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El-Dash HA, Yousef NE, Aboelazm AA, Awan ZA, Yahya G, El-Ganiny AM. Optimizing Eco-Friendly Degradation of Polyvinyl Chloride (PVC) Plastic Using Environmental Strains of Malassezia Species and Aspergillus fumigatus. Int J Mol Sci 2023; 24:15452. [PMID: 37895132 PMCID: PMC10607177 DOI: 10.3390/ijms242015452] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Worldwide, huge amounts of plastics are being introduced into the ecosystem, causing environmental pollution. Generally, plastic biodegradation in the ecosystem takes hundreds of years. Hence, the isolation of plastic-biodegrading microorganisms and finding optimum conditions for their action is crucial. The aim of the current study is to isolate plastic-biodegrading fungi and explore optimum conditions for their action. Soil samples were gathered from landfill sites; 18 isolates were able to grow on SDA. Only 10 isolates were able to the degrade polyvinyl chloride (PVC) polymer. Four isolates displayed promising depolymerase activity. Molecular identification revealed that three isolates belong to genus Aspergillus, and one isolate was Malassezia sp. Three isolates showed superior PVC-biodegrading activity (Aspergillus-2, Aspergillus-3 and Malassezia) using weight reduction analysis and SEM. Two Aspergillus strains and Malassezia showed optimum growth at 40 °C, while the last strain grew better at 30 °C. Two Aspergillus isolates grew better at pH 8-9, and the other two isolates grow better at pH 4. Maximal depolymerase activity was monitored at 50 °C, and at slightly acidic pH in most isolates, FeCl3 significantly enhanced depolymerase activity in two Aspergillus isolates. In conclusion, the isolated fungi have promising potential to degrade PVC and can contribute to the reduction of environmental pollution in eco-friendly way.
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Affiliation(s)
- Heba A. El-Dash
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (H.A.E.-D.); (N.E.Y.); (G.Y.)
| | - Nehal E. Yousef
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (H.A.E.-D.); (N.E.Y.); (G.Y.)
| | - Abeer A. Aboelazm
- Microbiology and Immunology Department, Faculty of Medicine, Benha University, Benha 13518, Egypt;
| | - Zuhier A. Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (H.A.E.-D.); (N.E.Y.); (G.Y.)
- Department of Molecular Genetics, Faculty of Biology, Technical University of Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - Amira M. El-Ganiny
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (H.A.E.-D.); (N.E.Y.); (G.Y.)
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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Wani AK, Akhtar N, Naqash N, Rahayu F, Djajadi D, Chopra C, Singh R, Mulla SI, Sher F, Américo-Pinheiro JHP. Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:1-24. [PMID: 36637649 PMCID: PMC9838310 DOI: 10.1007/s11356-023-25192-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/04/2023] [Indexed: 06/01/2023]
Abstract
Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Nafiaah Naqash
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Farida Rahayu
- Research Center for Applied Microbiology, National Research and Innovation Agency, Bogor, 16911, Indonesia
| | - Djajadi Djajadi
- Research Center for Horticulture and Plantation, National Research Innovation Agency, Bogor, 16111, Indonesia
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Punjab, 144411, India
| | - Sikandar I Mulla
- Department of Biochemistry, School of Allied Health Sciences, REVA University, Bengaluru, 560064, Karnataka, India
| | - Farooq Sher
- Department of Engineering, School of Science and Technology, Nottingham Trent University, Nottingham, NG11 8NS, UK
| | - Juliana Heloisa Pinê Américo-Pinheiro
- Department of Forest Science, Soils and Environment, School of Agronomic Sciences, São Paulo State University (UNESP), Ave. Universitária, 3780, Botucatu, SP, 18610-034, Brazil.
- Graduate Program in Environmental Sciences, Brazil University, Street Carolina Fonseca, 584, São Paulo, SP, 08230-030, Brazil.
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Chen XQ, Guo ZY, Wang L, Yan ZF, Jin CX, Huang QS, Kong DM, Rao DM, Wu J. Directional-path modification strategy enhances PET hydrolase catalysis of plastic degradation. JOURNAL OF HAZARDOUS MATERIALS 2022; 433:128816. [PMID: 35390614 DOI: 10.1016/j.jhazmat.2022.128816] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Poly (ethylene terephthalate) (PET) is a widely used type of general plastic that produces a significant amount of waste due to its non-degradable properties. We propose a novel directional-path modification (DPM) strategy, involving positive charge amino acid introduction and binding groove remodeling, and apply it to Thermobifida fusca cutinase to enhance PET degradation. The highest value of PET degradation (90%) was achieved in variant 4Mz (H184S/Q92G/F209I/I213K), exhibiting values almost 30-fold that of the wild-type. We employed molecular docking, molecular dynamics simulations, and QM/MM MD for the degradation process of PET, accompanied by acylation and deacylation. We found that the distance of nucleophilic attack was reduced from about 4.6 Å in the wild type to 3.8 Å in 4Mz, and the free energy barrier of 4Mz dropped from 14.3 kcal/mol to 7.1 kcal/mol at the acylation which was the rate-limiting step. Subsequently, the high efficiency and universality of the DPM strategy were successfully demonstrated in LCC, Est119, and BhrPETase enhancing the degradation activity of PET. Finally, the highest degradation rate of the pretreated commercial plastic bottles had reached to 73%. The present study provides insight into the molecular binding mechanism of PET into the PET hydrolases structure and proposes a novel DPM strategy that will be useful for the engineering of more efficient enzymes for PET degradation.
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Affiliation(s)
- Xiao-Qian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhi-Yong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zheng-Fei Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chang-Xu Jin
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Qing-Song Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - De-Min Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - De-Ming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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Dalal V, Golemi-Kotra D, Kumar P. Quantum Mechanics/Molecular Mechanics Studies on the Catalytic Mechanism of a Novel Esterase (FmtA) of Staphylococcus aureus. J Chem Inf Model 2022; 62:2409-2420. [PMID: 35475370 DOI: 10.1021/acs.jcim.2c00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
FmtA is a novel esterase that shares the penicillin-binding protein (PBP) core structural folding but found to hydrolyze the removal of d-Ala from teichoic acids. Molecular docking, dynamics, and MM-GBSA of FmtA and its variants S127A, K130A, Y211A, D213A, and K130AY211A, in the presence or absence of wall teichoic acid (WTA), suggest that active site residues S127, K130, Y211, D213, N343, and G344 play a role in substrate binding. Quantum mechanics (QM)/molecular mechanics (MM) calculations reveal that during WTA catalysis, K130 deprotonates S127, and the nucleophilic S127 attacks the carbonyl carbon of d-Ala bound to WTA. The tetrahedral intermediate (TI) complex is stabilized by hydrogen bonding to the oxyanion holes. The TI complex displays a high energy gap and collapses to an energetically favorable acyl-enzyme complex.
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Affiliation(s)
- Vikram Dalal
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
| | - Dasantila Golemi-Kotra
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, IIT Roorkee, Roorkee, Uttrakhand 247667, India
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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Carniel A, Waldow VDA, Castro AMD. A comprehensive and critical review on key elements to implement enzymatic PET depolymerization for recycling purposes. Biotechnol Adv 2021; 52:107811. [PMID: 34333090 DOI: 10.1016/j.biotechadv.2021.107811] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022]
Abstract
Plastics production and recycling chains must be refitted to a circular economy. Poly(ethylene terephthalate) (PET) is especially suitable for recycling because of its hydrolysable ester bonds and high environmental impact due to employment in single-use packaging, so that recycling processes utilizing enzymes are a promising biotechnological route to monomer recovery. However, enzymatic PET depolymerization still faces challenges to become a competitive route at an industrial level. In this review, PET characteristics as a substrate for enzymes are discussed, as well as the analytical methods used to evaluate the reaction progress. A comprehensive view on the biocatalysts used is discussed. Subsequently, different strategies pursued to improve enzymatic PET depolymerization are presented, including enzyme modification through mutagenesis, utilization of multiple enzymes, improvement of the interaction between enzymes and the hydrophobic surface of PET, and various reaction conditions (e.g., particle size, reaction medium, agitation, and additives). All scientific developments regarding these different aspects of PET depolymerization are crucial to offer a scalable and competitive technology. However, they must be integrated into global processes from upstream to downstream, discussed here at the final sections, which must be evaluated for their economic feasibility and life cycle assessment to check if PET recycling chains can be broadly incorporated into the future circular economy.
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Affiliation(s)
- Adriano Carniel
- School of Chemistry, Federal University of Rio de Janeiro (UFRJ) - Cidade Universitária, Rio de Janeiro, RJ CEP 21949-900, Brazil
| | - Vinicius de Abreu Waldow
- Petrobras Research, Development and Innovation Center (Cenpes), Av. Horácio Macedo, n° 950 - Cidade Universitária, Rio de Janeiro, RJ CEP 21941-915, Brazil
| | - Aline Machado de Castro
- Petrobras Research, Development and Innovation Center (Cenpes), Av. Horácio Macedo, n° 950 - Cidade Universitária, Rio de Janeiro, RJ CEP 21941-915, Brazil.
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Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11146291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The main protease (Mpro) of SARS-CoV-2 is a current target for the inhibition of viral replication. Through a combined Docking and Density Functional Theory (DFT) approach, we investigated in-silico the molecular mechanism by which ebselen (IUPAC: 2-phenyl-1,2-benzoselenazol-3-one), the most famous and pharmacologically active organoselenide, inhibits Mpro. For the first time, we report on a mechanistic investigation in an enzyme for the formation of the covalent -S-Se- bond between ebselen and a key enzymatic cysteine. The results highlight the strengths and weaknesses of ebselen and provide hints for a rational drug design of bioorganic selenium-based inhibitors.
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