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Lin Y, Cai Y, Li H, Li L, Jiang Z, Ni H. Efficiency enhancement in Aspergillus niger α-L-rhamnosidase reverse hydrolysis by using a tunnel site rational design strategy. Enzyme Microb Technol 2024; 180:110484. [PMID: 39079223 DOI: 10.1016/j.enzmictec.2024.110484] [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: 04/19/2024] [Revised: 06/08/2024] [Accepted: 07/14/2024] [Indexed: 09/15/2024]
Abstract
There has been ongoing interest in improving the efficiency of glycoside hydrolase for synthesizing glycoside compounds through protein engineering, given the potential applications of glycoside compounds. In this study, a strategy of modifying the substrate access tunnel was proposed to enhance the efficiency of reverse hydrolysis catalyzed by Aspergillus niger α-L-rhamnosidase. Analysis of the tunnel dynamics identified Tyr299 as a key modifiable residue in the substrate access tunnel. The location of Tyr299 was near the enzyme surface and at the outermost end of the substrate access tunnel, suggested its role in substrate recognition and throughput. Based on the properties of side chains, six mutants were designed and expressed by Pichia pastoris. Compared to WT, the reverse hydrolysis efficiencies of mutants Y299P and Y299W were increased by 21.3 % and 11.1 %, respectively. The calculation results of binding free energy showed that the binding free energy was inversely proportional to the reverse hydrolysis efficiency. Further, when binding free energy levels were comparable, the mutants with shorter side chains displayed a higher reverse hydrolysis efficiency. These results proved that substrate access tunnel modification was an effective method to improve the reverse hydrolysis efficacy of α-L-rhamnosidase and also provided new insights for modifying other glycoside hydrolases.
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Affiliation(s)
- Yanling Lin
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yuchen Cai
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Han Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Lijun Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China.
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China; Xiamen Ocean Vocational College, Xiamen 361021, China
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Sibiya A, Selvaraj C, Singh SK, Baskaralingam V. Toxicological study on ibuprofen and selenium in freshwater mussel Lamellidens marginalis and exploring the microbial cytochrome through modelling and quantum mechanics approaches for its toxicity degradation in contaminated environment. ENVIRONMENTAL RESEARCH 2024; 257:119331. [PMID: 38851371 DOI: 10.1016/j.envres.2024.119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/16/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Toxicological stress in aquatic organisms is caused by the discharge of hundreds of toxic pollutants and contaminants among which the current study concentrates on the toxic effect of non-steroidal anti-inflammatory drug ibuprofen (IBF) and the trace element selenium (Se). In this study, IBF and Se toxicity on freshwater mussel Lamellidens marginalis was studied for 14 days, and in silico predictions for their degradation were made using Molecular modelling and Quantum Mechanical approaches. The degrading propensity of cytochrome c oxidase proteins from Trametes verticillatus and Thauera selenatis (Turkey tail fungi and Gram-negative bacteria) is examined into atom level. The results of molecular modelling study indicate that ionic interactions occur in the T. selenatis-HEME bound complex by Se interacting directly with HEME, and in the T. versicolor-HEME bound complex by IBF bound to a nearby region of HEME. Experimental and theoretical findings suggest that, the toxicological effects of Se and IBF pollution can be reduced by bioremediation with special emphasis on T. versicolor, and T. selenatis, which can effectively interact with Se and IBF present in the environment and degrade them. Besides, this is the first time in freshwater mussel L. marginalis that ibuprofen and selenium toxicity have been studied utilizing both experimental and computational methodologies for their bioremediation study.
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Affiliation(s)
- Ashokkumar Sibiya
- Nano Biosciences and Nanopharmacology Division, Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Science Campus 6th Floor, Alagappa University, Karaikudi, 630004, Tamil Nadu, India
| | - Chandrabose Selvaraj
- CsrDD LAB, Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha Nagar, Thandalam, Chennai, Tamil Nadu 602105, India
| | - Sanjeev Kumar Singh
- CADD and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Science Block, Karaikudi, Tamil Nadu, 630004, India
| | - Vaseeharan Baskaralingam
- Nano Biosciences and Nanopharmacology Division, Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Science Campus 6th Floor, Alagappa University, Karaikudi, 630004, Tamil Nadu, India.
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Brandhorst E, Xu L, Klimezak M, Goegan B, Hong H, Hammes HP, Specht A, Cambridge S. In Vivo Optogenetic Manipulation of Transgene Expression in Retinal Neurovasculature. JACS AU 2024; 4:2818-2825. [PMID: 39211617 PMCID: PMC11350597 DOI: 10.1021/jacsau.4c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/27/2024] [Accepted: 06/14/2024] [Indexed: 09/04/2024]
Abstract
The retina is prone to developing pathological neovascularization, a leading cause of blindness in humans. Because excess neovascularization does not affect the entire retina, global inhibition treatment of angiogenesis critically interferes with healthy, unaffected retinal tissue. We therefore established an in vivo photoactivated gene expression paradigm which would allow light-mediated targeting of antiangiogenic genetic treatment only to affected retinal regions. We synthesized a "caged" (i.e., reversibly inhibited) photosensitive 4-hydroxytamoxifen analog. Molecular docking analyses validated its reduced transcriptional activity. Caged 4-hydroxytamoxifen was intravitreally injected into mice harboring the inducible Cre/lox system, with CreERT2 being expressed via the Tie2 promoter in the neurovasculature. Subsequent in vivo irradiation of eyes significantly induced retinal expression of a Cre-dependent transgene in retinal blood vessels. Using GFAP-CreERT2 mice, successful photoactivation was also achieved in eyes and also in ex vivo brain slices for validation of the approach. This highlights the possibility of light-mediated gene therapies specific for the retina, a key first step in personalized medicine.
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Affiliation(s)
- Eric Brandhorst
- Fifth Medical Department, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Liang Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Maxime Klimezak
- Laboratoire de Chémo-Biologie Synthétique et Thérapeutique, Equipe Nanoparticule Intelligentes, Université de Strasbourg, CNRS, CBST UMR 7199, F-67000 Strasbourg, France
| | - Bastien Goegan
- Laboratoire de Chémo-Biologie Synthétique et Thérapeutique, Equipe Nanoparticule Intelligentes, Université de Strasbourg, CNRS, CBST UMR 7199, F-67000 Strasbourg, France
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, United States
| | - Hans-Peter Hammes
- Fifth Medical Department, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Alexandre Specht
- Laboratoire de Chémo-Biologie Synthétique et Thérapeutique, Equipe Nanoparticule Intelligentes, Université de Strasbourg, CNRS, CBST UMR 7199, F-67000 Strasbourg, France
| | - Sidney Cambridge
- Dr. Senckenberg Anatomy, Anatomy II, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany
- Department of Medicine, Health and Medical University Potsdam, 14471 Potsdam, Germany
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Selvaraj C, Pedone E, Lee JK, Singh SK. Editorial: Molecular level atomistic and structural insights on biological macromolecules, inhibition, and dynamics studies. Front Mol Biosci 2024; 11:1362215. [PMID: 38516195 PMCID: PMC10955358 DOI: 10.3389/fmolb.2024.1362215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Chandrabose Selvaraj
- Computational and Structural Research in Drug Discovery Lab (CSRDD), Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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Ezhilarasan D, Shree Harini K, Karthick M, Selvaraj C. Ethyl gallate concurrent administration protects against acetaminophen-induced acute liver injury in mice: An in vivo and in silico approach. Chem Biol Drug Des 2024; 103:e14369. [PMID: 37817304 DOI: 10.1111/cbdd.14369] [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: 07/31/2023] [Revised: 09/13/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023]
Abstract
Acetaminophen (APAP) in high doses causes acute liver injury and acute liver failure. Ethyl gallate (EG) is a natural polyphenol, possessing antioxidant, anti-inflammatory, and anti-microbial properties. Therefore, in this study, we evaluated the protective role of EG against APAP-induced acute liver injury in mice. Acute liver injury was induced by a single dose of APAP (400 mg/kg., i.p.). In separate groups, EG (10 mg/kg), EG (20 mg/kg), and N-acetylcysteine (NAC; 1200 mg/kg., i.p.) were administered concurrently with APAP. The mice were sacrificed after 24 h of treatment. Liver marker enzymes of hepatotoxicity, antioxidant markers, inflammatory markers, and histopathological studies were done. APAP administration caused a significant elevation of marker enzymes of hepatotoxicity and lipid peroxidation. APAP administration also decreased enzymic and nonenzymic antioxidants. Acute APAP intoxication induced nuclear factor κ B, tumor necrosis factor-α, interleukin-1, p65, and p52 and downregulated IκB gene expressions. Our histopathological studies have confirmed the presence of centrilobular necrosis, 24 h after APAP intoxication. All the above abnormalities were significantly inhibited in groups of mice that were concurrently administered with APAP + EG and APAP + NAC. Our in silico analysis further confirms that hydroxyl groups of EG interact with the above inflammatory proteins at the 3,4,5-trihydroxybenzoic acid region. These effects of EG against APAP-induced acute liver injury could be attributed to its antioxidative, free radical scavenging, and anti-inflammatory potentials. Therefore, this study suggests that EG can be an efficient therapeutic approach to protect the liver from APAP intoxication.
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Affiliation(s)
- Devaraj Ezhilarasan
- Department of Pharmacology, Hepatology and Molecular Medicine Lab, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Karthik Shree Harini
- Department of Pharmacology, Hepatology and Molecular Medicine Lab, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Munusamy Karthick
- Department of Pharmacology, Hepatology and Molecular Medicine Lab, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Chandrabose Selvaraj
- Department of Pharmacology, Hepatology and Molecular Medicine Lab, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, India
- Laboratory for Artificial Intelligence and Molecular Modelling, Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, India
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Selvaraj C, Panwar U, Ramalingam KR, Vijayakumar R, Singh SK. Exploring the macromolecules for secretory pathway in cancer disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 133:55-83. [PMID: 36707206 DOI: 10.1016/bs.apcsb.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Secretory proteins play an important role in the tumor microenvironment and are widely distributed throughout tumor tissues. Tumor cells secrete a protein that mediates communication between tumor cells and stromal cells, thereby controlling tumor growth and affecting the success of cancer treatments in the clinic. The cancer secretome is produced by various secretory pathways and has a wide range of applications in oncoproteomics. Secretory proteins are involved in cancer development and tumor cell migration, and thus serve as biomarkers or effective therapeutic targets for a variety of cancers. Several proteomic strategies have recently been used for the analysis of cancer secretomes in order to gain a better understanding and elaborate interpretation. For instance, the development of exosome proteomics, degradomics, and tumor-host cell interaction provide clear information regarding the mechanism of cancer pathobiology. In this chapter, we emphasize the recent advances in secretory protein and the challenges in the field of secretome analysis and their clinical applications.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Umesh Panwar
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Karthik Raja Ramalingam
- Department of Biotechnology, Division of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai, Tamil Nadu, India
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Gupta M, Kumar A, Prasun C, Nair MS, Kini SG, Yadav D, Nain S. Design, synthesis, extra-precision docking, and molecular dynamics simulation studies of pyrrolidin-2-one derivatives as potential acetylcholinesterase inhibitors. J Biomol Struct Dyn 2022:1-13. [PMID: 35921217 DOI: 10.1080/07391102.2022.2106515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Inhibition of acetylcholinesterase (AChE) has been widely explored to develop novel molecules for management of Alzheimer's disease. In past research finding reported molecule 3-(4-(4-fluorobenzoyl)piperidin-1-yl)-1-(4-methoxybenzyl)pyrrolidin-2-one displayed a spectrum of anti-Alzheimer's properties herein, we report a library of 18 novel molecules that were rationally designed and synthesized employing known literature to mimic and explore the novel chemical space around the lead compound 6e and donepezil. All the compounds were docked in extra-precision mode with AChE (PDB ID 4EY7) using the Glide module. Molecular dynamics (MD) simulation studies were carried out for 100 ns along with MM-PBSA studies of the trajectory frames generated post-MD simulations. Docking and MD simulation studies suggested that the synthesized compounds showed a good binding affinity with AChE. and might form stable complexes. 3-(4-(benzyl(methyl)amino)piperidin-1-yl)-1-(3,4-dimethoxybenzyl)pyrrolidin-2-one (14a; docking score: -18.59) and 1-(3,4-dimethoxybenzyl)-3-(4-(methyl(thiazol-2-ylmethyl)amino)piperidin-1-yl)pyrrolidin-2-one (14d; docking score: -18.057) showed higher docking score than donepezil (docking score: -17.257) while most of the compounds had docking score >-10.0. ADMET study predicted these compounds to be CNS active and most of the compounds were drug-like molecules with no HERG blockade and good to excellent oral absorption. We developed an atom-based 3 D-QSAR model with R^2 and Q^2 values of 0.9639 and 0.8779 to predict the activity of the synthesized compounds. The model predicted these compounds to be potent AChE inhibitors with IC50 values in the lower micromolar range. Based on the in silico findings, we report these newly synthesized compounds 3-(4-(benzyl(methyl)amino)piperidin-1-yl)-1-(3,4-dimethoxybenzyl)pyrrolidin-2-one (14a) and 7-(2,6-difluorobenzyl)-2-(4-methoxybenzyl)-2,7-diazaspiro[4.5]decan-1-one (20 b) as potential AChE inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohan Gupta
- Department of Pharmacy ,Banasthali Vidyapith, Newai, Rajasthan, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chakrawarti Prasun
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Maya S Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Yadav
- Department of Pharmacy ,Banasthali Vidyapith, Newai, Rajasthan, India
| | - Sumitra Nain
- Department of Pharmacy ,Banasthali Vidyapith, Newai, Rajasthan, India
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