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Nyambo K, Tapfuma KI, Adu-Amankwaah F, Julius L, Baatjies L, Niang IS, Smith L, Govender KK, Ngxande M, Watson DJ, Wiesner L, Mavumengwana V. Molecular docking, molecular dynamics simulations and binding free energy studies of interactions between Mycobacterium tuberculosis Pks13, PknG and bioactive constituents of extremophilic bacteria. Sci Rep 2024; 14:6794. [PMID: 38514663 PMCID: PMC10957976 DOI: 10.1038/s41598-024-57124-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Mycobacterial pathogens present a significant challenge to disease control efforts globally due to their inherent resistance to multiple antibiotics. The rise of drug-resistant strains of Mycobacterium tuberculosis has prompted an urgent need for innovative therapeutic solutions. One promising way to discover new tuberculosis drugs is by utilizing natural products from the vast biochemical space. Multidisciplinary methods can used to harness the bioactivity of these natural products. This study aimed to evaluate the antimycobacterial efficacy of functional crude extracts from bacteria isolated from gold mine tailings in South Africa. Bacterial strains were identified using 16S rRNA sequencing. The crude extracts obtained from the bacteria were tested against Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. Untargeted HPLC-qTOF and molecular networking were used to identify the functional constituents present in extracts that exhibited inhibitory activity. A virtual screening workflow (VSW) was used to filter compounds that were strong binders to Mycobacterium tuberculosis Pks13 and PknG. The ligands returned from the VSW were subjected to optimization using density functional theory (DFT) at M06-2X/6-311++ (d,p) level of theory and basis set implemented in Gaussian16 Rev.C01. The optimized ligands were re-docked against Mycobacterium tuberculosis Pks13 and PknG. Molecular dynamics simulation and molecular mechanics generalized born surface area were used to evaluate the stability of the protein-ligand complexes formed by the identified hits. The hit that showed promising binding characteristics was virtually modified through multiple synthetic routes using reaction-driven enumeration. Three bacterial isolates showed significant activity against the two strains of Mycobacterium, while only two, Bacillus subtilis and Bacillus licheniformis, exhibited activity against both Mycobacterium tuberculosis H37Rv, Mycobacterium smegmatis mc2155, and Mycobacterium aurum A+. The tentatively identified compounds from the bacterial crude extracts belonged to various classes of natural compounds associated with antimicrobial activity. Two compounds, cyclo-(L-Pro-4-OH-L-Leu) and vazabitide A, showed strong binding against PknG and Pks13, with pre-MD MM-GBSA values of - 42.8 kcal/mol and - 47.6 kcal/mol, respectively. The DFT-optimized compounds exhibited the same docking scores as the ligands optimized using the OPSL-4 force field. After modifying vazabitide A, its affinity to the Pks13 binding site increased to - 85.8 kcal/mol, as revealed by the post-MD MM-GBSA analysis. This study highlights the potential of bacteria isolates from gold mine tailings as a source of new scaffolds for designing and optimizing anti-Mycobacterium agents. These agents synthesized in-silico can be further tested in-vitro to evaluate their efficacy.
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Affiliation(s)
- Kudakwashe Nyambo
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Kudzanai Ian Tapfuma
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Francis Adu-Amankwaah
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lauren Julius
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Lucinda Baatjies
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Idah Sithole Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, B064, Mount Pleasant, Harare, Zimbabwe
| | - Liezel Smith
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa
| | - Krishna Kuben Govender
- Department of Chemical Sciences, University of Johannesburg, Doornfontein Campus, P.O. Box 17011, Johannesburg, 2028, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Cape Town, South Africa
| | - Mkhuseli Ngxande
- Computer Science Division, Department of Mathematical Sciences, Faculty of Science, University of Stellenbosch, Matieland, South Africa
| | - Daniel J Watson
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lubbe Wiesner
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vuyo Mavumengwana
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, 7505, Cape Town, South Africa.
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Cheng S, Han Y, Tang Z, Li W. Producing magnetite concentrate from iron tailings via suspension magnetization roasting: A pilot-scale study. SEP SCI TECHNOL 2023. [DOI: 10.1080/01496395.2023.2189055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Shaokai Cheng
- School of Resources and Civil Engineering, Northeastern University, Shenyang, PR China
- National-local Joint Engineering Research Center of High-efficient exploitation technology for Refractory Iron Ore Resources, Shenyang, PR China
| | - Yuexin Han
- School of Resources and Civil Engineering, Northeastern University, Shenyang, PR China
- National-local Joint Engineering Research Center of High-efficient exploitation technology for Refractory Iron Ore Resources, Shenyang, PR China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, PR China
| | - Zhidong Tang
- School of Resources and Civil Engineering, Northeastern University, Shenyang, PR China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, PR China
| | - Wenbo Li
- School of Resources and Civil Engineering, Northeastern University, Shenyang, PR China
- State Key Laboratory of Rolling and Automation, Northeastern University, Shenyang, PR China
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Liu Q, Luo Y, Shi J, Wu Z, Wang Q. Synergistic detoxification by combined reagents and safe filling utilization of cyanide tailings. CHEMOSPHERE 2023; 312:137157. [PMID: 36368542 DOI: 10.1016/j.chemosphere.2022.137157] [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: 07/03/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Cyanide tailings are the major hazardous wastes generated in the production process of the gold industry, which not only contain highly toxic cyanide, but also contain heavy metals with recycling value and other substances suitable for building materials or filling. These tailings are in urgent need of purification treatment and safe utilization. In this study, the impacts of treatment methods, types and combinations of reagents on decyanation effect were researched. Gold in cyanide tailings was recovered by flotation, and flotation tailings were used for filling after identifying the properties of solid waste. Results are as follows: (1) INCO method and 5 reagents (sodium sulfite, sodium persulfate, copper sulfate, ferrous sulfate and zinc sulfate) were selected for synergistic decyanation treatment, and cyanide concents in slurry and leaching solution were decreased to the minimum. (2) The gold recovery rate of the tailings through flotation was increased by 27.8% than without detoxification. (3) Flotation tailings were identified as general industrial solid wastes by leaching toxicity and toxic substance content analysis. (4) As filling aggregate, under the conditions of slurry concentration of 63% and cement-sand ratio of 1:6, the strength filling body of flotation tailings reached 1.32 Mpa after 28 days of maintenance. (5) This process and combined reagents were applied to engineering. The cyanide content in the leaching solution and the flotation recovery rate of gold were kept below 0.2 mg/L and above 60% respectively, and the strength of the filling body was stable to meet the requirements of underground filling.
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Affiliation(s)
- Qiang Liu
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China; State Key of Comprehensive Utilization of Low-grade Refractory Gold Ores, Shanghang, 364200, China; Xiamen Zijin Mining & Metallurgy Technology Co., Lid., Xiamen, 361101, China
| | - Yating Luo
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Science, Zhejiang University, Hangzhou, 310058, China.
| | - Zengling Wu
- State Key of Comprehensive Utilization of Low-grade Refractory Gold Ores, Shanghang, 364200, China; Xiamen Zijin Mining & Metallurgy Technology Co., Lid., Xiamen, 361101, China
| | - Qiankun Wang
- State Key of Comprehensive Utilization of Low-grade Refractory Gold Ores, Shanghang, 364200, China; Xiamen Zijin Mining & Metallurgy Technology Co., Lid., Xiamen, 361101, China
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Kanta Das S, Kundu T, Dash N, Angadi S. Separation behavior of Falcon concentrator for the recovery of ultrafine scheelite particles from the gold mine tailings. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.123065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Effect and Mechanism of CaO on Iron Recovery and Desulfurization by Reduction Roasting-Magnetic Separation of High-Sulfur Cyanide Tailings. MINERALS 2022. [DOI: 10.3390/min12020239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The increasing demand for iron ore in the world causes the continuous exhaustion of mineral resources. The utilization of iron in secondary resources has become of focus. The present study was carried out to recover iron from high-sulfur cyanide tailings by coal-based reduction roasting-magnetic separation. The mechanism of CaO to increase iron recovery and reduce sulfur was investigated by observing CO and CO2 gas composition produced by the reaction, mineral composition and microstructure, distribution characteristics of sulfur, and the intercalation relationship between iron particles and gangue minerals. The results showed that the addition of CaO could increase the gasification rate of the reducing agent, increase the amount of CO2 gas produced, promote the reduction of iron minerals, and improve the metallization degree of iron. When CaO was not added, sulfur was mainly transformed into troilite, which was closely connected with iron particles and was difficult to remove by grinding and magnetic separation. With the addition of CaO, CaO preferentially formed oldhamite with active sulfur, which reduced the formation of troilite. Oldhamite was basically distributed in an independent gangue structure. There was a clear boundary between iron particles and gangue minerals. Oldhamite could be removed by grinding-magnetic separation.
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Zhang H, Chen G, Cai X, Fu J, Liu M, Zhang P, Yu H. The leaching behavior of copper and iron recovery from reduction roasting pyrite cinder. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126561. [PMID: 34252668 DOI: 10.1016/j.jhazmat.2021.126561] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/22/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Pyrite cinder (PyC) is an iron-enriched solid waste material, which is an important iron resource for steel industry. However, the separation or extraction of iron minerals and heavy metals from PyC was ineffective, because of the fine disseminated granularity and the intergrowth between iron minerals and toxic heavy metals during high temperature roasting. In this paper, a novel method to extract copper and iron from the PyC by reduction roasting-leaching-magnetic separation was proposed. The effect of various parameters on the copper leaching behavior were studied, and the corresponding kinetics model was established. Under the optimized leaching conditions, the maximum copper leaching recovery of 82.18% was reached. A high-quality iron concentrate with Fe content of 65.58% and copper content of 0.17% was obtained subsequently from the leaching residuals through magnetic separation. It showed that the leaching process was controlled by mixed diffusion and chemical reaction, with a corresponding activation energy of 27.97 kJ/mol. The free copper oxide, combined copper oxide and secondary copper sulfide were extracted completely in H2SO4 solution. However, chalcopyrite as a form of primary copper sulfide dissolved partly. The leaching mechanism was confirmed by chemical phase and XPS analysis.
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Affiliation(s)
- Hanquan Zhang
- School of Resources & Safety Engineering, Wuhan Institute of Technology, Wuhan 430073, China
| | - Guanhua Chen
- School of Resources & Safety Engineering, Wuhan Institute of Technology, Wuhan 430073, China
| | - Xiang Cai
- GEM (Jingmen) Recycling Industrial Park GEM Co. Ltd., Jingmen 448000, China
| | - Jintao Fu
- West Mining Group Co. Ltd., Xitieshan Branch, Xining 810001, China
| | - Mingxia Liu
- School of Resources & Safety Engineering, Wuhan Institute of Technology, Wuhan 430073, China
| | - Pengfei Zhang
- School of Resources & Safety Engineering, Wuhan Institute of Technology, Wuhan 430073, China
| | - Hong Yu
- School of Resources & Safety Engineering, Wuhan Institute of Technology, Wuhan 430073, China.
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