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de Souza BB, Meegoda J. Insights into PFAS environmental fate through computational chemistry: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171738. [PMID: 38494023 DOI: 10.1016/j.scitotenv.2024.171738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are widely used chemicals that exhibit exceptional chemical and thermal stability. However, their resistance to degradation has led to their widespread environmental contamination. PFAS also negatively affect the environment and other organisms, highlighting the need for effective remediation methods to mitigate their presence and prevent further contamination. Computational chemistry methods, such as Density Functional Theory (DFT) and Molecular Dynamics (MD) offer valuable tools for studying PFAS and simulating their interactions with other molecules. This review explores how computational chemistry methods contribute to understanding and tackling PFAS in the environment. PFAS have been extensively studied using DFT and MD, each method offering unique advantages and computational limitations. MD simulates large macromolecules systems however it lacks the ability model chemical reactions, while DFT provides molecular insights however at a high computational cost. The integration of DFT with MD shows promise in predicting PFAS behavior in different environments. This work summarizes reported studies on PFAS compounds, focusing on adsorption, destruction, and bioaccumulation, highlighting contributions of computational methods while discussing the need for continued research. The findings emphasize the importance of computational chemistry in addressing PFAS contamination, guiding risk assessments, and informing future research and innovations in this field.
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Affiliation(s)
- Bruno Bezerra de Souza
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Jay Meegoda
- John A. Reif, Jr. Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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El Mazouri S, Essabbar A, Aanniz T, Eljaoudi R, Belyamani L, Ibrahimi A, Ouadghiri M. Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco. Pathog Glob Health 2024; 118:241-252. [PMID: 37635364 PMCID: PMC11221468 DOI: 10.1080/20477724.2023.2250942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Among the numerous variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that have been reported worldwide, the emergence of the Omicron variant has drastically changed the landscape of the coronavirus disease (COVID-19) pandemic. Here, we analyzed the genetic diversity of Moroccan SARS-CoV-2 genomes with a focus on Omicron variant after one year of its detection in Morocco in order to understand its genomic dynamics, features and its potential introduction sources. From 937 Omicron genomes, we identified a total of 999 non-unique mutations distributed across 92 Omicron lineages, of which 13 were specific to the country. Our findings suggest multiple introductory sources of the Omicron variant to Morocco. In addition, we found that four Omicron clades are more infectious in comparison to other Omicron clades. Remarkably, a clade of Omicron is particularly more transmissible and has become the dominant variant worldwide. Moreover, our assessment of Receptor-Binding Domain (RBD) mutations showed that the Spike K444T and N460K mutations enabled a clade higher ability of immune vaccine escape. In conclusion, our analysis highlights the unique genetic diversity of the Omicron variant in Moroccan SARS-CoV-2 genomes, with multiple introductory sources and the emergence of highly transmissible clades. The distinctiveness of the Moroccan strains compared to global ones underscores the importance of ongoing surveillance and understanding of local genomic dynamics for effective response strategies in the evolving COVID-19 pandemic.
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Affiliation(s)
- Safae El Mazouri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Abdelmounim Essabbar
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Tarik Aanniz
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Rachid Eljaoudi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Lahcen Belyamani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Mouna Ouadghiri
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
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Bai J, Xie Y, Li M, Huang X, Guo Y, Sun J, Tang Y, Liu X, Wei C, Li J, Yang Y. Ultrasound-assisted extraction of emodin from Rheum officinale Baill and its antibacterial mechanism against Streptococcus suis based on CcpA. ULTRASONICS SONOCHEMISTRY 2024; 102:106733. [PMID: 38150957 PMCID: PMC10765492 DOI: 10.1016/j.ultsonch.2023.106733] [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: 03/01/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Emodin was extracted from Rheum officinale Baill by ultrasound-assisted extraction (UAE), and ethanol was chosen as the suitable solvent through SEM and molecular dynamic simulation. Under the optimum conditions (power 541 W, time 23 min, liquid to material ratio 13:1 mL/g, ethanol concentration 83 %) predicted by RSM, the yield of emodin was 2.18 ± 0.11 mg/g. Moreover, ultrasound power and time displayed the significant effects on the extraction process. Extracting dynamics analysis indicated that the extraction process of emodin by UAE conformed to Fick's second diffusion law. The results of antibacterial experiments suggested that emodin can damage cell membrane and inhibit the expression of cps2A, sao, mrp, epf, neu and the hemolytic activity of S. suis. Biolayer interferometry and FT-IR multi-peak fitting assays demonstrated that emodin induced a secondary conformational shift in CcpA. Molecular docking and molecular dynamics confirmed that emodin bound to CcpA through hydrogen bonding (ALA248, GLU249, GLY129 and ASN196) and π-π T-shaped interaction (TYR225 and TYR130), and the mutation of amino acid residues affected the affinity of CcpA to emodin. Therefore, emodin inhibited the sugar utilization of S. suis through binding to CcpA, and CcpA may be a potential target to inhibit the growth of S. suis.
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Affiliation(s)
- Jingwen Bai
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Xie
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Miao Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xianjun Huang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yujia Guo
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jingwen Sun
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yang Tang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xuantong Liu
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Chi Wei
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jianqiang Li
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yu Yang
- College of Art and Science, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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Zhu Y, Xiong H, Liu S, Wu D, Zhang X, Shi X, Qu J, Chen L, Liu Z, Peng B, Zhang D. Combining MOE Bioinformatics Analysis and In Vitro Pseudovirus Neutralization Assays to Predict the Neutralizing Ability of CV30 Monoclonal Antibody on SARS-CoV-2 Variants. Viruses 2023; 15:1565. [PMID: 37515251 PMCID: PMC10386485 DOI: 10.3390/v15071565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Combining bioinformatics and in vitro cytology assays, a predictive method was established to quickly evaluate the protective effect of immunity acquired through SARS-CoV-2 infection against variants. Bioinformatics software was first used to predict the changes in the affinity of variant antigens to the CV30 monoclonal antibody by integrating bioinformatics and cytology assays. Then, the ability of the antibody to neutralize the variant antigen was further verified, and the ability of the CV30 to neutralize the new variant strain was predicted through pseudovirus neutralization experiments. The current study has demonstrated that when the Molecular Operating Environment (MOE) predicts |ΔBFE| ≤ 3.0003, it suggests that the CV30 monoclonal antibody exhibits some affinity toward the variant strain and can potentially neutralize it. However, if |ΔBFE| ≥ 4.1539, the CV30 monoclonal antibody does not display any affinity for the variant strain and cannot neutralize it. In contrast, if 3.0003 < |ΔBFE| < 4.1539, it is necessary to conduct a series of neutralization tests promptly with the CV30 monoclonal antibody and the variant pseudovirus to obtain results and supplement the existing method, which is faster than the typical procedures. This approach allows for a rapid assessment of the protective efficacy of natural immunity gained through SARS-CoV-2 infection against variants.
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Affiliation(s)
- Yajuan Zhu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
| | - Husheng Xiong
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
| | - Shuang Liu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
| | - Dawei Wu
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaomin Zhang
- Department of Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xiaolu Shi
- Department of Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Jing Qu
- Department of Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Long Chen
- Department of Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Bo Peng
- Department of Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Dingmei Zhang
- School of Public Health, Sun Yat-Sen University, Guangzhou 510080, China
- NMPA Key Laboratory for Quality Monitoring and Evaluation of Vaccines and Biological Products, Guangzhou 510080, China
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