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Gufe C, Jambwa P, Marumure J, Makuvara Z, Khunrae P, Kayoka-Kabongo PN. Are phenolic compounds produced during the enzymatic production of prebiotic xylooligosaccharides (XOS) beneficial: a review. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:867-882. [PMID: 38594834 DOI: 10.1080/10286020.2024.2328723] [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: 09/25/2023] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
Phenolics produced during xylooligosaccharide production might inhibit xylanases and enhance the antioxidant and antimicrobial activities of XOS. The effects of phenolic compounds on xylanases may depend on the type and concentration of the compound, the plant biomass used, and the enzyme used. Understanding the effects of phenolic compounds on xylanases and their impact on XOS is critical for developing viable bioconversion of lignocellulosic biomass to XOS. Understanding the complex relationship between phenolic compounds and xylanases can lead to the development of strategies that improve the efficiency and cost-effectiveness of XOS manufacturing processes and optimise enzyme performance.
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Affiliation(s)
- Claudious Gufe
- Department of Veterinary Technical Services, Central Veterinary Laboratories, Borrowdale Road, Harare, Zimbabwe
| | - Prosper Jambwa
- Department of Veterinary Biosciences, Faculty of Veterinary Science, University of Zimbabwe, Mount Pleasant, Harare, Zimbabwe
| | - Jerikias Marumure
- School of Natural Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
| | - Zakio Makuvara
- School of Natural Sciences, Great Zimbabwe University, Masvingo, Zimbabwe
| | - Pongsak Khunrae
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, Thailand
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Mir SA, Razzokov J, Mukherjee V, Baitharu I, Nayak B. An exploration of the binding prediction of anatoxin-a and atropine to acetylcholinesterase enzyme using multi-level computer simulations. Phys Biol 2023; 21:016002. [PMID: 37963412 DOI: 10.1088/1478-3975/ad0caa] [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: 07/15/2023] [Accepted: 11/14/2023] [Indexed: 11/16/2023]
Abstract
Acetylcholinesterase (AChE) is crucial for the breakdown of acetylcholine to acetate and choline, while the inhibition of AChE by anatoxin-a (ATX-a) results in severe health complications. This study explores the structural characteristics of ATX-a and its interactions with AChE, comparing to the reference molecule atropine for binding mechanisms. Molecular docking simulations reveal strong binding affinity of both ATX-a and atropine to AChE, interacting effectively with specific amino acids in the binding site as potential inhibitors. Quantitative assessment using the MM-PBSA method demonstrates a significantly negative binding free energy of -81.659 kJ mol-1for ATX-a, indicating robust binding, while atropine exhibits a stronger binding affinity with a free energy of -127.565 kJ mol-1. Umbrella sampling calculates the ΔGbindvalues to evaluate binding free energies, showing a favorable ΔGbindof -36.432 kJ mol-1for ATX-a and a slightly lower value of -30.12 kJ mol-1for atropine. This study reveals the dual functionality of ATX-a, acting as both a nicotinic acetylcholine receptor agonist and an AChE inhibitor. Remarkably, stable complexes form between ATX-a and atropine with AChE at its active site, exhibiting remarkable binding free energies. These findings provide valuable insights into the potential use of ATX-a and atropine as promising candidates for modulating AChE activity.
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Affiliation(s)
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- School of Engineering, Central Asian University, Milliy Bog Street 264, Tashkent 111221, Uzbekistan
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Chemistry, Termez State University, Barkamol Avlod Street 43, Termez 190111, Uzbekistan
| | | | - Iswar Baitharu
- Department of Environmental Sciences, Sambalpur University, Odisha 768019, India
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Odisha 768019, India
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Insight into the glycerol extraction from biodiesel using deep eutectic solvents. J Mol Model 2023; 29:54. [PMID: 36701046 DOI: 10.1007/s00894-023-05453-3] [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: 11/05/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023]
Abstract
CONTEXT The main challenge of large-scale biofuel production is related to the extraction of its undesired impurities including glycerol, water, methanol, soap/catalyst, free fatty acids, glycerides, and others. There are many ways to remove glycerol, and herein, the one alternative is the extraction of glycerol from biodiesel by deep eutectic solvents. In this regard, the mixture of a choline chloride (ChCl) and urea, methyltriphenylphosphonium chloride (MTPPCl), and ethylene glycol (EGL), as a deep eutectic solvent (DES), is effective in removing glycerol from biofuel. METHODS In this work, we have investigated the formation mechanism of ChCl and urea, and then MTPPCl and EGL, as a DES, and then extraction of glycerol from biofuel via DES implementing density functional theory (DFT) by Gaussian09 software, B3LYP basis set, and classical all-atom molecular dynamics (MD) simulations by Gromacs software, GROMOS force field. DFT approximation demonstrates that Cl ion plays an important binding role in the formation of complexes ChCl/urea-based DES + biofuel and in MTPPCl/EGL-based DES + biofuel. We have also considered the formation and change of hydrogen bonds upon the formation of these systems using the DFT method. Large HOMO-LUMO gaps in ChCl/urea-based DES + biofuel and in MTPPCl/urea-based DES + biofuel demonstrate the stability of the complexes. The results of MD work have stated that the chloride ion formed bonding with the choline/ethylene glycol EGL, while still weakly intermolecular interacting with the urea/methyltriphenylphosphonium in ChCl/urea- and MTPPCl/EGL-based DESs. Further results of MD simulations stated that the DESs had a higher intermolecular interaction with glycerol in comparison with biofuel, thereby favoring the extraction process of glycerol from model biofuel. HIGHLIGHTS • Intermolecular interactions of choline chloride and urea, methyl triphenyl phosphonium chloride, and ethylene glycol-based DESs and their applications in the extraction of glycerol from biofuel studied by DFT calculations and classical all-atom molecular dynamics simulations. • Calculated outputs of DFT calculations and classical all-atom molecular dynamics simulations for DESs and their applications in the extraction of glycerol from biofuel were discussed in detail. • The molecular formation mechanism of choline and methyl triphenyl phosphonium-based DESs and their application in the extraction process of glycerol from biofuel were summarized.
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Mir SA, Muhammad A, Padhiary A, Ekka NJ, Baitharu I, Naik PK, Nayak B. Identification of potent EGFR-TKD inhibitors from NPACT database through combined computational approaches. J Biomol Struct Dyn 2023; 41:12063-12076. [PMID: 36695102 DOI: 10.1080/07391102.2023.2171133] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/27/2022] [Indexed: 01/26/2023]
Abstract
Cancer is the world's second leading cause of death, and there are no approved herbal therapies. The epidermal growth factor receptor tyrosine kinase (EGFR-TK) receptor is a transmembrane protein with eight domains that is found in almost every cancer type and plays an important role in abnormal cell cellular function and causes malignant outcomes. The current study aimed to virtually screen phytochemicals from the NPACT database against EGFR-TKD and also to identify potential inhibitors of this transmembrane protein among plant candidates for anticancer drug development. The docking scores of the chosen phytochemicals were compared with the control (erlotinib). Kurarinone, (2S)-2-methoxykurarnione, and Sophoraflavanone-G exhibited a stronger binding affinity of -18.102 kcal/mol, -14.243 kcal/mol, and -13.759 kcal/mol than erlotinib -12.783 kcal/mol. Moreover, several online search engines were used to predict ADME and toxicity. The drug-likeness of selected phytochemicals was higher than the reference (erlotinib). A 100 ns molecular dynamic (MD) simulation was also applied to the docked conformations to examine the stability and molecular mechanics of protein-ligand interactions. Furthermore, the calculated molecular mechanics Poisson Boltzmann surface area energy of (2S)-2-methoxykurarnione was found to be -129.555 ± 0.512 kJ/mol, which approximately corresponds to the free energy of the reference molecule -130.595 ± 0.908 kJ/mol. We identify phytoconstituents present in Sophora flavescens from the NPACT database, providing key insights into tyrosine kinase inhibition and may serve as better chemotherapeutic agents. Experimental validation is required to determine the anti-EGFR potency of the potent lead molecules discussed in this study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Showkat Ahmad Mir
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Odisha, India
| | - Auwal Muhammad
- Department of Physics, Kano University of Science and Technology, Wudil, Nigeria
| | - Archana Padhiary
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Odisha, India
| | - Nirius Jenen Ekka
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Odisha, India
| | - Iswar Baitharu
- Department of Environmental Sciences, Sambalpur University, Jyoti Vihar, Odisha, India
| | - Pradeep Kumar Naik
- Department of Biotechnology and Bioinformatics, Sambalpur University, Jyoti Vihar, Odisha, India
| | - Binata Nayak
- School of Life Sciences, Sambalpur University, Jyoti Vihar, Odisha, India
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Charupanit K, Tipmanee V, Sutthibutpong T, Limsakul P. In Silico Identification of Potential Sites for a Plastic-Degrading Enzyme by a Reverse Screening through the Protein Sequence Space and Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103353. [PMID: 35630830 PMCID: PMC9143596 DOI: 10.3390/molecules27103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
The accumulation of polyethylene terephthalate (PET) seriously harms the environment because of its high resistance to degradation. The recent discovery of the bacteria-secreted biodegradation enzyme, PETase, sheds light on PET recycling; however, the degradation efficiency is far from practical use. Here, in silico alanine scanning mutagenesis (ASM) and site-saturation mutagenesis (SSM) were employed to construct the protein sequence space from binding energy of the PETase–PET interaction to identify the number and position of mutation sites and their appropriate side-chain properties that could improve the PETase–PET interaction. The binding mechanisms of the potential PETase variant were investigated through atomistic molecular dynamics simulations. The results show that up to two mutation sites of PETase are preferable for use in protein engineering to enhance the PETase activity, and the proper side chain property depends on the mutation sites. The predicted variants agree well with prior experimental studies. Particularly, the PETase variants with S238C or Q119F could be a potential candidate for improving PETase. Our combination of in silico ASM and SSM could serve as an alternative protocol for protein engineering because of its simplicity and reliability. In addition, our findings could lead to PETase improvement, offering an important contribution towards a sustainable future.
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Affiliation(s)
- Krit Charupanit
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand; (K.C.); (V.T.)
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand;
- Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Praopim Limsakul
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Center of Excellence for Trace Analysis and Biosensor (TAB-CoE), Faculty of Science, Prince of Songkla University, Songkhla 90110, Thailand
- Correspondence:
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Gufe C, Sutthibutpong T, Muhammad A, Ngenyoung A, Rattanarojpong T, Khunrae P. Role of F124 in the inhibition of Bacillus firmus K-1 Xyn11A by monomeric aromatic phenolic compounds. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Effects of the outer-cleft aromatic ring deletion on the resistivity of a GH11 xylanase to the lignin-like monolignol aggregates. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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A Computational Study to Identify Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) from Eucalyptus Active Compounds. COMPUTATION 2020. [DOI: 10.3390/computation8030079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found to be a severe threat to global public health in late 2019. Nevertheless, no approved medicines have been found to inhibit the virus effectively. Anti-malarial and antiviral medicines have been reported to target the SARS-CoV-2 virus. This paper chose eight natural eucalyptus compounds to study their binding interactions with the SARS-CoV-2 main protease (Mpro) to assess their potential for becoming herbal drugs for the new SARS-CoV-2 infection virus. In-silico methods such as molecular docking, molecular dynamics (MD) simulations, and Molecular Mechanics Poisson Boltzmann Surface Area (MM/PBSA) analysis were used to examine interactions at the atomistic level. The results of molecular docking indicate that Mpro has good binding energy for all compounds studied. Three docked compounds, α-gurjunene, aromadendrene, and allo-aromadendrene, with highest binding energies of −7.34 kcal/mol (−30.75 kJ/mol), −7.23 kcal/mol (−30.25 kJ/mol), and −7.17 kcal/mol (−29.99 kJ/mol) respectively, were simulated with GROningen MAchine for Chemical Simulations (GROMACS) to measure the molecular interactions between Mpro and inhibitors in detail. Our MD simulation results show that α-gurjunene has the strongest binding energy of −20.37 kcal/mol (−85.21 kJ/mol), followed by aromadendrene with −18.99 kcal/mol (−79.45 kJ/mol), and finally allo-aromadendrene with −17.91 kcal/mol (−74.95 kJ/mol). The findings indicate that eucalyptus may be used to inhibit the Mpro enzyme as a drug candidate. This is the first computational analysis that gives an insight into the potential role of structural flexibility during interactions with eucalyptus compounds. It also sheds light on the structural design of new herbal medicinal products against Mpro.
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Mathibe BN, Malgas S, Radosavljevic L, Kumar V, Shukla P, Pletschke BI. Lignocellulosic pretreatment-mediated phenolic by-products generation and their effect on the inhibition of an endo-1,4-β-xylanase from Thermomyces lanuginosus VAPS-24. 3 Biotech 2020; 10:349. [PMID: 32728516 DOI: 10.1007/s13205-020-02343-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
The inhibitory effect of eight model lignin derivatives (ferulic acid, guaiacol, kraft lignin (alkali, low sulfonate content), p-coumaric acid, gallic acid, syringic acid, vanillin and vanillic acid) on XynA activity was evaluated. The model lignin derivatives viz. gallic acid, vanillic acid and vanillin were inhibitory to XynA activity, with an over 50% reduction in activity at concentrations as low as 0.5 mg/ml. However, enzyme deactivation studies in the absence of substrate showed that these pretreatment by-products do not interact with the enzyme except when in the presence of its substrate. The effect of the main structural properties of the pretreatment-derived phenolics, for example their hydroxyl and carbonyl group types, on XynA enzyme inhibition was investigated. The presence of carbonyl groups in phenolics appeared to confer stronger inhibitory effects than hydroxyl groups on XynA activity. The hydrolytic potential of XynA was not inhibited by a mixture of phenolics derived after steam pretreatment of woody biomass (Douglas fir and Black wattle). It appears as if the liquors from steam-pretreated woody biomass did not possess high enough phenolic content to confer XynA inhibition. The xylanase (XynA from Thermomyces lanuginosus) is, therefore, a striking choice for application in biofuel and fine chemical industries for the xylan degradation in steam-pretreated biomass.
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Affiliation(s)
- Brian N Mathibe
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 Eastern Cape South Africa
| | - Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 Eastern Cape South Africa
| | - Layla Radosavljevic
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 Eastern Cape South Africa
| | - Vishal Kumar
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 Haryana India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 Haryana India
| | - Brett I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 Eastern Cape South Africa
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