalization of an inorganic nanoparticle (NP) with an organic ligand determines the interaction of the functionalized NPs with various cellular components, leading to the desired therapeutic effect, while diminishing adverse side effects. Apart from the therapeutic effect of the nanoparticles, other physical properties of the organic-inorganic complex (nanohybrid) including fluorescence, X-ray or MRI contrast offer diagnosis of the anomalous target cell. In this study we functionalized Mn3 O4 NPs with organic citrate (C-Mn3 O4 ) and folic acid (FA-Mn3 O4 ) ligands and investigated their antimicrobial activities using Staphylococcus hominis as a model bacteria, which can be remediated through their membrane rupture. While high-resolution transmission microscopy (HR-TEM), XRD, DLS, absorbance and fluorescence spectroscopy were used for structural characterisation of the functionalised NPs, zeta potential measurements and temperature-dependent reactive oxygen speices (ROS) generation reveal their drug action. We used high-end density functional theory (DFT) calculations to rationalise the specificity of the drug action of the NPs. Picosecond-resolved FRET studies confirm the enhanced affinity of FA-Mn3 O4 to the bacteria relative to C-Mn3 O4 , leading to enhanced antimicrobial activity. We have shown that the functionalised nanoparticles offer significant X-ray contrast in in-vitro studies, indicating the FA-Mn3 O4 NPs to be a potential theranostic agent against bacterial infection.
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Affiliation(s)
- Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Ria Ghosh
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India.,Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.,Technical Research Centre, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Pritam Biswas
- Department of Microbiology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata, 700016, India
| | - Soumendra Darbar
- Research & Development Division, Dey's Medical Stores (Mfg.) Ltd., 62, Bondel Road, Ballygunge, Kolkata, 700019, India
| | - Soumendra Singh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Surajit Bose
- Department of Dentistry, Bharat Sevashram Sangha Hospital, Diamond Harbour Road, Kolkata, 700104, India.,Department of Oraland Maxillofacial Pathology, KSDJ Dental College and Hospital, 6 Ram Gopal Ghosh Road, Cossipore, Kolkata, 700002, India
| | - Tanusri Saha-Dasgupta
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India.,Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India.,Technical Research Centre, S. N. Bose National Centre for Basic Sciences Block JD, Sector 3, Salt Lake, Kolkata, 700106, India
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10
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Uday RVS, Misra R, Harika A, Dolui S, Saha A, Pal U, Ravichandiran V, Maiti NC. Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease. PLoS One 2021; 16:e0257206. [PMID: 34506566 PMCID: PMC8432871 DOI: 10.1371/journal.pone.0257206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
Dengue virus (DENV) encodes a unique protease (NS3/NS2B) essential for its maturation and infectivity and, it has become a key target for anti-viral drug design to treat dengue and other flavivirus related infections. Present investigation established that some of the drug molecules currently used mainly in cancer treatment are susceptible to bind non-active site (allosteric site/ cavity) of the NS3 protease enzyme of dengue virus. Computational screening and molecular docking analysis found that dabrafenib, idelalisib and nintedanib can bind at the allosteric site of the enzyme. The binding of the molecules to the allosteric site found to be stabilized via pi-cation and hydrophobic interactions, hydrogen-bond formation and π-stacking interaction with the molecules. Several interacting residues of the enzyme were common in all the five serotypes. However, the interaction/stabilizing forces were not uniformly distributed; the π-stacking was dominated with DENV3 proteases, whereas, a charged/ionic interaction was the major force behind interaction with DENV2 type proteases. In the allosteric cavity of protease from DENV1, the residues Lys73, Lys74, Thr118, Glu120, Val123, Asn152 and Ala164 were involved in active interaction with the three molecules (dabrafenib, idelalisib and nintedanib). Molecular dynamics (MD) analysis further revealed that the molecules on binding to NS3 protease caused significant changes in structural fluctuation and gained enhanced stability. Most importantly, the binding of the molecules effectively perturbed the protein conformation. These changes in the protein conformation and dynamics could generate allosteric modulation and thus may attenuate/alter the NS3 protease functionality and mobility at the active site. Experimental studies may strengthen the notion whether the binding reduce/enhance the catalytic activity of the enzyme, however, it is beyond the scope of this study.
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Affiliation(s)
- R. V. Sriram Uday
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Rajdip Misra
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Annaram Harika
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, West Bengal, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - V. Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Chunilal Bhawan, Kolkata, West Bengal, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
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11
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Adhikari A, Pal U, Bayan S, Mondal S, Ghosh R, Darbar S, Saha-Dasgupta T, Ray SK, Pal SK. Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic, and Antimicrobial Study. ACS APPLIED BIO MATERIALS 2021; 4:5471-5484. [PMID: 35006728 PMCID: PMC8231689 DOI: 10.1021/acsabm.1c00238] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022]
Abstract
Centers for Disease Control and Prevention (CDC) warns the use of one-way valves or vents in face masks for potential threat of spreading COVID-19 through expelled respiratory droplets. Here, we have developed a nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanomaterial for potential use as a membrane filter in the one-way valve for the ease of breathing without the threat of COVID-19 spreading. A detailed computational study revealed that zinc oxide nanoflowers (ZnO NFs) with almost two-dimensional petals trap SARS-CoV-2 spike proteins, responsible to attach to ACE-2 receptors in human lung epithelial cells. The study also confirmed significant denaturation of the spike proteins on the ZnO surface, revealing removal of the virus upon efficient trapping. Following the computational study, we have synthesized ZnO NF on a cotton matrix using a hydrothermal-assisted strategy. Electron-microscopic, steady-state, and picosecond-resolved spectroscopic studies confirm attachment of ZnO NF to the cotton (i.e., cellulose) matrix at the atomic level to develop the nanoceutical fabric. A detailed antimicrobial assay using Pseudomonas aeruginosa bacteria (model SARS-CoV-2 mimic) reveals excellent antimicrobial efficiency of the developed nanoceutical fabric. To our understanding, the nanoceutical fabric used in the one-way valve of a face mask would be the choice to assure breathing comfort along with source control of COVID-19 infection. The developed nanosensitized cloth can also be used as an antibacterial/anti CoV-2 washable dress material in general.
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Affiliation(s)
- Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose
National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata
700106, India
| | - Sayan Bayan
- Department of Condensed Matter Physics and Material
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose
National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata
700106, India
| | - Soumendra Darbar
- Research & Development Division,
Dey’s Medical Stores (Mfg.) Ltd., 62, Bondel Road,
Ballygunge, Kolkata 700019, India
| | - Tanusri Saha-Dasgupta
- Technical Research Centre, S. N. Bose
National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata
700106, India
- Department of Condensed Matter Physics and Material
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Samit Kumar Ray
- Department of Condensed Matter Physics and Material
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Physics, Indian Institute
of Technology Kharagpur, Kharagpur 721302, India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular
Sciences, S. N. Bose National Centre for Basic Sciences, Block
JD, Sector 3, Salt Lake, Kolkata 700106, India
- Technical Research Centre, S. N. Bose
National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata
700106, India
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12
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Adhikari A, Pal U, Bayan S, Mondal S, Ghosh R, Darbar S, Saha-Dasgupta T, Ray SK, Pal SK. Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic, and Antimicrobial Study. ACS APPLIED BIO MATERIALS 2021. [PMID: 35006728 DOI: 10.1101/2021.02.20.432081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Centers for Disease Control and Prevention (CDC) warns the use of one-way valves or vents in face masks for potential threat of spreading COVID-19 through expelled respiratory droplets. Here, we have developed a nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanomaterial for potential use as a membrane filter in the one-way valve for the ease of breathing without the threat of COVID-19 spreading. A detailed computational study revealed that zinc oxide nanoflowers (ZnO NFs) with almost two-dimensional petals trap SARS-CoV-2 spike proteins, responsible to attach to ACE-2 receptors in human lung epithelial cells. The study also confirmed significant denaturation of the spike proteins on the ZnO surface, revealing removal of the virus upon efficient trapping. Following the computational study, we have synthesized ZnO NF on a cotton matrix using a hydrothermal-assisted strategy. Electron-microscopic, steady-state, and picosecond-resolved spectroscopic studies confirm attachment of ZnO NF to the cotton (i.e., cellulose) matrix at the atomic level to develop the nanoceutical fabric. A detailed antimicrobial assay using Pseudomonas aeruginosa bacteria (model SARS-CoV-2 mimic) reveals excellent antimicrobial efficiency of the developed nanoceutical fabric. To our understanding, the nanoceutical fabric used in the one-way valve of a face mask would be the choice to assure breathing comfort along with source control of COVID-19 infection. The developed nanosensitized cloth can also be used as an antibacterial/anti CoV-2 washable dress material in general.
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Affiliation(s)
- Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Sayan Bayan
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Soumendra Darbar
- Research & Development Division, Dey's Medical Stores (Mfg.) Ltd., 62, Bondel Road, Ballygunge, Kolkata 700019, India
| | - Tanusri Saha-Dasgupta
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Samit Kumar Ray
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Physics, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
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13
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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14
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Ghosh R, Singh S, Adhikari A, Mondal S, Mukherjee D, Bhattacharyya N, Halder A, Bhattacharyya M, Pal SK. Synthesis and characterization of a nano-formulation for long lasting sterilization effect. ACTA ACUST UNITED AC 2021; 80:1846-1851. [PMID: 34178606 PMCID: PMC8214171 DOI: 10.1016/j.matpr.2021.05.623] [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] [Indexed: 12/15/2022]
Abstract
The current COVID-19 pandemic has increased the use of alcohol based hand sanitisers globally. These available alcohol based sanitisers cannot provide an antibacterial effect for an extended period of time, after the evaporation of ethanol. Hence, the need for a sanitiser with an anti-microbial activity combined with a long lasting effect is the need of the hour. In this study, we report the synthesis of a long lasting sanitiser from ozonated omega 9 fatty acid esters in an ethanolic medium. The formed vesicles made of the fatty acids have been characterized by DLS, Zeta potential, and time resolved fluorescence anisotropy studies. Ethanol although, provides an antibacterial effect, the effect is more pronounced in our prepared formulation owing to its high peroxide value that generates additional oxidative stress. Finally, this additional antimicrobial effect will have relevance in the current COVID-19 scenario in providing a long lasting hand sanitiser.
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Affiliation(s)
- Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Ballygunge, Kolkata 700019, India
| | - Soumendra Singh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Neha Bhattacharyya
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Animesh Halder
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Applied Optics & Photonics, University of Calcutta, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
| | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Ballygunge, Kolkata 700019, India
- Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Kasba, Kolkata 700107, India
| | - Samir Kumar Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector 3, Salt Lake, Kolkata 700106, India
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15
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Host assisted molecular recognition by human serum albumin: Study of molecular recognition controlled protein/drug mimic binding in a microfluidic channel. Int J Biol Macromol 2021; 176:137-144. [PMID: 33548310 DOI: 10.1016/j.ijbiomac.2021.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/21/2022]
Abstract
Human serum albumin (HSA) plays a pivotal role in drug release from its delivery vehicles such as cyclodextrins (CDs) by binding to the drugs. Here molecular recognition and binding of a drug mimic (CD1) to HSA have been explored in a microfluidic channel when CD1 is encapsulated in β-cyclodextrin (βCD) and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TRIMEB), respectively, to investigate whether change of the host vehicle modulate the rate of drug binding to the serum protein. Molecular recognition of βCD encapsulated CD1 by HSA occurs by the conformational selection fit mechanism leading to rapid binding of CD1 to HSA (k1 ~ 700 s-11) when the βCD/CD1 complex interacts with HSA. In contrary, HSA recognizes CD1 encapsulated in TRIMEB by an induced fit mechanism leading to a significantly slower binding rate (k1 ~ 20.8 s-1) of the drug mimic to the protein. Thus molecular recognition controls the rate of HSA binding by CD1 which in turn modulates the rate of delivery of the drug mimic from its macrocyclic hosts. The remarkable change in the molecular recognition pathway of CD1 by HSA, upon change of the host from βCD to TRIMEB, originates from significantly different conformational flexibility of the host/drug mimic complexes.
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