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Akter N, Islam MSU, Rahman MS, Zohra FT, Rahman SM, Manirujjaman M, Sarkar MAR. Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses. PLoS One 2024; 19:e0298543. [PMID: 38507444 PMCID: PMC10954154 DOI: 10.1371/journal.pone.0298543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 01/25/2024] [Indexed: 03/22/2024] Open
Abstract
Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.
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Affiliation(s)
- Nasrin Akter
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Shohel Ul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - M. Manirujjaman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, New Orleans, Louisiana, LA, United States of America
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Liu JL, Yao J, Li R, Liu H, Zhu JJ, Sunahara G, Duran R. Unraveling assemblage of microbial community dwelling in Dabaoshan As/Pb/Zn mine-impacted area: A typical mountain mining area of South China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168850. [PMID: 38043811 DOI: 10.1016/j.scitotenv.2023.168850] [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: 09/19/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Microbial community assemblage includes microorganisms from the three domains including Bacteria, Archaea, and Eukarya (Fungi), which play a crucial role in geochemical cycles of metal(loid)s in mine tailings. Mine tailings harbor vast proportions of metal(loid)s, representing a unique source of co-contamination of metal(loid)s that threaten the environment. The elucidation of the assembly patterns of microbial communities in mining-impacted ecospheres has received little attention. To decipher the microbial community assembly processes, the microbial communities from the five sites of the Dabaoshan mine-impacted area were profiled by the MiSeq sequencing of 16S rRNA (Bacteria and Archaea) genes and internal transcribed spacers (Fungi). Results indicated that the coexistence of 31 bacterial, 10 fungal, and 3 archaeal phyla, were mainly dominated by Mucilaginibacter, Cladophialophora, and Candidatus Nitrosotalea, respectively. The distribution of microorganisms was controlled by deterministic processes. The combination of Cu, Pb, and Sb was the main factor explaining the structure of microbial communities. Functional predicting analysis of bacteria and archaea based on the phylogenetic investigation of communities by reconstruction of unobserved states analyses revealed that the metabolic pathways related to arsenite transporter, arsenate reductase, and FeS cluster were important for metal detoxification. Furthermore, the ecological guilds (pathogens, symbiotrophs, and saprotrophs) of fungal communities explained 44.5 % of functional prediction. In addition, metal-induced oxidative stress may be alleviated by antioxidant enzymes of fungi communities, such as catalase. Such information provides new insights into the microbial assembly rules in co-contaminated sites.
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Affiliation(s)
- Jian-Li Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China.
| | - Jun Yao
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Ruofei Li
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Houquan Liu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Jun-Jie Zhu
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China
| | - Geoffrey Sunahara
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China; Department of Natural Resource Sciences, McGill University, Montreal, Quebec H9X3V9, Canada
| | - Robert Duran
- School of Water Resources and Environment and Research Center of Environmental Science and Engineering, Sino-Hungarian Joint Laboratory of Environmental Science and Health, Beijing Key Laboratory of Water Resources & Environmental Engineering, China University of Geosciences (Beijing), 29 Xueyuan Road, Haidian District, 100083 Beijing, China; Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, BP 1155, 64013 Pau Cedex, France
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Bhati R, Nigam A, Ahmad S, Raza K, Singh R. Structural-functional analysis and molecular characterization of arsenate reductase from Enterobacter cloacae RSC3 for arsenic biotransformation. 3 Biotech 2023; 13:305. [PMID: 37593205 PMCID: PMC10427597 DOI: 10.1007/s13205-023-03730-9] [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: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023] Open
Abstract
Enterobacter cloacae RSC3 isolated from an industrial pesticide site transformed arsenate into arsenite. The arsenate is transported by membrane-bound phosphate transporter and transformed to arsenite by arsenate reductase (arsC). E. cloacae RSC3 produced an arsenate reductase enzyme with a maximum activity of 354 U after 72 h of incubation. Arsenate reductase was found to be active and stable at a wide range of temperatures (20 and 45 °C) and pH (5-10), with maximum activity at 35 °C and pH 7.0. The arsenate reductase protein was further characterised molecularly using different bioinformatics tools. The 3D structure of ArsC protein was predicted by homology modelling and validated by the Ramachandran plot with 91.9% residues in the most favoured region. ArsC protein of E. cloacae RSC3 revealed structural homology with ArsC from PDB ID: 1S3C. The gene ontology results also showed that the ArsC protein had a molecular functionality of the arsenate reductase (glutaredoxin) activity and the biological function of cellular response to DNA damage stimulus. Molecular docking analysis of 3D structures using AutoDock vina-1.5.7 server predicted four ligand binding active site residues at Gln70, Asp68, Leu68, and Leu63. Strong ArsC-arsenate ion interaction was observed with binding energy -1.03 kcal/mol, indicating significant arsenate reductase activity and specificity of ArsC protein. On the basis of molecular dynamics simulation analysis, the RMSD and RMSF values revealed the stability of ArsC protein from E. cloacae RSC3. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03730-9.
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Affiliation(s)
- Reeta Bhati
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
| | - Arti Nigam
- Institute of Home Economics, University of Delhi, New Delhi, 110016 India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
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Kabiraj A, Laha A, Panja AS, Bandopadhyay R. In silico comparative structural and functional analysis of arsenite methyltransferase from bacteria, fungi, fishes, birds, and mammals. J Genet Eng Biotechnol 2023; 21:64. [PMID: 37204693 DOI: 10.1186/s43141-023-00522-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Arsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. RESULTS Several arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from - 0.93 to - 1.30, ERRAT score (83-96), PROCHECK (88-92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein-protein interaction networks. CONCLUSION All of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation.
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Affiliation(s)
- Ashutosh Kabiraj
- Department of Botany, UGC-Centre for Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
| | - Anubhab Laha
- Department of Botany, UGC-Centre for Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India
- Department of Botany, Chandernagore College, Hooghly, Chandernagore, West Bengal, 712136, India
| | - Anindya Sundar Panja
- Molecular Informatics Laboratory, Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Rajib Bandopadhyay
- Department of Botany, UGC-Centre for Advanced Study, The University of Burdwan, Golapbag, Bardhaman, West Bengal, 713104, India.
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Khazamipour A, Gholampour-Faroji N, Zeraati T, Vakilian F, Haddad-Mashadrizeh A, Ghayour Mobarhan M, Pasdar A. A novel causative functional mutation in GATA6 gene is responsible for familial dilated cardiomyopathy as supported by in silico functional analysis. Sci Rep 2022; 12:13752. [PMID: 35962153 PMCID: PMC9374661 DOI: 10.1038/s41598-022-13993-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Dilated cardiomyopathy (DCM), one of the most common types of cardiomyopathies has a heterogeneous nature and can be seen in Mendelian forms. Next Generation Sequencing is a powerful tool for identifying novel variants in monogenic disorders. We used whole-exome sequencing (WES) and Sanger sequencing techniques to identify the causative mutation of DCM in an Iranian pedigree. We found a novel variant in the GATA6 gene, leading to substituting Histidine by Tyrosine at position 329, observed in all affected family members in the pedigree, whereas it was not established in any of the unaffected ones. We hypothesized that the H329Y mutation may be causative for the familial pattern of DCM in this family. The predicted models of GATA6 and H329Y showed the high quality according to PROCHECK and ERRAT. Nonetheless, simulation results revealed that the protein stability decreased after mutation, while the flexibility may have been increased. Hence, the mutation led to the increased compactness of GATA6. Overall, these data indicated that the mutation could affect the protein structure, which may be related to the functional impairment of GATA6 upon H329Y mutation, likewise their involvement in pathologies. Further functional investigations would help elucidating the exact mechanism.
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Affiliation(s)
- Afrouz Khazamipour
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Nazanin Gholampour-Faroji
- Biotechnology Department, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Tina Zeraati
- Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farveh Vakilian
- Atherosclerosis Prevention Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aliakbar Haddad-Mashadrizeh
- Industrial Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Majid Ghayour Mobarhan
- Metabolic Syndrome Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Division of Applied Medicine, Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK. .,Bioinformatics Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran.
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Zhan Y, Wang M, Ma T, Li Z. Enhancing the potential production of bioethanol with bamboo by γ-valerolactone/water pretreatment. RSC Adv 2022; 12:16942-16954. [PMID: 35754883 PMCID: PMC9171899 DOI: 10.1039/d2ra02421g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
In this study, the effect of the γ-valerolactone (GVL)/H2O pretreatment system on bamboo (Neosinocalamus affinis) for enzymatic hydrolysis and ethanol fermentation was investigated. The performance characterization of the pretreated bamboo substrates, including the chemical composition, the structural characteristics, and the ability to produce bioethanol, were evaluated. The recovered substrates were enzymatically hydrolyzed for 48 h and then fermented to bioethanol. For the cellulose in the raw bamboo material, the highest cellulose-to-glucose conversion yield (CGCY) was achieved at 140 °C for 2 h with GVL : H2O = 8 : 2, which was 73.39%, and the cellulose-to-ethanol conversion yield (CECY) was 67.00%. This indicated that 183.5 kg of bioethanol could be produced per ton of bamboo, which was 9.71-folds higher than that directly converted from the untreated raw bamboo powder. Under these conditions, 50.60% of the active lignin can be recovered and be used as a wood-derived feedstock for further high-valued utilization. Meanwhile, the maximum concentration of fermentation inhibitors formed after pretreatment was about 140.9 mmol L-1, and had weak inhibition to the subsequent reaction. It has been shown that the cellulose could be effectively separated from bamboo and converted into bioethanol through the GVL/H2O pretreatment system.
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Affiliation(s)
- Yawei Zhan
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology Beijing 100102 China
| | - Meixin Wang
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology Beijing 100102 China
| | - Tengfei Ma
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology Beijing 100102 China
| | - Zhiqiang Li
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology Beijing 100102 China
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Lin C, Cheruiyot NK, Bui XT, Ngo HH. Composting and its application in bioremediation of organic contaminants. Bioengineered 2022; 13:1073-1089. [PMID: 35001798 PMCID: PMC8805880 DOI: 10.1080/21655979.2021.2017624] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
This review investigates the findings of the most up-to-date literature on bioremediation via composting technology. Studies on bioremediation via composting began during the 1990s and have exponentially increased over the years. A total of 655 articles have been published since then, with 40% published in the last six years. The robustness, low cost, and easy operation of composting technology make it an attractive bioremediation strategy for organic contaminants prevalent in soils and sediment. Successful pilot-and large-scale bioremediation of organic contaminants, e.g., total petroleum hydrocarbons, plasticizers, and persistent organic pollutants (POPs) by composting, has been documented in the literature. For example, composting could remediate >90% diesel with concentrations as high as 26,315 mg kg−a of initial composting material after 24 days. Composting has unique advantages over traditional single- and multi-strain bioaugmentation approaches, including a diverse microbial community, ease of operation, and the ability to handle higher concentrations. Bioremediation via composting depends on the diverse microbial community; thus, key parameters, including nutrients (C/N ratio = 25–30), moisture (55–65%), and oxygen content (O2 > 10%) should be optimized for successful bioremediation. This review will provide bioremediation and composting researchers with the most recent finding in the field and stimulate new research ideas.
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Affiliation(s)
- Chitsan Lin
- Maritime Science and Technology, College of Maritime, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan (R.O.C.).,Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan (R.O.C.)
| | - Nicholas Kiprotich Cheruiyot
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung, Taiwan (R.O.C.)
| | - Xuan-Thanh Bui
- Key Laboratory of Advanced Waste Treatment Technology, Ho Chi Minh City University of Technology (HCMUT), Vietnam National University Ho Chi Minh (VNU-HCM), Ho Chi Minh City, Vietnam.,Faculty of Environment & Natural Resources, Ho Chi Minh City University of Technology (Hcmut), Ho Chi Minh City, Vietnam
| | - Huu Hao Ngo
- Centre for Technology in Water and Wastewater, School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, Australia
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Zheng X, Zheng T, Liao Y, Luo L. Identification of Potential Inhibitors of MurD Enzyme of Staphylococcus aureus from a Marine Natural Product Library. Molecules 2021; 26:molecules26216426. [PMID: 34770835 PMCID: PMC8587310 DOI: 10.3390/molecules26216426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that can cause fatal bacterial infections. MurD catalyzes the formation of peptide bond between UDP-N-acetylehyl-l-alanine and d-glutamic acid, which plays an important role in the synthesis of peptidoglycan and the formation of cell wall by S. aureus. Because S. aureus is resistant to most existing antibiotics, it is necessary to develop new inhibitors. In this study, Schrodinger 11.5 Prime homology modeling was selected to prepare the protein model of MurD enzyme, and its structure was optimized. We used a virtual screening program and similarity screening to screen 47163 compounds from three marine natural product libraries to explore new inhibitors of S. aureus. ADME provides analysis of the physicochemical properties of the best performing compounds during the screening process. To determine the stability of the docking effect, a 100 ns molecular dynamics was performed to verify how tightly the compound was bound to the protein. By docking analysis and molecular dynamics analysis, both 46604 and 46608 have strong interaction with the docking pocket, have good pharmacological properties, and maintain stable conformation with the target protein, so they have a chance to become drugs for S. aureus. Through virtual screening, similarity screening, ADME study and molecular dynamics simulation, 46604 and 46608 were selected as potential drug candidates for S. aureus.
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Affiliation(s)
- Xiaoqi Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Tongyu Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524023, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
- Correspondence:
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