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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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Shahmoradipour P, Zaboli M, Torkzadeh-Mahani M. Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation. J Biol Eng 2024; 18:10. [PMID: 38254151 PMCID: PMC10804793 DOI: 10.1186/s13036-023-00397-x] [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: 10/04/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy.
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Affiliation(s)
- Parisa Shahmoradipour
- Department of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Maryam Zaboli
- Department of chemistry, faculty of science, University of Birjand, Birjand, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
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Meng Y, Wei Z, Xue C. Deciphering the interaction mechanism and binding mode between chickpea protein isolate and flavonoids based on experimental studies and molecular simulation. Food Chem 2023; 429:136848. [PMID: 37454615 DOI: 10.1016/j.foodchem.2023.136848] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Chickpea protein isolate (CPI) is a promising novel plant protein, and protein-flavonoid system has also been applied in various food products. However, the interaction mechanism between CPI and flavonoids remains to be elucidated. In this paper, the affinity behavior between flavonoids and CPI was explained by constructing the three-dimensional quantitative structure-activity relationship (R2 = 0.988, Q2 = 0.777). Subsequently, four representative flavonoids were selected for further study. Multi-spectroscopy analysis showed that the sequence of affinity for CPI was puerarin > apigenin > naringenin > epigallocatechin gallate. Meanwhile, flavonoids altered the secondary structure and spatial conformation of CPI, leading to the static quenching of CPI. Additionally, thermodynamic analysis indicated that hydrogen bonding and van der Waals forces were the main driving forces for complex binding. Molecular docking and molecular dynamics simulations further explored the binding sites and conformations of complexes. This study provides theoretical guidance for in-depth research on the interaction patterns between biomacromolecules and small molecules in food matrices.
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Affiliation(s)
- Yuan Meng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Zihao Wei
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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Roman BH, Charęza M, Janus E, Drozd R. Evaluation of new L-amino acids triethanolammonium salts usability for controlling protease activity. Int J Biol Macromol 2023; 231:123218. [PMID: 36634803 DOI: 10.1016/j.ijbiomac.2023.123218] [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: 09/05/2022] [Revised: 12/23/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
Twenty new triethanolammonium amino acid salts (TEA AA) have been prepared from triethanolammonium hydroxide and L-amino acids. The physicochemical properties of TEA AA depended on the applied amino acid. Five of the synthesised salts, i.e. mono- and bis-salts of L-glutamic acid, L-aspartic acid, and TEA salt of l-glutamine were solids with melting points between 127.32 °C to 171.51 °C. The other TEA AA exhibited glass transition temperatures from -68.45 °C for TEA Ser to -6.27 °C for TEA Trp and were assigned as amino acid ionic liquids (AAILs). The TEA His was characterised by the highest thermal stability, with an average temperature of 5 % weight loss at 186.4 °C, whereas the lowest stability was determined for TEA Asp (107.5 °C). The developed salts were tested as reaction medium additives for proteolytic enzymes (papain, subtilisin, bromelain). Most AAILs showed an inhibitory effect on tested proteases but with different mechanisms related to the enzyme substrate specificity and structural diversity. The TEA Ser was the most effective competitive inhibitor (Ki = 0.24 10-4 mol/L) for bromelain, while TEA Val uncompetitive inhibitor for papain (Ki = 0.25 10-4 mol/L). The developed TEA AA salts exhibit potential as enzyme-controlling agents for use in industrial processes.
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Affiliation(s)
- Barbara Hanna Roman
- West Pomeranian University of Technology Szczecin, Faculty of Chemical Technology and Engineering, Department of Organic Chemical Technology and Polymeric Materials, Pułaski Ave.10, PL, 70-322 Szczecin, Poland
| | - Magdalena Charęza
- West Pomeranian University of Technology Szczecin, Faculty of Biotechnology and Animal Husbandry, Department of Microbiology and Biotechnology, Piastów Ave. 45, 70-311 Szczecin, Poland
| | - Ewa Janus
- West Pomeranian University of Technology Szczecin, Faculty of Chemical Technology and Engineering, Department of Organic Chemical Technology and Polymeric Materials, Pułaski Ave.10, PL, 70-322 Szczecin, Poland
| | - Radosław Drozd
- West Pomeranian University of Technology Szczecin, Faculty of Biotechnology and Animal Husbandry, Department of Microbiology and Biotechnology, Piastów Ave. 45, 70-311 Szczecin, Poland.
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Kalpana K, Rani VA, Ranga A, Perumandla R, Ramani R. One-Pot Synthesis of 6-Amino-4-(furan/thiophen/pyrrol-2-yl)-3-methyl-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitriles, Evaluation of Anticancer Activity and Molecular Modelling Studies. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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6
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Srinivas A, Shree AJ, Goud SSK. [BMIM][OH]-Mediated One-Pot Synthesis of 2-Amino-5-oxo-4-(1H-pyrazol-5-yl)-5H-chromeno[4,3-b]pyridine-3-carbonitriles as Potential Anticancer Agents. RUSS J GEN CHEM+ 2023. [DOI: 10.1134/s1070363223010279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Electrochemical enzyme-based blood uric acid biosensor: new insight into the enzyme immobilization on the surface of electrode via poly-histidine tag. Mikrochim Acta 2022; 189:326. [PMID: 35948696 DOI: 10.1007/s00604-022-05408-0] [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: 04/18/2022] [Accepted: 07/06/2022] [Indexed: 10/15/2022]
Abstract
In a new approach, we considered the special affinity between Ni and poly-histidine tags of recombinant urate oxidase to utilize Ni-MOF for immobilizing the enzyme. In this study, a carbon paste electrode (CPE) was modified by histidine-tailed urate oxidase (H-UOX) and nickel-metal-organic framework (Ni-MOF) to construct H-UOX/Ni-MOF/CPE, which is a rapid, sensitive, and simple electrochemical biosensor for UA detection. The use of carboxy-terminal histidine-tailed urate oxidase in the construction of the electrode allows the urate oxidase enzyme to be positioned correctly in the electrode. This, in turn, enhances the efficiency of the biosensor. Characterization was carried out by X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDX), Fourier transform infrared spectroscopy (FTIR), Brunauer-Emmett-Teller (BET), and field emission scanning electron microscopy (FE-SEM). At optimum conditions, the biosensor provided a short response time, linear response within 0.3-10 µM and 10-140 µM for UA with a detection limit of 0.084 µM, repeatability of 3.06%, and reproducibility of 4.9%. Furthermore, the biosensor revealed acceptable stability and selectivity of UA detection in the presence of the commonly coexisted ascorbic acid, dopamine, L-cysteine, urea, and glucose. The detection potential was at 0.4 V vs. Ag/AgCl.
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Kumar VH, Tamminana R. Copper‐catalyzed multicomponent green reaction approach: Synthesis of dihydropyrano [2, 3‐c] pyrazoles and evaluation of their anti‐cancer activity. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Venkata Hema Kumar
- Department of Chemistry GITAM Deemed to be University, NH‐207, Doddaballapur Taluk Bengaluru Rural Karnataka Inida
| | - Ramana Tamminana
- Department of Chemistry GITAM Deemed to be University, NH‐207, Doddaballapur Taluk Bengaluru Rural Karnataka Inida
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Zhu H, Zhang M, Wang P, Sun C, Xu W, Ma J, Zhu Y, Wang D. Exploring the regulating mechanism of heat induced gelation of myosin by binding with Mb hemin prosthetic group. Food Chem 2022; 382:132354. [DOI: 10.1016/j.foodchem.2022.132354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 01/30/2023]
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Chen L, Zhu M, Hu X, Pan J, Zhang G. Exploring the binding mechanism of ferulic acid and ovalbumin: insights from spectroscopy, molecular docking and dynamics simulation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3835-3846. [PMID: 34927253 DOI: 10.1002/jsfa.11733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Ferulic acid (FA), a phenolic acid widely occurring in nature, has attracted extensive attention because of its biological activity. Ovalbumin (OVA) is a commonly used carrier protein. The mechanism of FA binding with OVA was investigated by utilizing a variety of spectral analyses, accompanied by computer simulation. RESULTS It was discovered that the fluorescence quenching mechanism of OVA by FA was a static mode as a result of the formation of an FA-OVA complex, which was verified by the concentration distributions and pure spectrum of the constituents decomposed from the high overlap spectrum signals using multivariate curve resolution-alternate least squares algorithm. Hydrogen bonds and Van der Waals forces drove the formation of FA-OVA complex with a binding constant of 1.69 × 104 L mol-1 . The presence of FA induced the loose structure of OVA with an attenuation of α-helix content and improved the thermal stability of OVA. Computer docking indicated that FA interacted with the amino acid residues Arg84, Asn88, Leu101 and Ser103 of OVA through hydrogen bonds. Molecular dynamics simulation proved that the combination of FA with OVA boosted the conformational stability of OVA and hydrogen bonds brought a crucial part in stabilizing the structure of the complex. CONCLUSIONS The study may supply the theoretical basis for the design of FA transport system using OVA as carrier protein to improve the instability and low bioavailability of FA. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Lei Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Miao Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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Gorla MR, Sarma M. Synthesis of Pyrazole–Oxothiazolidine Hybrids as Potential Anticancer Agents in [Bmim]OH Ionic Liquid Medium. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022040157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kalpana K, Rani VA, Kiran BR. One-Pot Pseudo-Five-Component Synthesis of 2,3-Dihydroquinazolin-4(1H)-one Derivatives via [DBU][OAc] as Ionic Liquid, and Their Anti-Cancer Evaluation and Molecular Modelling. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222060196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Synthesis, in-vivo anti-diabetic & anticancer activities and molecular modelling studies of tetrahydrobenzo[d]thiazole tethered nicotinohydrazide derivatives. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Kalpana K, Rani VA, Seshadri S, Kiran BR. BMIM[BF4]: An Efficient Ionic Liquid Medium for the Synthesis of Chromeno[b]pyridines as Potential Anticancer Agents. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021090177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kalpana K, Syed R, Saranya J, Rafi M, Kiran BR. Synthesis and Theoretical Study of Novel Imidazo[4,5-b]pyrazine-Conjugated Benzamides as Potential Anticancer Agents. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021090153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Imam HT, Krasňan V, Rebroš M, Marr AC. Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis. Molecules 2021; 26:4791. [PMID: 34443378 PMCID: PMC8399596 DOI: 10.3390/molecules26164791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.
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Affiliation(s)
- Hasan Tanvir Imam
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
| | - Vladimír Krasňan
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Andrew Craig Marr
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
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Kadaf Manea Y, Banu A, Qashqoosh MT, Mumtaz Khan A, Alahdal FM, Ahmad Wani A, Salem MA, Naqvi S. Interaction of AMOT@CS NPs and AMOT drug with bovine serum albumin: Insights from spectroscopic and molecular docking techniques. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Ghorbani SM, Housaindokht MR, Bozorgmehr MR. Investigating the effect of 1-Butyl-3-methylimidazolium bromide and 1-Butyl-3-methylimidazolium methyl sulfate ionic liquids on structure and function of Chloroproxidase by molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Qureshi S, Khandelwal R, Madhavi M, Khurana N, Gupta N, Choudhary SK, Suresh RA, Hazarika L, Srija CD, Sharma K, Hindala MR, Hussain T, Nayarisseri A, Singh SK. A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma. Curr Top Med Chem 2021; 21:790-818. [PMID: 33463471 DOI: 10.2174/1568026621666210119112336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). AIM The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. METHODOLOGY Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhibitor (PubChem ID: 66760355) were recognized as drugs with high binding capacity with their respective protein receptors. 41, 72, 102 and 3 virtual screened compounds were obtained after the similarity search with compound (PubChem ID:102173753), PubChem compound SCHEMBL15569297 (PubChem ID:72374403), PubChem compound SCHEMBL17075298 (PubChem ID:136970120) and compound CID: 71814473 with best virtual screened compounds. RESULT MMP9 inhibitors show commendable affinity and good interaction profile of compound holding PubChem ID:102173753 over the most effective established inhibitor SB-3CT. The pharmacophore study of the best virtual screened compound reveals its high efficacy based on various interactions. The virtual screened compound's better affinity with the target MMP9 protein was deduced using toxicity and integration profile studies. CONCLUSION Based on the ADMET profile, the compound (PubChem ID: 102173753) could be a potent drug for MCL treatment. Similar to the established SB-3CT, the compound was non-toxic with LD50 values for both the compounds lying in the same range.
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Affiliation(s)
- Shahrukh Qureshi
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Ravina Khandelwal
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Maddala Madhavi
- Department of Zoology, Nizam College, Osmania University, Hyderabad - 500001, Telangana State, India
| | - Naveesha Khurana
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Neha Gupta
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Saurav K Choudhary
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Revathy A Suresh
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Lima Hazarika
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Chillamcherla D Srija
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Khushboo Sharma
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Mali R Hindala
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Tajamul Hussain
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
| | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi-630 003, Tamil Nadu, India
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20
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Investigation of interactions between zein and natamycin by fluorescence spectroscopy and molecular dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Zaboli M, Saeidnia F, Zaboli M, Torkzadeh-Mahani M. Stabilization of recombinant d-Lactate dehydrogenase enzyme with trehalose: Response surface methodology and molecular dynamics simulation study. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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Zhao H. What do we learn from enzyme behaviors in organic solvents? - Structural functionalization of ionic liquids for enzyme activation and stabilization. Biotechnol Adv 2020; 45:107638. [PMID: 33002582 DOI: 10.1016/j.biotechadv.2020.107638] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/05/2020] [Accepted: 09/25/2020] [Indexed: 12/16/2022]
Abstract
Enzyme activity in nonaqueous media (e.g. conventional organic solvents) is typically lower than in water by several orders of magnitude. There is a rising interest of developing new nonaqueous solvent systems that are more "water-like" and more biocompatible. Therefore, we need to learn from the current state of nonaqueous biocatalysis to overcome its bottleneck and provide guidance for new solvent design. This review firstly focuses on the discussion of how organic solvent properties (such as polarity and hydrophobicity) influence the enzyme activity and stability, and how these properties impact the enzyme's conformation and dynamics. While hydrophobic organic solvents usually lead to the maintenance of enzyme activity, solvents carrying functional groups like hydroxys and ethers (including crown ethers and cyclodextrins) can lead to enzyme activation. Ionic liquids (ILs) are designable solvents that can conveniently incorporate these functional groups. Therefore, we systematically survey these ether- and/or hydroxy-functionalized ILs, and find most of them are highly compatible with enzymes leading to high activity and stability. In particular, ILs carrying both ether and tert-alcohol groups are among the most enzyme-activating solvents. Future direction is to learn from enzyme behaviors in both water and nonaqueous media to design biocompatible "water-like" solvents.
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Affiliation(s)
- Hua Zhao
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO 80639, United States.
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Taherimehr Z, Zaboli M, Torkzadeh-Mahani M. New insight into the molecular mechanism of the trehalose effect on urate oxidase stability. J Biomol Struct Dyn 2020; 40:1461-1471. [PMID: 33000700 DOI: 10.1080/07391102.2020.1828167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinant expression of UOX in E. coli BL21 cells, firstly the coding sequence was subcloned into the pET-28a vector and after induction with IPTG, the recombinant UOX was purified by affinity chromatography using a Ni-NTA agarose column. To specify the trehalose effects on the urate oxidase (UOX) structure, optimum pH, optimum temperature, kinetic and thermodynamic parameters and also, the intrinsic fluorescence of UOX in the absence and presence of trehalose were examined. The UOX half-life is 24.32 min at 40 °C, whereas the UOX-TRE has a higher half-life (32.09 min) at this temperature. Generally, our findings confirm that trehalose has a protective effect on the enzyme structure. Optimum pH and temperature were 9 and 25 °C, respectively for both the naked and treated enzymes and their activity retained 42.18 and 64.80%, respectively after 48 h of incubation at room temperature. Also, theoretical results indicate that the random coil of the enzyme was converted to α-helix and β-sheet in the presence of trehalose which may preserve the integrity of the active site of the enzyme and increased the enzymatic activity. The MD simulation results indicated greater stability of the uricase structure in the presence of trehalose.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Taherimehr
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
| | - Maryam Zaboli
- Department of chemistry, Faculty of science, University of Birjand, Birjand, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
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Torkzadeh‐Mahani M, Zaboli M, Barani M, Torkzadeh‐Mahani M. A combined theoretical and experimental study to improve the thermal stability of recombinant D‐lactate dehydrogenase immobilized on a novel superparamagnetic Fe3O4NPs@metal–organic framework. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5581] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Mahdieh Torkzadeh‐Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental SciencesGraduate University of Advanced Technology Kerman‐Iran Iran
| | - Maryam Zaboli
- Department of Chemistry, Faculty of ScienceUniversity of Birjand Birjand Iran
| | - Mahmood Barani
- Department of ChemistryShahid Bahonar University of Kerman Kerman Iran
| | - Masoud Torkzadeh‐Mahani
- Department of Biotechnology, Institute of Science and High Technology and Environmental SciencesGraduate University of Advanced Technology Kerman‐Iran Iran
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