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Wu F, Du M, Ling J, Wang R, Hao N, Wang Z, Li X. In silico degradation of fluoroquinolones by a microalgae-based constructed wetland system. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134946. [PMID: 38941832 DOI: 10.1016/j.jhazmat.2024.134946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
Fluoroquinolone antibiotics (FQs) have been used worldwide due to their extended antimicrobial spectrum. However, the overuse of FQs leads to frequent detection in the environment and cannot be efficiently removed. Microalgae-based constructed wetland systems have been proven to be a relatively proper method to treat FQs, mainly by microalgae, plants, microorganisms, and sediments. To improve the removal efficiency of microalgae-constructed wetland, a systematic molecular design, screening, functional, and risk evaluation method was developed using three-dimensional quantitative structure-activity relationship models, molecular dynamics simulation, molecular docking, and TOPKAT approaches. Five designed ciprofloxacin alternatives with improved bactericidal effects and lower human health risks were found to be more easily degraded by microalgae (16.11-167.88 %), plants (6.72-58.86 %), microorganisms (9.10-15.02 %), and sediments (435.83 %-1763.51 %) compared with ciprofloxacin. According to the mechanism analysis, the removal effect of the FQs can be affected via changes in the number, bond energy, and molecular descriptors of favorable and unfavorable amino acids. To the best of our knowledge, this is the first comprehensive study of improving the microalgae, plants, microorganisms, and sediment removal efficiency of FQs in constructed wetlands, which provides theoretical support for the treatment of FQ pollution.
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Affiliation(s)
- Fuxing Wu
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun 130062, China
| | - Meijin Du
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Jianglong Ling
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Renjie Wang
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun 130062, China
| | - Ning Hao
- College of New Energy and Environment, Jilin University, Changchun 130012, China
| | - Zini Wang
- College of Plant Science, Jilin University, 5333 Xian Road, Changchun 130062, China
| | - Xixi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, State Environmental Protection Key Laboratory of Ecological Effect and Risk Assessment of Chemicals, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada.
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Ling J, Niu Y, Liu D, Li R, Ruan Y, Li X. Inhibition of algal blooms by residual antibiotics in aquatic environments: Design, screening, and validation of antibiotic alternatives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167914. [PMID: 37858809 DOI: 10.1016/j.scitotenv.2023.167914] [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: 09/08/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Water blooms frequently appear in the aquatic environment with global warming. However, traditional methods for treating water bloom usually require the addition of algaecides, which may lead to secondary environmental pollution problems in the water environment. To solve this problem, researchers have initiated efforts to harness pre-existing chemical substances within aquatic environments to regulate algal blooms, thereby pioneering novel avenues for water body management. Therefore, an integrated approach involving molecular docking, molecular dynamics simulations, three-dimensional quantitative structure-activity relationship (3D-QSAR), and toxicokinetics methods were utilized for the molecular modification of fluoroquinolone antibiotics, to design and screen fluoroquinolone substitutes with improved toxicity of cyanobacteria and green algae, functionality, and environmental friendliness. A total of 143 fluoroquinolone alternatives were designed in this study, and lomefloxacin-6 (LOM6) was found as the optimum alternative to lomefloxacin (LOM), with increased toxicity to cyanobacteria and green algae by 31 % and 72 %. Molecular docking of LOM before and after modification with seven other cyanobacterial and green algal photosynthetic proteins revealed that LOM6 exhibited varying degrees of increased toxicity towards 6 of these photosynthetic proteins, of which 2J96 protein increased the most (136.25 %). It shows that the residual LOM6 in the water environment has a certain inhibitory effect on the algae bloom. In addition, results showed that LOM6 had synergistic toxic effects on cyanobacteria and green algae with other pollutants residual in the aqueous environment, such as trichloroethyl phosphate, triethyl phosphate, perfluorononanoic acid, perfluorooctanoic acid. This indicates that LOM6 has better algal removal effectiveness in aqueous environments where organophosphate flame retardants and perfluorinated compounds exist together. In this paper, a novel method was developed to remove cyanobacteria and green algae in water environment and reduce the secondary pollution through theoretical simulation, which provides theoretical support for the control of water blooms.
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Affiliation(s)
- Jianglong Ling
- School of Public Health, Lanzhou University, Lanzhou 730000, China.
| | - Yong Niu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Di Liu
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Rui Li
- Center for Environmental Health Risk Assessment and Research, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Ye Ruan
- School of Public Health, Lanzhou University, Lanzhou 730000, China.
| | - Xixi Li
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's A1B 3X5, Canada.
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Wang Y, Yang H, He W, Sun P, Zhao W, Liu M. Exploring the Potential Hormonal Effects of Tire Polymers (TPs) on Different Species Based on a Theoretical Computational Approach. Polymers (Basel) 2023; 15:polym15071719. [PMID: 37050333 PMCID: PMC10097371 DOI: 10.3390/polym15071719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Tire polymers (TPs) are the most prevalent type of microplastics and are of great concern due to their potential environmental risks. This study aims to determine the toxicity of TPs with the help of molecular-dynamics simulations of their interactions with receptors and to highlight the differences in the toxicity characteristics of TPs in different environmental media (marine environment, freshwater environment, soil environment). For this purpose, five TPs—natural rubber, styrene–butadiene rubber (SBR), butadiene rubber, nitrile–butadiene rubber, and isobutylene–isoprene rubber—were analyzed. Molecular-dynamics calculations were conducted on their binding energies to neurotoxic, developmental, and reproductive receptors of various organisms to characterize the toxic effects of the five TPs. The organisms included freshwater species (freshwater nematodes, snails, shrimp, and freshwater fish), marine species (marine nematodes, mussels, crab, and marine fish), and soil species (soil nematodes, springtails, earthworms, and spiders). A multilevel empowerment method was used to determine the bio-toxicity of the TPs in various environmental media. A coupled-normalization method–principal-component analysis–factor-analysis weighting method—was used to calculate the weights of the TP toxicity (first level) categories. The results revealed that the TPs were the most biologically neurotoxic to three environmental media (20.79% and 10.57% higher compared with developmental and reproductive toxicity, respectively). Regarding the effects of TPs on organisms in various environmental media (second level), using a subjective empowerment approach, a gradual increase in toxicity was observed with increasing trophic levels due to the enrichment of TPs and the feeding behavior of organisms. TPs had the greatest influence in the freshwater-environment organisms according to the subjective empowerment approach employed to weight the three environmental media (third level). Therefore, using the minimum-value method coupled with the feature-aggregation method, the interval-deflation method coupled with the entropy-weighting method, and the standard-deviation normalization method, the three toxicity characteristics of SBR in three environmental media and four organisms were determined. SBR was found to have the greatest impact on the overall toxicity of the freshwater environment (12.38% and 9.33% higher than the marine and soil environments, respectively). The greatest contribution to neurotoxicity (26.01% and 15.95% higher than developmental and reproductive toxicity, respectively) and the greatest impact on snails and shrimp among organisms in the freshwater environment were observed. The causes of the heterogeneity of SBR’s toxicity were elucidated using amino-acid-residue analysis. SBR primarily interacted with toxic receptors through van der Waals, hydrophobic, π-π, and π-sigma interactions, and the more stable the binding, the more toxic the effect. The toxicity characteristics of TMPs to various organisms in different environments identified in this paper provide a theoretical basis for subsequent studies on the prevention and control of TMPs in the environment.
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Overview of Side-Effects of Antibacterial Fluoroquinolones: New Drugs versus Old Drugs, a Step Forward in the Safety Profile? Pharmaceutics 2023; 15:pharmaceutics15030804. [PMID: 36986665 PMCID: PMC10056716 DOI: 10.3390/pharmaceutics15030804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
Antibacterial fluoroquinolones (FQs) are frequently used in treating infections. However, the value of FQs is debatable due to their association with severe adverse effects (AEs). The Food and Drug Administration (FDA) issued safety warnings concerning their side-effects in 2008, followed by the European Medicine Agency (EMA) and regulatory authorities from other countries. Severe AEs associated with some FQs have been reported, leading to their withdrawal from the market. New systemic FQs have been recently approved. The FDA and EMA approved delafloxacin. Additionally, lascufloxacin, levonadifloxacin, nemonoxacin, sitafloxacin, and zabofloxacin were approved in their origin countries. The relevant AEs of FQs and their mechanisms of occurrence have been approached. New systemic FQs present potent antibacterial activity against many resistant bacteria (including resistance to FQs). Generally, in clinical studies, the new FQs were well-tolerated with mild or moderate AEs. All the new FQs approved in the origin countries require more clinical studies to meet FDA or EMA requirements. Post-marketing surveillance will confirm or infirm the known safety profile of these new antibacterial drugs. The main AEs of the FQs class were addressed, highlighting the existing data for the recently approved ones. In addition, the general management of AEs when they occur and the rational use and caution of modern FQs were outlined.
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Dube PS, Legoabe LJ, Beteck RM. Quinolone: a versatile therapeutic compound class. Mol Divers 2022:10.1007/s11030-022-10581-8. [PMID: 36527518 PMCID: PMC9758687 DOI: 10.1007/s11030-022-10581-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 12/23/2022]
Abstract
The discovery of nalidixic acid is one pinnacle in medicinal chemistry, which opened a new area of research that has led to the discovery of several life-saving antimicrobial agents (generally referred to as fluoroquinolones) for over decades. Although fluoroquinolones are frequently encountered in the literature, the utility of quinolone compounds extends far beyond the applications of fluoroquinolones. Quinolone-based compounds have been reported for activity against malaria, tuberculosis, fungal and helminth infections, etc. Hence, the quinolone scaffold is of great interest to several researchers in diverse disciplines. This article highlights the versatility of the quinolone pharmacophore as a therapeutic agent beyond the fluoroquinolone profile.
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Affiliation(s)
- Phelelisiwe S. Dube
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, 2520 South Africa
| | - Lesetja J. Legoabe
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, 2520 South Africa
| | - Richard M. Beteck
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, 2520 South Africa
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Fu R, Li X, Zhao Y, Pu Q, Li Y, Gu W. Efficient and synergistic degradation of fluoroquinolones by bacteria and microalgae: Design of environmentally friendly substitutes, risk regulation and mechanism analysis. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129384. [PMID: 35897172 DOI: 10.1016/j.jhazmat.2022.129384] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/02/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Fluoroquinolones (FQs) are widely used as antimicrobial agents, and their nonbiodegradable in sewage has become an increasingly concerning. High-biochemical substitutes of FQs were designed with bacteria and microalgae as driving forces of biodegradation, and this is the first study on efficient synergistic degradation of FQs by multiple microorganisms. Among 143 designed FQ substitutes, only one was screened with high biodegradability (increased by 120.51 %), improved functional properties (genotoxicity: 13.66 %), less environmental impacts (bio-accumulation: -44.81 %), less human health and ecological risk (hepatotoxicity: -106.21 %). The complex functional protein with the synergistic degradation effect of bacteria and microalgae was constructed, which proved their synergistic degradation and realized the effect of "1 + 1 > 2″. The best risk regulation scheme determined using molecular dynamics simulation proved the degradation ability of complex functional protein and found the CIP-129 was easy to be degraded in real environment compared with CIP, and the degradation rate increased by 70.42 %. The synthesis path of CIP-129 and CIP were inferred and calculated, and the results showed the Gibbs free energies of three CIP-129 synthetic paths (40.64 a.u.; 40.61 a.u.; 40.65 a.u.) were close to the energy required for the CIP (39.43 a.u.), indicating there was no significant difference in the energy consumption of CIP-129 in laboratory synthesis.
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Affiliation(s)
- Rui Fu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Xinao Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yuanyuan Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Qikun Pu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
| | - Wenwen Gu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
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Bio-Enhanced Degradation Strategies for Fluoroquinolones in the Sewage Sludge Composting Stage: Molecular Modification and Resistance Gene Regulation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19137766. [PMID: 35805422 PMCID: PMC9265465 DOI: 10.3390/ijerph19137766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023]
Abstract
The molecular/protein–protein docking and the index normalization method assisted by the entropy weight method were used to quantitatively evaluate the biodegradability of fluoroquinolones (FQs) under different biodegradation systems. Four biodegradability three-dimensional quantitative structure–activity relationship (3D-QSAR) models of FQs were constructed to design FQ derivatives with improved biodegradability. Through the evaluation of the environmental friendliness and functional properties, the FQ derivatives with high biodegradability, improved functionality, and environmental friendliness were screened. Moreover, four bio-enhanced degradation scenarios of FQs were set up according to the different temperatures and carbon–nitrogen ratio (C/N) in the sewage sludge composting stage, and the molecular dynamic (MD) simulation assisted by protein–protein docking was used to screen the external environmental factors that promote the degradation of FQs by thermophilic bacteria or group under different scenarios. Finally, MD simulation assisted by sampling method was used to validate and screen the application scheme of field measures to enhance the expression of antibacterial resistance of FQ derivatives in an agricultural soil environment after activated sludge land use. This study aims to provide theoretical support for the development of highly biodegradable FQ derivatives and the mitigation of potential risks that FQs may pose to the environment and humans through the food chain.
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Jian-Bo T, Xing Z, Shuai B, Ding L, Tian-Hao W. Topomer CoMFA and HQSAR Study on Benzimidazole Derivative as NS5B Polymerase Inhibitor. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804125607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In recent years, the number of people infected with the hepatitis C virus
(HCV) is increasing rapidly. This has become a major threat to global health, therefore, new anti-
HCV drugs are urgently needed. HCV NS5B polymerase is an RNA-dependent RNA polymerase
(RdRp), which plays an important role in virus replication, and can effectively prevent the replication
of HCV sub-genomic RNA in daughter cells. It is considered a very promising HCV therapeutic
target for the design of anti-HCV drugs.
Methods:
In order to explore the relationship between the structure of benzimidazole derivative and
its inhibitory activity on NS5B polymerase, holographic quantitative structure-activity relationship
(HQSAR) and Topomer comparative molecular field analysis (CoMFA) were used to establish benzimidazole
QSAR model of derivative inhibitors.
Results:
The results show that for the Topomer CoMFA model, the cross-validation coefficient q2
value is 0.883, and the non-cross-validation coefficient r2 value is 0.975. The model is reasonable,
reliable, and has a good predictive ability. For the HQSAR model, the cross-validated q2 value is
0.922, and the uncross-validated r2 value is 0.971, indicating that the model data fit well and has a
high predictive ability. Through the analysis of the contour map and color code diagram, 40 new
benzimidazole inhibitor molecules were designed, and all of them have higher activity than template
molecules, and the new molecules have significant interaction sites with protein 3SKE.
Conclusion:
The 3D-QSAR model established by Topomer CoMFA and HQSAR has good prediction
results and the statistical verification is valid. The newly designed molecules and docking results
provide theoretical guidance for the synthesis of new NS5B polymerase inhibitors and for the identification
of key residues that the inhibitors bind to NS5B, which helps to better understand their inhibitory
mechanism. These findings are helpful for the development of new anti-HCV drugs.
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Affiliation(s)
- Tong Jian-Bo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Zhang Xing
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Bian Shuai
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Luo Ding
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Wang Tian-Hao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
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Li X, Hou Y, Li Q, Gu W, Li Y. Molecular design of high-efficacy and high drug safety Fluoroquinolones suitable for a variety of aerobic biodegradation bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 299:113628. [PMID: 34461464 DOI: 10.1016/j.jenvman.2021.113628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
The present study attempted to improve the biodegradation removal rate of Fluoroquinolones (FQs) in sewage treatment plants. The similarity index analysis (CoMSIA) model for combined biodegradability was constructed, and 33 kinds of molecular derivatives of FQs suitable for a variety of aerobic biodegradation microorganisms were designed. Further, derivative-20 and derivative-28, with high drug efficiency, drug safety, and environmental friendliness were selected through pharmacokinetics (ADMET), toxicokinetics (TOPKAT), FQs functional characteristics, and environmental friendliness evaluations. Compared with the target molecules, the combined biodegradability of the above two FQ-derivative molecules were increased by 193.57 % and 205.07 %, respectively, while their environment-friendly characteristics were improved to a certain degree. Through molecular docking and molecular dynamic simulation analysis, it showed that van der Waals force (decreased by 2.73 %-61.74 %) was the main factor influencing the binding ability of the modified FQ molecules to the receptor proteins. In addition, the relationship among the non-bonding interaction resultant force, the binding effect of the FQ-derivative molecules, and the receptor protein-related amino acid residues were studied for the first time. It was observed that the higher the value of the non-bonding interaction resultant force, the better was the binding effect, which demonstrating the significantly improved biodegradability of the designed FQ-derivative molecules.
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Affiliation(s)
- Xinao Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; MOE Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing, 102206, China.
| | - Yilin Hou
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; MOE Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing, 102206, China.
| | - Qing Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; MOE Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing, 102206, China.
| | - Wenwen Gu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; MOE Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing, 102206, China.
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; MOE Key Laboratory of Resources and Environmental System Optimization, North China Electric Power University, Beijing, 102206, China.
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Ren Z, Wang S, Liu D, Yu J, Zhang X, Zhao P, Sun Y, Han S. Control strategies for the vertical gene transfer of quinolone ARGs in Escherichia coli through molecular modification and molecular dynamics. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126667. [PMID: 34329116 DOI: 10.1016/j.jhazmat.2021.126667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
This study investigates the regulation of the vertical gene transfer of quinolones' antibiotic resistance genes (ARGs) through a combination of source modification and process control. In source prevention, 29 Escherichia coli (E. coli) DNA gyrase subunit A mutant proteins were constructed, the B-G mutant protein displayed the greatest reduction in binding effect (-25.98%). Based on this, a 3D-QSAR model was constructed, and LEV-2 and LEV-9 QNs derivatives were designed based on Levofloxacin (LEV), and their binding effect with B-G mutant protein was found be increased by 13.24% and 19.40%. The drug resistance mechanism of E. coli was explored based on molecular docking technology and protein hydrophobic interaction theory. Most of the amino acid resistance mutations changed from hydrophilic to lipophilic, which inhibited the binding of QNs to mutant protein A subunit, and further reduced the bactericidal effect of QNs. In process control, Huoxiang-Zhengqi, stroke-physiological saline solution (SPSS), and Lycium barbarum (L. barbarum) was found to be 164.82% higher than that of the blank control group. The purpose of this study is to provide a theoretical support for the joint regulation of QNs' ARGs in organisms and the research and development on green alternatives to QNs compounds.
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Affiliation(s)
- Zhixing Ren
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Shen Wang
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Dong Liu
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Jie Yu
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Xiaoyuan Zhang
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Pingnan Zhao
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Yuxuan Sun
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
| | - Song Han
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin 150040, China.
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Sun P, Zhao W. Strategies to Control Human Health Risks Arising from Antibiotics in the Environment: Molecular Modification of QNs for Enhanced Plant-Microbial Synergistic Degradation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10610. [PMID: 34682354 PMCID: PMC8536065 DOI: 10.3390/ijerph182010610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/30/2022]
Abstract
In the present work, a comprehensive screening and evaluation system was established to improve the plant-microbial synergistic degradation effects of QNs. The study included the construction of a 3D-QSAR model, the molecular modification, environmental friendliness and functional evaluation of drugs, degradation pathway simulation, and human health risk assessment. Molecular dynamics was applied to quantify the binding capacity of QNs toward the plant degradation enzyme (peroxidase) and microbial degradation enzymes (manganese peroxidase, lignin peroxidase, and laccase). The fuzzy comprehensive evaluation method was used in combination with the weighted average method for normalization and assigning equal weights to the plant and microbial degradation effect values of the QNs. Considering the synergistic degradation effect value as the dependent variable and the molecular information of the QNs as the independent variable, a 3D-QSAR model was constructed for the plant-microbial synergistic degradation effect of QNs. The constructed model was then employed to conduct the molecular modification, environmental friendliness and functional evaluation, degradation pathway simulation, and human health risk assessment of transformation products using pharmacokinetics and toxicokinetics. The results revealed that the synergistic degradation effect 3D-QSAR (CoMSIA) model exhibited good internal and external prediction ability, fitting ability, stability, and no overfitting phenomenon. Norfloxacin (NOR) was used as the target molecule in the molecular modification. A total of 35 NOR derivatives with enhanced plant-microbial synergistic degradation effect (1.32-21.51%) were designed by introducing small-volume, strongly electronegative, and hydrophobic hydrogen bond receptor groups into the active group of the norfloxacin structure. The environment-friendliness and the functionality of NOR were evaluated prior to and after the modification, which revealed seven environment-friendly FQs derivatives exhibiting moderate improvement in stability and bactericidal efficacy. The simulation of the NOR plant and microbial degradation pathways prior to and after the modification and the calculation of the reaction energy barrier revealed Pathway A (D-17 to D-17-2) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in plants and Pathway A (D-17 to D-17-1) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in microorganisms. This demonstrated that the degradation of the modified NOR derivatives was significantly enhanced, with the hydroxylation and piperazine ring substitution reaction playing an important role in the degradation process. Finally, the parameters, including hepatotoxicity, mutagenicity, and rodent carcinogenicity, among others, predicted using the pharmacokinetics and toxicokinetics analyses revealed a significant reduction in the human health risk associated with the modified NOR, along with a considerable reduction in the toxicity of its transformation products, implying that the human health risk associated with the transformation products was reduced remarkably. The present study provides a theoretical basis for novel ideas and evaluation programs for improving the plant-microbial synergistic degradation of the QNs antibiotics for source control and drug design, thereby reducing the residues of these antibiotics and the associated hazard in the complex plant-soil environment, ultimately decreasing the potential risks to human health.
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Affiliation(s)
| | - Wenjin Zhao
- College of New Energy and Environment, Jilin University, Changchun 130012, China;
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12
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Hou Y, Li Q, He W, Li M, Xue J, Li X, Li Y. Enhanced biodegradation of modified fluoroquinolone for aerobic, facultative, and anaerobic processes using quantitative structure-activity relationship, molecular docking, and molecular dynamics. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Ngoepe MP, Moeno S. Evaluation of Pipemidic Acid Derivatives for Potential Antimicrobial Activity Application: In silico Studies on Bioactivity. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999200730165219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Pipemidic acid is a broad-spectrum quinolone antibacterial agent for the
treatment of chronic urinary tract infections against both gram-positive and gram-negative bacteria.
Both quinolone and fluoroquinolone antibiotics have been useful in combating bacterial infections.
However, patients suffer severe side effects when they stop taking the medication. The piperazinyl
region of pipemidic acid is highly responsible for the side effects.
Objective:
The objective of this study is to design new compounds in which the piperazinyl region is
masked by way of conjugation to benzoic acid derivatives.
Methods:
In silico studies were conducted using AutoDockTools software for ligand-protein
docking. The docking scores were compared to the parent pipemidic acid docked to Bacterial DNA
(deoxyribonucleic acid) gyrase and GABA (gamma-Aminobutyric acid) receptor from the PDB
(Protein Data Bank) database. Sites of metabolism, biological activity, quantum chemical
descriptors, and ADME (absorption, distribution, metabolism, and excretion) property predictions
for each designed ligand were also evaluated.
Results:
The docking studies and biological activity predictions showed good anti-infective properties
(ligand PAR03) whilst also suggesting a reduction in GABA receptor agonist activity. The performance
of PAR03 correlates with its electronic properties showing electrophilic character (can
generate Reactive Electrophilic Species (RES)).
Conclusion:
The results from this study indicate that modification of the piperazinyl region of pipemidic
acid can be an effective way to improve the drug potency whilst also ensuring reduction of
the associated side effects.
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Affiliation(s)
- Mpho Phehello Ngoepe
- Department of Oral Biological Sciences, School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, South Africa
| | - Sharon Moeno
- Department of Oral Biological Sciences, School of Oral Health Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, South Africa
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14
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Zhang W, Gu W, Sun R, Zhou M, Han Z, Li Y. An adjusted 3D-QSAR model for the combined activity of fluoroquinolones photodegradation and microbial degradation assisted by dynamic simulation and its application in molecular modification. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111973. [PMID: 33516099 DOI: 10.1016/j.ecoenv.2021.111973] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
This study developed a comprehensive characterization method for the combined degradation effect of modified fluoroquinolones (FQs) photodegradation and microbial degradation. A combination of revised 3D-QSAR model, molecular docking, path simulation inference, pharmacokinetics, molecular dynamics (MD) simulation and toxicokinetics simulation was used to construct a systematic environment-friendly drug screening system. Five derivatives were screened with significantly improved combined degradation effect (over 20%) and functional characteristics and human health parameters through combined model verification, functional and human health risk assessment. The simulation path of photo- and microbial-degradation of gatifloxacin and new gatifloxacin molecules was derived, and the reaction energy barrier was also calculated. The ratio of the total rate-determining steps change rate of the decreased energy barrier (14.10%:26.30%) was consistent with the ratio of the increased degradation performance predicted by the model (22.87%:19.77%), demonstrating the reliability of revised 3D-QSAR model and it could be applied in molecular modification. MD and toxicokinetics simulation were used to predict the binding energy and aquatic toxicity between photo- and microbial-degradation products and the degradation enzymes, which further to screen the degradation pathways with low potential environmental risks. The findings will be helpful to screen environment-friendly drug and develop appropriate strategies for its risk management.
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Affiliation(s)
- Wenhui Zhang
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
| | - Wenwen Gu
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
| | - Ruihao Sun
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
| | - Mengying Zhou
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
| | - Zhenzhen Han
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
| | - Yu Li
- The Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing 102206, China.
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15
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Li M, Du M, Sun R, Zhang W, Hou Y, Li Y. Application of a 2D-QSAR with a sine normalization method for the biodegradation of fluoroquinolones to poison cyanobacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:11302-11316. [PMID: 33118068 DOI: 10.1007/s11356-020-11366-y] [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: 06/12/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Cyanobacteria are photosynthetic autotrophic aquatic prokaryotes. One of the methods for controlling cyanobacterial blooms is to destroy the phycobiliproteins required for photosynthesis. In this study, to improve the biodegradation of the fluoroquinolones through inhibit cyanobacteria, the molecular docking scores of 32 fluoroquinolones (FQs) with four categories of phycobiliproteins from cyanobacteria were calculated after sine normalization to characterize the binding ability between them. A two-dimensional quantitative structure-activity relationship (2D-QSAR) model was constructed based on the comprehensive scores. Danofloxacin (DAN) with the highest comprehensive score was chosen for molecular modification. When docking with four categories of phycobiliproteins from cyanobacteria, the docking values of DAN-11 and DAN-16 were increased up to 35.75%. Moreover, their functional characteristics and environmentally friendly predictive values were improved. When the DAN-11 and DAN-16 molecules docked with the other cyanobacterial phycobiliproteins, indicating that the designed DAN derivatives had general applicability to poison cyanobacteria, the weak interaction forces might increase the binding ability between the DAN derivatives and the receptor phycobiliprotein compared with the target molecule.
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Affiliation(s)
- Minghao Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Meijin Du
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Ruihao Sun
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Wenhui Zhang
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Yilin Hou
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China
| | - Yu Li
- The Moe Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing, 102206, China.
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16
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Tong JB, Luo D, Feng Y, Bian S, Zhang X, Wang TH. Structural modification of 4, 5-dihydro-[1, 2, 4] triazolo [4, 3-f] pteridine derivatives as BRD4 inhibitors using 2D/3D-QSAR and molecular docking analysis. Mol Divers 2021; 25:1855-1872. [PMID: 33392965 DOI: 10.1007/s11030-020-10172-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
Cancer treatment continues to be one of the most serious public health issues in the world. The overexpression of BRD4 protein has led to a series of malignant tumors, hence the development of small molecule BRD4 protease inhibitors has always been a hot spot in the field of medical research. In this study, a series of 4,5-dihydro-[1, 2, 4] triazolo [4, 3-f] pteridine derivatives were used to establish 3D/2D-QSAR models and to discuss the relationship between inhibitor structure and activity. Four ideal models were established, including the comparative molecular field analysis (CoMFA: [Formula: see text] = 0.574, [Formula: see text] = 0.947) model, comparative molecular similarity index analysis (CoMSIA: [Formula: see text]= 0.622, [Formula: see text] = 0.916) model, topomer CoMFA ([Formula: see text] = 0.691, [Formula: see text]= 0.912) model and hologram quantitative structure-activity relationship (HQSAR: [Formula: see text]= 0.759, [Formula: see text] = 0.963) model. They show quite good external predictive power for the test set, with [Formula: see text] values of 0.602, 0.624, 0.671 and 0.750, respectively. In addition, the contour and color code map given by the 2D/3D-QSAR model with the results of molecular docking analyzed to chalk up modification methods for improving inhibitory activity, which was verified by designing novel compounds. The analysis results are helpful to promote the modification of the inhibitor framework and to provide a reference for the construction of new and promising BRD4 inhibitor compounds.
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Affiliation(s)
- Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China.
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China.
| | - Ding Luo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Yi Feng
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Shuai Bian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Xing Zhang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
| | - Tian-Hao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an, 710021, China
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17
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Tong JB, Luo D, Xu HY, Bian S, Zhang X, Xiao XC, Wang J. A computational approach for designing novel SARS-CoV-2 M pro inhibitors: combined QSAR, molecular docking, and molecular dynamics simulation techniques. NEW J CHEM 2021. [DOI: 10.1039/d1nj02127c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The promising compound T21 for treating COVID-19 at the active site of SARS-CoV-2 Mpro.
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Affiliation(s)
- Jian-Bo Tong
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Ding Luo
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Hai-Yin Xu
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Shuai Bian
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Xing Zhang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Xue-Chun Xiao
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Jie Wang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
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18
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Sun P, Zhao Y, Yang L, Ren Z, Zhao W. Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E9398. [PMID: 33333906 PMCID: PMC7765274 DOI: 10.3390/ijerph17249398] [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: 10/29/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022]
Abstract
Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.
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Affiliation(s)
- Peixuan Sun
- College of New Energy and Environment, Jilin University, Changchun 130012, China; (P.S.); (L.Y.)
| | - Yuanyuan Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China;
| | - Luze Yang
- College of New Energy and Environment, Jilin University, Changchun 130012, China; (P.S.); (L.Y.)
| | - Zhixing Ren
- College of Forestry, Northeast Forestry University, Harbin 150040, China;
| | - Wenjin Zhao
- College of New Energy and Environment, Jilin University, Changchun 130012, China; (P.S.); (L.Y.)
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19
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Han Z, Chen X, Li G, Sun S. A novel 3D-QSAR model assisted by coefficient of variation method and its application in FQs’ modification. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-020-02052-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Environmentally Friendly Fluoroquinolone Derivatives with Lower Plasma Protein Binding Rate Designed Using 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186626. [PMID: 32932916 PMCID: PMC7560044 DOI: 10.3390/ijerph17186626] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 01/03/2023]
Abstract
Comparative molecular similarity index analysis (CoMSIA) was used to establish a three-dimensional quantitative structure–activity relationship (3D-QSAR) model with structural parameters of quinolones as the independent variables and plasma protein binding rate (logfb) as the dependent variable to predict the logfb values of remaining quinolones in this study. In addition, the mono-substituted and bis-substituted reaction schemes that significantly influenced the plasma protein binding rate of quinolones were determined through an analysis of the 3D-QSAR contour maps. It was found that the replacement of small groups, hydrophobic groups, electronegative groups, or hydrogen bond acceptor groups at the substitution sites significantly reduce the logfb values of quinolone derivatives. Furthermore, the mechanism of decrease in binding rate between trovafloxacin (TRO) derivatives and plasma protein was revealed qualitatively and quantitatively based on molecular docking and molecular dynamics simulation. After modification of the target molecule, 11 TRO derivatives with low plasma protein binding rates were screened (reduced by 0.50–24.18%). Compared with the target molecule, the molecular genotoxicity and photodegradability of the TRO derivatives was higher (genotoxicity increased by 4.89–21.36%, and photodegradability increased by 9.04–20.56%), and their bioconcentration was significantly lower (by 36.90–61.41%).
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21
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Zhang H, Zhao C, Na H. Enhanced Biodegradation of Phthalic Acid Esters' Derivatives by Plasticizer-Degrading Bacteria ( Burkholderia cepacia, Archaeoglobus fulgidus, Pseudomonas aeruginosa) Using a Correction 3D-QSAR Model. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17155299. [PMID: 32717867 PMCID: PMC7432126 DOI: 10.3390/ijerph17155299] [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: 06/27/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022]
Abstract
A phthalic acid ester’s (PAEs) comprehensive biodegradability three-dimensional structure-activity relationship (3D-QSAR) model was established, to design environmentally friendly PAE derivatives, which could be simultaneously degraded by plasticizer-degrading bacteria, such as Burkholderia cepacia, Archaeoglobus fulgidus, and Pseudomonas aeruginosa. Only three derivatives of diethyl phthalate (DEP (DEP-27, DEP-28 and DEP-29)) were suited for their functionality and environmental friendliness, which had an improved stability in the environment and improved the characteristics (bio-toxicity, bioaccumulation, persistence, and long-range migration) of the persistent organic pollutants (POPs). The simulation inference of the microbial degradation path before and after DEP modification and the calculation of the reaction energy barrier exhibited the energy barrier for degradation being reduced after DEP modification and was consistent with the increased ratio of comprehensive biodegradability. This confirmed the effectiveness of the comparative molecular similarity index analysis (CoMSIA) model of the PAE’s comprehensive biodegradability. In addition, a molecular dynamics simulation revealed that the binding of the DEP-29 derivative with the three plasticizer-degradation enzymes increased significantly. DEP-29 could be used as a methyl phthalate derivative that synergistically degrades with microplastics, providing directional selection and theoretical designing for plasticizer replacement.
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Affiliation(s)
- Haigang Zhang
- Correspondence: ; Tel.: +86-0431-85168870; Fax: +86-0431-85168870
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22
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Li X, Zhang B, Huang W, Cantwell C, Chen B. Integration of Fuzzy Matter-Element Method and 3D-QSAR Model for Generation of Environmentally Friendly Quinolone Derivatives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17093239. [PMID: 32384726 PMCID: PMC7246649 DOI: 10.3390/ijerph17093239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
The environmental pollution of quinolone antibiotics (QAs) has caused rising public concern due to their widespread usage. In this study, Gaussian 09 software was used to obtain the infrared spectral intensity (IRI) and ultraviolet spectral intensity (UVI) of 24 QAs based on the Density Functional Theory (DFT). Rather than using two single-factor inputs, a fuzzy matter-element method was selected to calculate the combined effects of infrared and ultraviolet spectra (CI). The Comparative Molecular Field Analysis (CoMFA) was then used to construct a three-dimensional quantitative structure–activity relationship (3D-QSAR) with QAs’ molecular structure as the independent variable and CI as the dependent variable. Using marbofloxacin and levofloxacin as target molecules, the molecular design of 87 QA derivatives was carried out. The developed models were further used to determine the stability, functionality (genetic toxicity), and the environmental effects (bioaccumulation, biodegradability) of these designed QA derivatives. Results indicated that all QA derivatives are stable in the environment with their IRI, UVI, and CI enhanced. Meanwhile, the genetic toxicity of the 87 QA derivatives increased by varying degrees (0.24%–29.01%), among which the bioaccumulation and biodegradability of 43 QA derivatives were within the acceptable range. Through integration of fuzzy matter-element method and 3D-QSAR, this study advanced the QAs research with the enhanced CI and helped to generate the proposed environmentally friendly quinolone derivatives so as to aid the management of this class of antibiotics.
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A Double-Activity (Green Algae Toxicity and Bacterial Genotoxicity) 3D-QSAR Model Based on the Comprehensive Index Method and Its Application in Fluoroquinolones' Modification. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17030942. [PMID: 32028728 PMCID: PMC7037916 DOI: 10.3390/ijerph17030942] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 11/17/2022]
Abstract
The comparative molecular similarity index analysis (CoMSIA) model of double-activity quinolones targeting green algae toxicity and bacterial genotoxicity (8:2) was constructed in this paper on the basis of the comprehensive index method. The contour maps of the model were analyzed for molecular modifications with high toxicities. In the CoMSIA model, the optimum number of components n was 7, the cross-validated q2 value was 0.58 (>0.5), the standard deviation standard error of estimate (SEE) was 0.02 (<0.95), F was 1265.33, and the non-cross-validated R2 value was 1 (>0.9), indicating that the model had a good fit and predicting ability. The scrambling stability test parameters Q2, cross-validated standard error of prediction (cSDEP), and dq2/dr2yy were 0.54, 0.25, and 0.8 (<1.2), respectively, indicating that the model had good stability. The external verification coefficient r2pred was 0.73 (>0.6), and standard error of prediction (SEP) was 0.17, indicating that the model had a good external prediction ability. The contribution rates of the steric fields, electrostatic fields, hydrophobic fields, hydrogen bond donor, and acceptor fields were 10.9%, 19.8%, 32.7%, 13.8%, and 22.8%, respectively. Large volume groups were selected for modification of ciprofloxacin (CIP), and the derivatives with increased double-activity characterization values were screened; the increase ratio ranged from 12.31-19.09%. The frequency of derivatives were positive and total energy, bioaccumulation, and environmental persistence was reduced, indicating that the CIP derivatives had good environmental stability and friendliness. Predicted values and CoMSIA model constructed of single activities showed that the CoMSIA model of double activities had accuracy and reliability. In addition, the total scores of the derivatives docking with the D1 protein, ferredoxin-NADP (H) reductases (FNRs), and DNA gyrase increased, indicating that derivatives can be toxic to green algae by affecting the photosynthesis of green algae. The mechanism behind the bactericidal effect was also explained from a molecular perspective.
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24
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Zhang W, Sun R, Zhao X, Li Y. Environmental Conversion Path Inference of New Designed Fluoroquinolones and Their Potential Environmental Risk. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2020; 78:310-328. [PMID: 31605151 DOI: 10.1007/s00244-019-00672-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
Fluoroquinolone (FQ) derivatives with environmental friendliness regarding photodegradation, bioconcentration, and genotoxicity were selected from our previous works so that their transformation pathways of biological metabolism, photodegradation, microbial degradation, and chlorination disinfection could be studied. The pathways of these molecules and their derivatives were simulated to investigate the genotoxicity of their transformation products. The results showed that the genotoxicity of the biological metabolites, photodegradation products, and microbial degradation products of the maternal FQ derivatives partially increased, whereas the disinfection by-products exhibited lower genotoxicity than their precursors. Some designed FQ molecular derivatives still had potential environmental risks in biological metabolism, photodegradation, and microbial degradation. This study demonstrated that it is necessary to take into account the potential environmental risks of the transformed products of the modified FQs molecules during biometabolism, photodegradation, microbial degradation, and chlorination processes when designing novel FQ molecules. In future studies, assessing the potential environmental risks during various artificial or natural processes can be applied to screen environmentally friendly novel FQ molecules to avoid and or reduce their threat to environmental and human health.
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Affiliation(s)
- Wenhui Zhang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
- The State Key Laboratory of Regional Optimisation of Energy System, North China Electric Power University, Beijing, 102206, China
| | - Ruihao Sun
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
- The State Key Laboratory of Regional Optimisation of Energy System, North China Electric Power University, Beijing, 102206, China
| | - Xiaohui Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
- The State Key Laboratory of Regional Optimisation of Energy System, North China Electric Power University, Beijing, 102206, China
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
- The State Key Laboratory of Regional Optimisation of Energy System, North China Electric Power University, Beijing, 102206, China.
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25
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Balasubramaniyan S, Irfan N, Senthilkumar C, Umamaheswari A, Puratchikody A. The synthesis and biological evaluation of virtually designed fluoroquinolone analogs against fluoroquinolone-resistant Escherichia coliintended for UTI treatment. NEW J CHEM 2020. [DOI: 10.1039/d0nj00657b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthesis and evaluvate the supercoiling activity of the virtually screened novel fluoroquinolone analogs against fluoroquinolone-resistantEscherichia colifor the treatment of urinary tract infections (UTIs).
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Affiliation(s)
- Sakthivel Balasubramaniyan
- Drug Discovery and Development Research Group
- Department of Pharmaceutical Technology
- University College of Engineering
- Anna University
- BIT Campus
| | - Navabshan Irfan
- School of Pharmacy
- B.S. Abdur Rahman Crescent Institute of Science & Technology
- Chennai 600048
- India
| | | | - Appavoo Umamaheswari
- Drug Discovery and Development Research Group
- Department of Pharmaceutical Technology
- University College of Engineering
- Anna University
- BIT Campus
| | - Ayarivan Puratchikody
- Drug Discovery and Development Research Group
- Department of Pharmaceutical Technology
- University College of Engineering
- Anna University
- BIT Campus
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Du M, Zhang D, Hou Y, Zhao X, Li Y. Combined 2D-QSAR, Principal Component Analysis and Sensitivity Analysis Studies on Fluoroquinolones' Genotoxicity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E4156. [PMID: 31661905 PMCID: PMC6862474 DOI: 10.3390/ijerph16214156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/22/2019] [Accepted: 10/25/2019] [Indexed: 01/19/2023]
Abstract
In this paper, two-dimensional quantitative structure-activity relationship (2D-QSAR) and principal component analysis (PCA) methods were employed to screen the main parameters affecting the genotoxicity of fluoroquinolones (FQs), and the rules affecting the genetic toxicity of FQs were investigated by combining 2D-QSAR and PCA with the sensitivity analysis method. First, four types of parameters were calculated, namely, the geometric parameters (7), electronic parameters (5), physical and chemical parameters (8), and spectral parameters (7), but the physical and chemical parameters heat of formation (HF) and critical volume (CV) were excluded after the establishment of the 2D-QSAR model. Then, after PCA, it was found that the first principal component represented the main driving factors affecting the molecular genetic toxicity of FQs. In addition, after comprehensive analysis of the factor loading of the first, second, and third principal components, seven parameters affecting the genotoxicity of the FQs were screened out, namely, total energy (TE), critical temperature (CT), and molecular weight (Mol Wt) (increased with increasing genotoxicity of the FQs) and steric parameter (MR), quadrupole moment QXX (QXX), quadrupole moment QYY (QYY), and boiling point (BP) (decreased with increasing genotoxicity of the FQs); the above key parameters were also verified by sensitivity analysis. The obtained rules could be used to determine the substitution sites and the substitution groups associated with higher genotoxicity in the process of FQ modification, and these rules agreed well with the hologram quantitative structure-activity relationship (HQSAR) model. Finally, it was also found through SPSS analysis that the parameters screened in this paper were significantly correlated with FQ derivatives' genetic toxicity.
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Affiliation(s)
- Meijin Du
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Dan Zhang
- Jilin Province Shize Environmental Protection Technology Co., Ltd, Jilin 130012, China.
| | - Yilin Hou
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Xiaohui Zhao
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China.
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China.
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