1
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Jaito N, Phetlum S, Saeoung T, Tiyasakulchai T, Srimongkolpithak N, Uengwetwanit T. Improving stereoselectivity of phosphotriesterase (PTE) for kinetic resolution of chiral phosphates. Front Bioeng Biotechnol 2024; 12:1446566. [PMID: 39139291 PMCID: PMC11319162 DOI: 10.3389/fbioe.2024.1446566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
Specific stereoisomer is paramount as it is vital for optimizing drug efficacy and safety. The quest for the isolation of desired stereoisomer of active pharmaceutical ingredients or key intermediates drives innovation in drug synthetic and biocatalytic methods. Chiral phosphoramidate is an important building block for the synthesis of antiviral drugs such as remdesivir and sofosbuvir. Given the clinical potency of the (Sp)-diastereomer of the drugs, an enzyme capable of completely hydrolyzing the (Rp)-diastereomer is needed to achieve the purified diastereomers via biocatalytic reaction. In this study, protein engineering of phosphotriesterase (PTE) was aimed to improve the specificity. Employing rational design and site-directed mutagenesis, we generated a small library comprising 24 variants for activity screening. Notably, W131M and I106A/W131M variants demonstrated successful preparation of pure (Sp)-diastereomer of remdesivir and sofosbuvir precursors within a remarkably short hydrolysis time (<20 min). Our work unveils a promising methodology for producing pure stereoisomeric compounds, utilizing novel biocatalysts to enable the chemoenzymatic synthesis of phosphoramidate nucleoside prodrugs.
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Affiliation(s)
| | | | | | | | | | - Tanaporn Uengwetwanit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
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2
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Mohite SV, Sharma KK. Gut microbial metalloproteins and its role in xenobiotics degradation and ROS scavenging. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 141:495-538. [PMID: 38960484 DOI: 10.1016/bs.apcsb.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The gut microbial metalloenzymes play an important role in maintaining the balance between gut microbial ecosystem, human physiologically processes and immune system. The metals coordinated into active site contribute in various detoxification and defense strategies to avoid unfavourable environment and ensure bacterial survival in human gut. Metallo-β-lactamase is a potent degrader of antibiotics present in periplasmic space of both commensals and pathogenic bacteria. The resistance to anti-microbial agents developed in this enzyme is one of the global threats for human health. The organophosphorus eliminator, organophosphorus hydrolases have evolved over a course of time to hydrolyze toxic organophosphorus compounds and decrease its effect on human health. Further, the redox stress responders namely superoxide dismutase and catalase are key metalloenzymes in reducing both endogenous and exogenous oxidative stress. They hold a great importance for pathogens as they contribute in pathogenesis in human gut along with reduction of oxidative stress. The in-silico study on these enzymes reveals the importance of point mutation for the evolution of these enzymes in order to enhance their enzyme activity and stability. Various mutation studies were conducted to investigate the catalytic activity of these enzymes. By using the "directed evolution" method, the enzymes involved in detoxification and defense system can be engineered to produce new variants with enhance catalytic features, which may be used to predict the severity due to multi-drug resistance and degradation pattern of organophosphorus compounds in human gut.
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Affiliation(s)
- Shreya Vishwas Mohite
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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3
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Song Z, Zhang Q, Wu W, Pu Z, Yu H. Rational design of enzyme activity and enantioselectivity. Front Bioeng Biotechnol 2023; 11:1129149. [PMID: 36761300 PMCID: PMC9902596 DOI: 10.3389/fbioe.2023.1129149] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023] Open
Abstract
The strategy of rational design to engineer enzymes is to predict the potential mutants based on the understanding of the relationships between protein structure and function, and subsequently introduce the mutations using the site-directed mutagenesis. Rational design methods are universal, relatively fast and have the potential to be developed into algorithms that can quantitatively predict the performance of the designed sequences. Compared to the protein stability, it was more challenging to design an enzyme with improved activity or selectivity, due to the complexity of enzyme molecular structure and inadequate understanding of the relationships between enzyme structures and functions. However, with the development of computational force, advanced algorithm and a deeper understanding of enzyme catalytic mechanisms, rational design could significantly simplify the process of engineering enzyme functions and the number of studies applying rational design strategy has been increasing. Here, we reviewed the recent advances of applying the rational design strategy to engineer enzyme functions including activity and enantioselectivity. Five strategies including multiple sequence alignment, strategy based on steric hindrance, strategy based on remodeling interaction network, strategy based on dynamics modification and computational protein design are discussed and the successful cases using these strategies are introduced.
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Affiliation(s)
- Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang, China
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4
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Job L, Köhler A, Testanera M, Escher B, Worek F, Skerra A. Engineering of a phosphotriesterase with improved stability and enhanced activity for detoxification of the pesticide metabolite malaoxon. Protein Eng Des Sel 2023; 36:gzad020. [PMID: 37941439 DOI: 10.1093/protein/gzad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Organophosphorus (OP) pesticides are still widely applied but pose a severe toxicological threat if misused. For in vivo detoxification, the application of hydrolytic enzymes potentially offers a promising treatment. A well-studied example is the phosphotriesterase of Brevundimonas diminuta (BdPTE). Whereas wild-type BdPTE can hydrolyse pesticides like paraoxon, chlorpyrifos-oxon and mevinphos with high catalytic efficiencies, kcat/KM >2 × 107 M-1 min-1, degradation of malaoxon is unsatisfactory (kcat/KM ≈ 1 × 104 M-1 min-1). Here, we report the rational engineering of BdPTE mutants with improved properties and their efficient production in Escherichia coli. As result, the mutant BdPTE(VRNVVLARY) exhibits 37-fold faster malaoxon hydrolysis (kcat/KM = 4.6 × 105 M-1 min-1), together with enhanced expression yield, improved thermal stability and reduced susceptibility to oxidation. Therefore, this BdPTE mutant constitutes a powerful candidate to develop a biocatalytic antidote for the detoxification of this common pesticide metabolite as well as related OP compounds.
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Affiliation(s)
- Laura Job
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Anja Köhler
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
- Institut für Pharmakologie und Toxikologie der Bundeswehr, Neuherbergstr, 11, 80937 München, Germany
| | - Mauricio Testanera
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Benjamin Escher
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Franz Worek
- Institut für Pharmakologie und Toxikologie der Bundeswehr, Neuherbergstr, 11, 80937 München, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
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5
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Mali H, Shah C, Patel DH, Trivedi U, Subramanian RB. Bio-catalytic system of metallohydrolases for remediation of neurotoxin organophosphates and applications with a future vision. J Inorg Biochem 2022; 231:111771. [DOI: 10.1016/j.jinorgbio.2022.111771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 12/29/2022]
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6
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Bigley AN, Harvey SP, Narindoshvili T, Raushel FM. Substrate Analogues for the Enzyme-Catalyzed Detoxification of the Organophosphate Nerve Agents-Sarin, Soman, and Cyclosarin. Biochemistry 2021; 60:2875-2887. [PMID: 34494832 DOI: 10.1021/acs.biochem.1c00361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The G-type nerve agents, sarin (GB), soman (GD), and cyclosarin (GF), are among the most toxic compounds known. Much progress has been made in evolving the enzyme phosphotriesterase (PTE) from Pseudomonas diminuta for the decontamination of the G-agents; however, the extreme toxicity of the G-agents makes the use of substrate analogues necessary. Typical analogues utilize a chromogenic leaving group to facilitate high-throughput screening, and substitution of an O-methyl for the P-methyl group found in the G-agents, in an effort to reduce toxicity. Till date, there has been no systematic evaluation of the effects of these substitutions on catalytic activity, and the presumed reduction in toxicity has not been tested. A series of 21 G-agent analogues, including all combinations of O-methyl, p-nitrophenyl, and thiophosphate substitutions, have been synthesized and evaluated for their ability to unveil the stereoselectivity and catalytic activity of PTE variants against the authentic G-type nerve agents. The potential toxicity of these analogues was evaluated by measuring the rate of inactivation of acetylcholinesterase (AChE). All of the substitutions reduced inactivation of AChE by more than 100-fold, with the most effective being the thiophosphate analogues, which reduced the rate of inactivation by about 4-5 orders of magnitude. The analogues were found to reliably predict changes in catalytic activity and stereoselectivity of the PTE variants and led to the identification of the BHR-30 variant, which has no apparent stereoselectivity against GD and a kcat/Km of 1.4 × 106, making it the most efficient enzyme for GD decontamination reported till date.
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Affiliation(s)
- Andrew N Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven P Harvey
- US Army DEVCOM-CBC, FCDD-CBR-CC E3400, 5183 Blackhawk Rd. Aberdeen Proving Ground, Aberdeen, Maryland 21010, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.,Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 7784, United States
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7
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Liu C, Jiang X, Chi S, Bo D, Liu G. Contribution of the mutation T865G in TPH1 gene to the genetic potentiality of housed Mongolian sheep to year-round breeding. Reprod Domest Anim 2021; 56:1406-1412. [PMID: 34390051 DOI: 10.1111/rda.14005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/13/2023]
Abstract
Seasonal breeding is widespread in sheep and significantly affects the development of the housed sheep industry. To improve and balance the reproduction performance of sheep, year-round breeding has the goal of modern sheep farming. The tryptophan hydroxylase (TPH), which initiates and regulates biosynthesis of melatonin, is an important player in the formation of mammalian year-round breeding. However, little is known about its role in regulation of sheep seasonal breeding. In this study, a missense mutation, T865G in TPH1 gene was detected in 328 individuals of six Mongolian sheep groups. It was positively selected among Mongolian sheep. This mutation may appear between 13,683 and 350,973 years ago and only exist in Hu sheep now. In Hu sheep, the frequency of allele T was 89.66%, and that of allele G was 10.34%. The TPH1 protein structure and property analysis suggested that this mutation from T to G affect the three-dimensional structure and reduce the hydropathicity of catalytic core. When the allele is T, the protein activity is twice that of the allele G, and their difference was significant (p < .05). In conclusion, T865G is an ancient mutation of TPH1 gene and affects the function of TPH protein, which may contribute to the genetic potentiality of Mongolian sheep to year-round breeding.
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Affiliation(s)
- Chenhui Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China.,Institute of Animal Science and Veterinary Medicine, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Shaxuan Chi
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Dongdong Bo
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, China
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8
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Köhler A, Escher B, Job L, Koller M, Thiermann H, Skerra A, Worek F. Catalytic activity and stereoselectivity of engineered phosphotriesterases towards structurally different nerve agents in vitro. Arch Toxicol 2021; 95:2815-2823. [PMID: 34160649 PMCID: PMC8298220 DOI: 10.1007/s00204-021-03094-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/15/2021] [Indexed: 12/20/2022]
Abstract
Highly toxic organophosphorus nerve agents, especially the extremely stable and persistent V-type agents such as VX, still pose a threat to the human population and require effective medical countermeasures. Engineered mutants of the Brevundimonas diminuta phosphotriesterase (BdPTE) exhibit enhanced catalytic activities and have demonstrated detoxification in animal models, however, substrate specificity and fast plasma clearance limit their medical applicability. To allow better assessment of their substrate profiles, we have thoroughly investigated the catalytic efficacies of five BdPTE mutants with 17 different nerve agents using an AChE inhibition assay. In addition, we studied one BdPTE version that was fused with structurally disordered PAS polypeptides to enable delayed plasma clearance and one bispecific BdPTE with broadened substrate spectrum composed of two functionally distinct subunits connected by a PAS linker. Measured kcat/KM values were as high as 6.5 and 1.5 × 108 M-1 min-1 with G- and V-agents, respectively. Furthermore, the stereoselective degradation of VX enantiomers by the PASylated BdPTE-4 and the bispecific BdPTE-7 were investigated by chiral LC-MS/MS, resulting in a several fold faster hydrolysis of the more toxic P(-) VX stereoisomer compared to P(+) VX. In conclusion, the newly developed enzymes BdPTE-4 and BdPTE-7 have shown high catalytic efficacy towards structurally different nerve agents and stereoselectivity towards the toxic P(-) VX enantiomer in vitro and offer promise for use as bioscavengers in vivo.
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Affiliation(s)
- Anja Köhler
- Institut für Pharmakologie und Toxikologie der Bundeswehr, 80937, Munich, Germany
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Germany
| | - Benjamin Escher
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Germany
| | - Laura Job
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Germany
| | - Marianne Koller
- Institut für Pharmakologie und Toxikologie der Bundeswehr, 80937, Munich, Germany
| | - Horst Thiermann
- Institut für Pharmakologie und Toxikologie der Bundeswehr, 80937, Munich, Germany
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising, Germany.
| | - Franz Worek
- Institut für Pharmakologie und Toxikologie der Bundeswehr, 80937, Munich, Germany.
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9
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Wang L, Sun Y. Engineering organophosphate hydrolase for enhanced biocatalytic performance: A review. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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10
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Santillan JY, Rojas NL, Ghiringhelli PD, Nóbile ML, Lewkowicz ES, Iribarren AM. Organophosphorus compounds biodegradation by novel bacterial isolates and their potential application in bioremediation of contaminated water. BIORESOURCE TECHNOLOGY 2020; 317:124003. [PMID: 32810733 DOI: 10.1016/j.biortech.2020.124003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
Organophosphorus compounds (OPs), the major pesticides used worldwide, comprise an environmental hazard due to their harmful toxicity. Aimed to develop a bioreactor to remediate OPs contaminated wastewater, bacteria isolated from contaminated soils were identified and their ability to degrade OPs assessed, resulting in two main isolates, Sphingomonas sp. and Brevundimonas sp. Their OP degrading activities were characterized in terms of temperature, pH and substrates acceptance, resulting in high degradation rates at 60 °C, pH 10 and towards bulky OPs such as coroxon, coumaphos, and chlorpyrifos. Sphingomonas sp. cells were immobilized and 75.4% degradation of 0.15 mM chlorpyrifos was achieved after 21 days by immobilized cells in batch system, while this OP was completely degraded within 17 h when the biocatalyst is settled in a packed bed bioreactor, with a reusability of 8 cycles. These results suggest the potential application of this system in the bioremediation of contaminated wastewater.
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Affiliation(s)
- Julia Yamila Santillan
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Biocatálisis y Biotransformaciones, Roque Sáenz Peña 352, Quilmes 1876, Argentina.
| | - Natalia Lorena Rojas
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular- Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Roque Sáenz Peña 352, Quilmes 1876, Argentina
| | - Pablo Daniel Ghiringhelli
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Ingeniería Genética y Biología Celular y Molecular- Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Roque Sáenz Peña 352, Quilmes 1876, Argentina
| | - Matías Leonardo Nóbile
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Biocatálisis y Biotransformaciones, Roque Sáenz Peña 352, Quilmes 1876, Argentina
| | - Elizabeth Sandra Lewkowicz
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Biocatálisis y Biotransformaciones, Roque Sáenz Peña 352, Quilmes 1876, Argentina
| | - Adolfo Marcelo Iribarren
- Universidad Nacional de Quilmes, CONICET, Departamento de Ciencia y Tecnología, Laboratorio de Biocatálisis y Biotransformaciones, Roque Sáenz Peña 352, Quilmes 1876, Argentina
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11
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Bigley AN, Narindoshvili T, Raushel FM. A Chemoenzymatic Synthesis of the ( RP)-Isomer of the Antiviral Prodrug Remdesivir. Biochemistry 2020; 59:3038-3043. [PMID: 32786401 PMCID: PMC7418565 DOI: 10.1021/acs.biochem.0c00591] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/04/2020] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic threatens to overwhelm healthcare systems around the world. The only current FDA-approved treatment, which directly targets the virus, is the ProTide prodrug remdesivir. In its activated form, remdesivir prevents viral replication by inhibiting the essential RNA-dependent RNA polymerase. Like other ProTide prodrugs, remdesivir contains a chiral phosphorus center. The initial selection of the (SP)-diastereomer for remdesivir was reportedly due to the difficulty in producing the pure (RP)-diastereomer of the required precursor. However, the two currently known enzymes responsible for the initial activation step of remdesivir are each stereoselective and show differential tissue distribution. Given the ability of the COVID-19 virus to infect a wide array of tissue types, inclusion of the (RP)-diastereomer may be of clinical significance. To help overcome the challenge of obtaining the pure (RP)-diastereomer of remdesivir, we have developed a novel chemoenzymatic strategy that utilizes a stereoselective variant of the phosphotriesterase from Pseudomonas diminuta to enable the facile isolation of the pure (RP)-diastereomer of the chiral precursor for the chemical synthesis of the (RP)-diastereomer of remdesivir.
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Affiliation(s)
- Andrew N. Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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12
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Katyal P, Chu S, Montclare JK. Enhancing organophosphate hydrolase efficacy via protein engineering and immobilization strategies. Ann N Y Acad Sci 2020; 1480:54-72. [PMID: 32814367 DOI: 10.1111/nyas.14451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/21/2020] [Accepted: 07/07/2020] [Indexed: 01/30/2023]
Abstract
Organophosphorus compounds (OPs), developed as pesticides and chemical warfare agents, are extremely toxic chemicals that pose a public health risk. Of the different detoxification strategies, organophosphate-hydrolyzing enzymes have attracted much attention, providing a potential route for detoxifying those exposed to OPs. Phosphotriesterase (PTE), also known as organophosphate hydrolase (OPH), is one such enzyme that has been extensively studied as a catalytic bioscavenger. In this review, we will discuss the protein engineering of PTE aimed toward improving the activity and stability of the enzyme. In order to make enzyme utilization in OP detoxification more favorable, enzyme immobilization provides an effective means to increase enzyme activity and stability. Here, we present several such strategies that enhance the storage and operational stability of PTE/OPH.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, New York
| | - Stanley Chu
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, New York
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University, Tandon School of Engineering, Brooklyn, New York.,Department of Radiology, New York University Langone Health, New York, New York.,Department of Biomaterials, New York University College of Dentistry, New York, New York.,Department of Chemistry, New York University, New York, New York
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13
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Bigley AN, Narindoshvili T, Xiang DF, Raushel FM. Stereoselective Formation of Multiple Reaction Products by the Phosphotriesterase from Sphingobium sp. TCM1. Biochemistry 2020; 59:1273-1288. [PMID: 32167750 DOI: 10.1021/acs.biochem.0c00089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Organophosphate flame retardants are used to inhibit combustion and increase plasticity in plastics and durable foams. While not neurotoxic, these compounds are potential carcinogens, endocrine disrupters, and developmental toxins. The phosphotriesterase from Sphingobium sp. TCM1 (Sb-PTE) is unique among phosphotriesterase enzymes for its ability to hydrolyze these compounds and its ability to hydrolyze any one of the three different ester bonds within a given substrate. In some cases, the extent of hydrolysis of a methyl ester exceeds that of a p-nitrophenyl ester within a single substrate. There is a stereochemical component to this hydrolysis where the two enantiomers of chiral substrates give different product ratios. To investigate the stereoselectivity for the product distribution of Sb-PTE, a series of 24 phosphotriesters were synthesized with all possible combinations of methyl, cyclohexyl, phenyl, and p-nitrophenyl esters. Prochiral compounds were made chiral by differential isotopic labeling using a chemo/enzymatic strategy, which allowed the differentiation of hydrolysis for each ester in all but two compounds. The rate equations for this unique enzymatic mechanism were derived; the product ratios were determined for each substrate, and the individual kinetic constants for hydrolysis of each ester within each substrate were measured. The findings are consistent with the rate-limiting step for substrate hydrolysis catalyzed by Sb-PTE being the formation of a phosphorane-like intermediate and the kinetic constants and product ratios being dictated by a combination of transition state energies, inductive effects, and stereochemical constraints.
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Affiliation(s)
- Andrew N Bigley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tamari Narindoshvili
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dao Feng Xiang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Frank M Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.,Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 88743, United States
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14
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Theoretical analyses on enantiospecificity of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1 towards 2-chloropropionic acid. J Mol Graph Model 2019; 92:131-139. [DOI: 10.1016/j.jmgm.2019.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/02/2019] [Accepted: 07/20/2019] [Indexed: 11/24/2022]
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15
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Abstract
The role of phosphotriesterase as an enzyme which is able to hydrolyze organophosphate compounds cannot be disputed. Contamination by organophosphate (OP) compounds in the environment is alarming, and even more worrying is the toxicity of this compound, which affects the nervous system. Thus, it is important to find a safer way to detoxify, detect and recuperate from the toxicity effects of this compound. Phosphotriesterases (PTEs) are mostly isolated from soil bacteria and are classified as metalloenzymes or metal-dependent enzymes that contain bimetals at the active site. There are three separate pockets to accommodate the substrate into the active site of each PTE. This enzyme generally shows a high catalytic activity towards phosphotriesters. These microbial enzymes are robust and easy to manipulate. Currently, PTEs are widely studied for the detection, detoxification, and enzyme therapies for OP compound poisoning incidents. The discovery and understanding of PTEs would pave ways for greener approaches in biotechnological applications and to solve environmental issues relating to OP contamination.
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Xiang DF, Bigley AN, Desormeaux E, Narindoshvili T, Raushel FM. Enzyme-Catalyzed Kinetic Resolution of Chiral Precursors to Antiviral Prodrugs. Biochemistry 2019; 58:3204-3211. [PMID: 31268686 PMCID: PMC6822272 DOI: 10.1021/acs.biochem.9b00530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleoside analogues are among the most common medications given for the treatment of viral infections and cancers. The therapeutic effectiveness of nucleoside analogues can be dramatically improved by phosphorylation. The ProTide approach was developed using a phosphorylated nucleoside that is masked by esterification with an amino acid and phenol forming a chiral phosphorus center. The biological activity of the ProTides depends, in part, on the stereochemistry at phosphorus, and thus, it is imperative that efficient methods be developed for the chemical synthesis and isolation of diastereomerically pure ProTides. Chiral ProTides are often synthesized by direct displacement of a labile phenol (p-nitrophenol or pentafluorophenol) from a chiral phosphoramidate precursor with the appropriate nucleoside analogue. The ability to produce these chiral products is dictated by the synthesis of the chiral phosphoramidate precursors. The enzyme phosphotriesterase (PTE) from Pseudomonas diminuta is well-known for its high stereoselectivity and broad substrate profile. Screening PTE variants from enzyme evolution libraries enabled the identification of variants of PTE that can stereoselectively hydrolyze the chiral phosphoramidate precursors. The variant G60A-PTE exhibits a 165-fold preference for hydrolysis of the RP isomer, while the variant In1W-PTE has a 1400-fold preference for hydrolysis of the SP isomer. Using these mutants of PTE, the SP and RP isomers were isolated on a preparative scale with no detectable contamination of the opposite isomer. Combining the simplicity of the enzymatic resolution of the precursor with the latest synthetic strategy will facilitate the production of diastereometrically pure nucleotide phosphoramidate prodrugs.
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Affiliation(s)
- Dao Feng Xiang
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Andrew N Bigley
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Emily Desormeaux
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Tamari Narindoshvili
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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17
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The evolution of phosphotriesterase for decontamination and detoxification of organophosphorus chemical warfare agents. Chem Biol Interact 2019; 308:80-88. [PMID: 31100274 DOI: 10.1016/j.cbi.2019.05.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/22/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022]
Abstract
The organophosphorus chemical warfare agents were initially synthesized in the 1930's and are some of the most toxic compounds ever discovered. The standard means of decontamination are either harsh chemical hydrolysis or high temperature incineration. Given the continued use of chemical warfare agents there are ongoing efforts to develop gentle environmentally friendly means of decontamination and medical counter measures to chemical warfare agent intoxication. Enzymatic decontamination offers the benefits of extreme specificity and mild conditions, allowing their use for both environmental and medical applications. The most promising enzyme for decontamination of the organophosphorus chemical warfare agents is the enzyme phosphotriesterase from Pseudomonas diminuta. However, the catalytic activity of the wild-type enzyme with the chemical warfare agents falls far below that seen with its best substrates, and its stereochemical preference is for the less toxic enantiomer of the chiral phosphorus center found in most chemical warfare agents. Rational design efforts have succeeded in the dramatic improvement of the stereochemical preference of PTE for the more toxic enantiomers. Directed evolution experiments, including site-saturation mutagenesis, targeted error-prone PCR, computational design, and quantitative library analysis, have systematically improved the catalytic activity against the chemical warfare nerve agents. These efforts have resulted in greater than 4-orders of magnitude improvement in catalytic activity and have led to the identification of variants that are highly effective at detoxifying both G-type and V-type nerve agents. The best of these variants have the ability to prevent intoxication when delivered as a post-exposure treatment for VX and as a pre-exposure treatment for G-agent intoxication with observed protective factors up to 60-fold. Combining the best variant, H257Y/L303T, with a PCB polymer coating has enabled the development of a long lasting circulating prophylactic treatment that is highly effective against sarin.
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18
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Hussain I, Aleti G, Naidu R, Puschenreiter M, Mahmood Q, Rahman MM, Wang F, Shaheen S, Syed JH, Reichenauer TG. Microbe and plant assisted-remediation of organic xenobiotics and its enhancement by genetically modified organisms and recombinant technology: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 628-629:1582-1599. [PMID: 30045575 DOI: 10.1016/j.scitotenv.2018.02.037] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 05/18/2023]
Abstract
Environmental problems such as the deterioration of groundwater quality, soil degradation and various threats to human, animal and ecosystem health are closely related to the presence of high concentrations of organic xenobiotics in the environment. Employing appropriate technologies to remediate contaminated soils is crucial due to the site-specificity of most remediation methods. The limitations of conventional remediation technologies include poor environmental compatibility, high cost of implementation and poor public acceptability. This raises the call to employ biological methods for remediation. Bioremediation and microbe-assisted bioremediation (phytoremediation) offer many ecological and cost-associated benefits. The overall efficiency and performance of bio- and phytoremediation approaches can be enhanced by genetically modified microbes and plants. Moreover, phytoremediation can also be stimulated by suitable plant-microbe partnerships, i.e. plant-endophytic or plant-rhizospheric associations. Synergistic interactions between recombinant bacteria and genetically modified plants can further enhance the restoration of environments impacted by organic pollutants. Nevertheless, releasing genetically modified microbes and plants into the environment does pose potential risks. These can be minimized by adopting environmental biotechnological techniques and guidelines provided by environmental protection agencies and other regulatory frameworks. The current contribution provides a comprehensive overview on enhanced bioremediation and phytoremediation approaches using transgenic plants and microbes. It also sheds light on the mitigation of associated environmental risks.
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Affiliation(s)
- Imran Hussain
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria; Department of Molecular Systems Biology, Faculty of Life Sciences, University of Vienna, Austria
| | - Gajender Aleti
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria
| | - Ravi Naidu
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Markus Puschenreiter
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Mohammad Mahmudur Rahman
- Global Centre for Environmental Remediation (GCER), Faculty of Science, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shahida Shaheen
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Jabir Hussain Syed
- Department of Meteorology, COMSATS Institute of Information Technology, Park Road Tarlai Kalan 45550, Islamabad, Pakistan; Department of Civil and Environmental Engineering, Hong Kong Polytechnic University, Hong Kong.
| | - Thomas G Reichenauer
- AIT Austrian Institute of Technology, Centre for Energy, Environmental Resources and Technologies, Tulln, Austria.
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19
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de Castro AA, Assis LC, Silva DR, Corrêa S, Assis TM, Gajo GC, Soares FV, Ramalho TC. Computational enzymology for degradation of chemical warfare agents: promising technologies for remediation processes. AIMS Microbiol 2017; 3:108-135. [PMID: 31294152 PMCID: PMC6604975 DOI: 10.3934/microbiol.2017.1.108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/14/2017] [Indexed: 11/18/2022] Open
Abstract
Chemical weapons are a major worldwide problem, since they are inexpensive, easy to produce on a large scale and difficult to detect and control. Among the chemical warfare agents, we can highlight the organophosphorus compounds (OP), which contain the phosphorus element and that have a large number of applications. They affect the central nervous system and can lead to death, so there are a lot of works in order to design new effective antidotes for the intoxication caused by them. The standard treatment includes the use of an anticholinergic combined to a central nervous system depressor and an oxime. Oximes are compounds that reactivate Acetylcholinesterase (AChE), a regulatory enzyme responsible for the transmission of nerve impulses, which is one of the molecular targets most vulnerable to neurotoxic agents. Increasingly, enzymatic treatment becomes a promising alternative; therefore, other enzymes have been studied for the OP degradation function, such as phosphotriesterase (PTE) from bacteria, human serum paraoxonase 1 (HssPON1) and diisopropyl fluorophosphatase (DFPase) that showed significant performances in OP detoxification. The understanding of mechanisms by which enzymes act is of extreme importance for the projection of antidotes for warfare agents, and computational chemistry comes to aid and reduce the time and costs of the process. Molecular Docking, Molecular Dynamics and QM/MM (quantum-mechanics/molecular-mechanics) are techniques used to investigate the molecular interactions between ligands and proteins.
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Affiliation(s)
| | - Letícia C. Assis
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Daniela R. Silva
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Silviana Corrêa
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Tamiris M. Assis
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Giovanna C. Gajo
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Flávia V. Soares
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
| | - Teodorico C. Ramalho
- Department of Chemistry, Federal University of Lavras, 37200-000, Lavras, Brazil
- Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Rokitanskeho 62, 50003, Czech Republic
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20
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Poirier L, Jacquet P, Elias M, Daudé D, Chabrière E. [Decontamination of organophosphorus compounds: Towards new alternatives]. ANNALES PHARMACEUTIQUES FRANÇAISES 2017; 75:209-226. [PMID: 28267954 DOI: 10.1016/j.pharma.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 01/20/2023]
Abstract
Organophosphorus coumpounds (OP) are toxic chemicals mainly used for agricultural purpose such as insecticides and were also developed and used as warfare nerve agents. OP are inhibitors of acetylcholinesterase, a key enzyme involved in the regulation of the central nervous system. Chemical, physical and biological approaches have been considered to decontaminate OP. This review summarizes the current and emerging strategies that are investigated to tackle this issue with a special emphasis on enzymatic remediation methods. During the last decade, many studies have been dedicated to the development of biocatalysts for OP removal. Among these, recent reports have pointed out the promising enzyme SsoPox isolated from the archaea Sulfolobus solfataricus. Considering both its intrinsic stability and activity, this hyperthermostable enzyme is highly appealing for the decontamination of OP.
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Affiliation(s)
- L Poirier
- Inserm, CNRS, IRD, URMITE, Aix Marseille université, Marseille, France
| | - P Jacquet
- Inserm, CNRS, IRD, URMITE, Aix Marseille université, Marseille, France
| | - M Elias
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, MN 55108, États-Unis
| | - D Daudé
- Gene&GreenTK, faculté de médecine, 27, boulevard Jean-Moulin, 13385 Marseille cedex 5, France.
| | - E Chabrière
- Inserm, CNRS, IRD, URMITE, Aix Marseille université, Marseille, France; Gene&GreenTK, faculté de médecine, 27, boulevard Jean-Moulin, 13385 Marseille cedex 5, France.
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21
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Lutz S, Williams E, Muthu P. Engineering Therapeutic Enzymes. DIRECTED ENZYME EVOLUTION: ADVANCES AND APPLICATIONS 2017:17-67. [DOI: 10.1007/978-3-319-50413-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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22
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Iyengar ARS, Pande AH. Organophosphate-Hydrolyzing Enzymes as First-Line of Defence Against Nerve Agent-Poisoning: Perspectives and the Road Ahead. Protein J 2016; 35:424-439. [DOI: 10.1007/s10930-016-9686-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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23
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Zhu J, Li X, Zhang S, Ye H, Zhao H, Jin H, Han W. Exploring stereochemical specificity of phosphotriesterase by MM-PBSA and MM-GBSA calculation and steered molecular dynamics simulation. J Biomol Struct Dyn 2016; 35:3140-3151. [DOI: 10.1080/07391102.2016.1244494] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
| | - Xin Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
| | - Siqi Zhang
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
| | - Hen Ye
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
| | - Hui Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Changchun 130023, China
| | - Hanyong Jin
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130023, China
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24
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Mabanglo MF, Xiang DF, Bigley AN, Raushel FM. Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1: A Familiar Binuclear Metal Center Embedded in a Seven-Bladed β-Propeller Protein Fold. Biochemistry 2016; 55:3963-74. [DOI: 10.1021/acs.biochem.6b00364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark F. Mabanglo
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Dao Feng Xiang
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Andrew N. Bigley
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842, United States
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25
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Bisterfeld C, Classen T, Küberl I, Henßen B, Metz A, Gohlke H, Pietruszka J. Redesigning Aldolase Stereoselectivity by Homologous Grafting. PLoS One 2016; 11:e0156525. [PMID: 27327271 PMCID: PMC4915726 DOI: 10.1371/journal.pone.0156525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/16/2016] [Indexed: 11/18/2022] Open
Abstract
The 2-deoxy-d-ribose-5-phosphate aldolase (DERA) offers access to highly desirable building blocks for organic synthesis by catalyzing a stereoselective C-C bond formation between acetaldehyde and certain electrophilic aldehydes. DERA´s potential is particularly highlighted by the ability to catalyze sequential, highly enantioselective aldol reactions. However, its synthetic use is limited by the absence of an enantiocomplementary enzyme. Here, we introduce the concept of homologous grafting to identify stereoselectivity-determining amino acid positions in DERA. We identified such positions by structural analysis of the homologous aldolases 2-keto-3-deoxy-6-phosphogluconate aldolase (KDPG) and the enantiocomplementary enzyme 2-keto-3-deoxy-6-phosphogalactonate aldolase (KDPGal). Mutation of these positions led to a slightly inversed enantiopreference of both aldolases to the same extent. By transferring these sequence motifs onto DERA we achieved the intended change in enantioselectivity.
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Affiliation(s)
- Carolin Bisterfeld
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Irene Küberl
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Birgit Henßen
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Alexander Metz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jörg Pietruszka
- Institut für Bioorganische Chemie, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- * E-mail:
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26
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Jacquet P, Daudé D, Bzdrenga J, Masson P, Elias M, Chabrière E. Current and emerging strategies for organophosphate decontamination: special focus on hyperstable enzymes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:8200-18. [PMID: 26832878 DOI: 10.1007/s11356-016-6143-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/20/2016] [Indexed: 06/05/2023]
Abstract
Organophosphorus chemicals are highly toxic molecules mainly used as pesticides. Some of them are banned warfare nerve agents. These compounds are covalent inhibitors of acetylcholinesterase, a key enzyme in central and peripheral nervous systems. Numerous approaches, including chemical, physical, and biological decontamination, have been considered for developing decontamination methods against organophosphates (OPs). This work is an overview of both validated and emerging strategies for the protection against OP pollution with special attention to the use of decontaminating enzymes. Considerable efforts have been dedicated during the past decades to the development of efficient OP degrading biocatalysts. Among these, the promising biocatalyst SsoPox isolated from the archaeon Sulfolobus solfataricus is emphasized in the light of recently published results. This hyperthermostable enzyme appears to be particularly attractive for external decontamination purposes with regard to both its catalytic and stability properties.
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Affiliation(s)
- Pauline Jacquet
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - David Daudé
- Gene&GreenTK, Faculté de Médecine, 27 boulevard Jean Moulin, Cedex 5, Marseille, 13385, France
| | - Janek Bzdrenga
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kazan, 420008, Russia
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric Chabrière
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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27
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Jang YJ, Kim K, Tsay OG, Atwood DA, Churchill DG. Update 1 of: Destruction and Detection of Chemical Warfare Agents. Chem Rev 2015; 115:PR1-76. [DOI: 10.1021/acs.chemrev.5b00402] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yoon Jeong Jang
- Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea
| | - Kibong Kim
- Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea
| | - Olga G. Tsay
- Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea
| | - David A. Atwood
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - David G. Churchill
- Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), 373-1 Guseong-dong, Yuseong-gu, Daejeon, 305−701, Republic of Korea
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28
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Tanaka SI, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nat Chem Biol 2015; 11:762-4. [PMID: 26322825 DOI: 10.1038/nchembio.1896] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/11/2015] [Indexed: 12/16/2022]
Abstract
Current methods for engineering enzymes modify enzymes themselves and require a detailed mechanistic understanding or a high-throughput assay. Here, we describe a new approach where catalytic properties are modulated with synthetic binding proteins, termed monobodies, directed to an unmodified enzyme. Using the example of a β-galactosidase from Bacillus circulans, we efficiently identified monobodies that restricted its substrates for its transgalactosylation reaction and selectively enhanced the production of small oligosaccharide prebiotics.
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Affiliation(s)
- Shun-Ichi Tanaka
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.,Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Tetsuya Takahashi
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
| | - Satoru Ishihara
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Satoshi Koikeda
- Frontier Research Department, Gifu R&D Center, Amano Enzyme, Inc., Gifu, Japan
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA
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29
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Zhan D, Guan S, Jin H, Han W, Wang S. Stereoselectivity of phosphotriesterase with paraoxon derivatives: a computational study. J Biomol Struct Dyn 2015; 34:600-11. [PMID: 25929154 DOI: 10.1080/07391102.2015.1046937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The bacterial enzyme phosphotriesterase (PTE) exhibits stereoselectivity toward hydrolysis of chiral substrates with a preference for the Sp enantiomer. In this work, docking analysis and two explicit-solvent molecular dynamics (MD) simulations were performed to characterize and differentiate the structural dynamics of PTE bound to the Sp and Rp paraoxon derivative enantiomers (Rp-1 and Sp-1) hydrolyzed with distinct catalytic efficiencies. Comparative analysis of the molecular trajectories for PTE bound to Rp-1 and Sp-1 suggested that substrate binding induced conformational changes in the loops near the active site. After 100 ns of MD simulation, the Zn β(2+) metal ion formed hexacoordinated- and tetracoordinated geometries in the Sp-1-PTE and Rp-1-PTE ensembles, respectively. Simulation results further showed that the hydrogen bond between Asp301 and His254 occurred with a higher probability after Sp-1 binding to PTE (47.5%) than that after Rp-1 binding (22.2%). These results provide a qualitative and molecular-level explanation for the 10 orders of magnitude increase in the catalytic efficiency of PTE toward the Sp enantiomer of paraoxon.
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Affiliation(s)
- Dongling Zhan
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China.,b College of Food Science and Engineering , Jilin Agricultural University , Changchun 130118 , China
| | - Shanshan Guan
- c State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun 130023 , China
| | - Hanyong Jin
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China
| | - Weiwei Han
- a Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science , Jilin University , Changchun 130023 , China
| | - Song Wang
- c State Key Laboratory of Theoretical and Computational Chemistry , Institute of Theoretical Chemistry, Jilin University , Changchun 130023 , China
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30
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Makhlynets OV, Raymond EA, Korendovych IV. Design of allosterically regulated protein catalysts. Biochemistry 2015; 54:1444-56. [PMID: 25642601 DOI: 10.1021/bi5015248] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Activity of allosteric protein catalysts is regulated by an external stimulus, such as protein or small molecule binding, light activation, pH change, etc., at a location away from the active site of the enzyme. Since its original introduction in 1961, the concept of allosteric regulation has undergone substantial expansion, and many, if not most, enzymes have been shown to possess some degree of allosteric regulation. The ability to create new catalysts that can be turned on and off using allosteric interactions would greatly expand the chemical biology toolbox and will allow for detection of environmental pollutants and disease biomarkers and facilitate studies of cellular processes and metal homeostasis. Thus, design of allosterically regulated protein catalysts represents an actively growing area of research. In this paper, we describe various approaches to achieving regulation of catalysis.
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
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31
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Iyer R, Iken B. Protein engineering of representative hydrolytic enzymes for remediation of organophosphates. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Tsai PC, Fox N, Bigley AN, Harvey SP, Barondeau DP, Raushel FM. Enzymes for the homeland defense: optimizing phosphotriesterase for the hydrolysis of organophosphate nerve agents. Biochemistry 2012; 51:6463-75. [PMID: 22809162 DOI: 10.1021/bi300811t] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphotriesterase (PTE) from soil bacteria is known for its ability to catalyze the detoxification of organophosphate pesticides and chemical warfare agents. Most of the organophosphate chemical warfare agents are a mixture of two stereoisomers at the phosphorus center, and the S(P)-enantiomers are significantly more toxic than the R(P)-enantiomers. In previous investigations, PTE variants were created through the manipulation of the substrate binding pockets and these mutants were shown to have greater catalytic activities for the detoxification of the more toxic S(P)-enantiomers of nerve agent analogues for GB, GD, GF, VX, and VR than the less toxic R(P)-enantiomers. In this investigation, alternate strategies were employed to discover additional PTE variants with significant improvements in catalytic activities relative to that of the wild-type enzyme. Screening and selection techniques were utilized to isolate PTE variants from randomized libraries and site specific modifications. The catalytic activities of these newly identified PTE variants toward the S(P)-enantiomers of chromophoric analogues of GB, GD, GF, VX, and VR have been improved up to 15000-fold relative to that of the wild-type enzyme. The X-ray crystal structures of the best PTE variants were determined. Characterization of these mutants with the authentic G-type nerve agents has confirmed the expected improvements in catalytic activity against the most toxic enantiomers of GB, GD, and GF. The values of k(cat)/K(m) for the H257Y/L303T (YT) mutant for the hydrolysis of GB, GD, and GF were determined to be 2 × 10(6), 5 × 10(5), and 8 × 10(5) M(-1) s(-1), respectively. The YT mutant is the most proficient enzyme reported thus far for the detoxification of G-type nerve agents. These results support a combinatorial strategy of rational design and directed evolution as a powerful tool for the discovery of more efficient enzymes for the detoxification of organophosphate nerve agents.
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Affiliation(s)
- Ping-Chuan Tsai
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, TX 77842, USA
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Bigley AN, Raushel FM. Catalytic mechanisms for phosphotriesterases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:443-53. [PMID: 22561533 DOI: 10.1016/j.bbapap.2012.04.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/31/2012] [Accepted: 04/13/2012] [Indexed: 01/04/2023]
Abstract
Phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. Wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. A wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (PTE), methyl parathion hydrolase (MPH), organophosphorus acid anhydrolase (OPAA), diisopropylfluorophosphatase (DFP), and paraoxonase 1 (PON1). These enzymes differ widely in protein sequence and three-dimensional structure, as well as in catalytic mechanism, but they also share several common features. All of the enzymes identified as phosphotriesterases are metal-dependent hydrolases that contain a hydrophobic active site with three discrete binding pockets to accommodate the substrate ester groups. Activation of the substrate phosphorus center is achieved by a direct interaction between the phosphoryl oxygen and a divalent metal in the active site. The mechanistic details of the hydrolytic reaction differ among the various enzymes with both direct attack of a hydroxide as well as covalent catalysis being found. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Affiliation(s)
- Andrew N Bigley
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
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Wales ME, Reeves TE. Organophosphorus hydrolase as an in vivo catalytic nerve agent bioscavenger. Drug Test Anal 2012; 4:271-81. [DOI: 10.1002/dta.381] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/03/2011] [Accepted: 10/03/2011] [Indexed: 11/12/2022]
Affiliation(s)
- Melinda E. Wales
- Department of Biochemistry & Biophysics; Texas A&M University; College Station; TX; USA
| | - Tony E. Reeves
- Southwest Research Institute; Microencapsulation and Nanomaterials, Chemistry and Chemical Engineering Division; San Antonio; TX; USA
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Gomes DEB, Lins RD, Pascutti PG, Lei C, Soares TA. Conformational variability of organophosphorus hydrolase upon soman and paraoxon binding. J Phys Chem B 2011; 115:15389-98. [PMID: 22098575 DOI: 10.1021/jp208787g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial enzyme organophosphorus hydrolase (OPH) exhibits both catalytic and substrate promiscuity. It hydrolyzes bonds in a variety of phosphotriester (P-O), phosphonothioate (P-S), phosphofluoridate (P-F), and phosphonocyanate (F-CN) compounds. However, its catalytic efficiency varies markedly for different substrates, limiting the broad-range application of OPH as catalyst in the bioremediation of pesticides and chemical war agents. In the present study, pK(a) calculations and multiple explicit-solvent molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of OPH bound to two substrates hydrolyzed with very distinct catalytic efficiencies: the nerve agent soman (O-pinacolylmethylphosphonofluoridate) and the pesticide paraoxon (diethyl p-nitrophenyl phosphate). pK(a) calculations for the substrate-bound and unbound enzyme showed a significant pK(a) shift from standard values (ΔpK(a) = ±3 units) for residues His254 and Arg275. MD simulations of protonated His254 revealed a dynamic hydrogen bond network connecting the catalytic residue Asp301 via His254 to Asp232, Asp233, Arg275, and Asp235, and is consistent with a previously postulated proton relay mechanism to ferry protons away from the active site with substrates that do not require activation of the leaving group. Hydrogen bonds between Asp301 and His254 were persistent in the OPH-paraoxon complex but not in the OPH-soman one, suggesting a potential role for such interaction in the more efficient hydrolysis of paraoxon over soman by OPH. These results are in line with previous mutational studies of residue His254, which led to an increase of the catalytic efficiency of OPH over soman yet decreased its efficiency for paraoxon. In addition, comparative analysis of the molecular trajectories for OPH bound to soman and paraoxon suggests that binding of the latter facilitates the conformational transition of OPH from the open to the closed substate promoting a tighter binding of paraoxon.
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Affiliation(s)
- Diego E B Gomes
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
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An isofenphos-methyl hydrolase (Imh) capable of hydrolyzing the P-O-Z moiety of organophosphorus pesticides containing an aryl or heterocyclic group. Appl Microbiol Biotechnol 2011; 94:1553-64. [PMID: 22120622 DOI: 10.1007/s00253-011-3709-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 10/23/2011] [Accepted: 11/05/2011] [Indexed: 10/15/2022]
Abstract
Organophosphorus pesticide (OP) hydrolases play key roles in the degradation and decontamination of agricultural and household OPs and in the detoxification of chemical warfare agents. In this study, an isofenphos-methyl hydrolase gene (imh) was cloned from the isocarbophos-degrading strain of Arthrobacter sp. scl-2 using the polymerase chain reaction method. Isofenphos-methyl hydrolase (Imh) showed 98% sequence identity with the isofenphos hydrolase from Arthrobacter sp. strain B-5. Imh was highly expressed in Escherichia coli BL21 (DE3), and the His(6)-tagged Imh was purified (1.7 mg/ml) with a specific activity of 14.35 U/mg for the substrate isofenphos-methyl. The molecular mass of the denatured Imh is about 44 kDa, and the isoelectric point (pI) value was estimated to be 3.4. The optimal pH and temperature for hydrolysis of isofenphos-methyl were pH 8.0 and 35 °C, respectively. The secondary structure of Imh shows that Imh is a metallo-dependent hydrolase, and it was found that Imh was completely inhibited by the metalloprotease inhibitor 1,10-phenanthroline (0.5 mM), and the catalytic activity was restored by the subsequent addition of Zn(2+). Interestingly, Imh had a relatively broader substrate specificity and was capable of hydrolyzing 12 of the tested oxon and thion OPs with the P-O-Z moiety instead of the P-S(C)-Z moiety. Furthermore, it was found that the existence of an aryl or heterocyclic group in the leaving group (Z) is also important in determining the substrate specificity. Among all the substrates hydrolyzed by Imh, it was assumed that Imh preferred P-O-Z substrates still with a phosphamide bond (P-N), such as isofenphos-methyl, isofenphos, isocarbophos, and butamifos. The newly characterized Imh has a great potential for use in the decontamination and detoxification of agricultural and household OPs and is a good candidate for the study of the catalytic mechanism and substrate specificity of OP hydrolases.
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Bornscheuer U, Kazlauskas RJ. Survey of protein engineering strategies. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 26:26.7.1-26.7.14. [PMID: 22045562 DOI: 10.1002/0471140864.ps2607s66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein engineering is altering the structure of a protein to improve or change its properties. This unit summarizes concepts for protein engineering using rational design, directed evolution, and combinations of them. Different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are given. This should enable researchers to choose the most promising tools to solve their protein engineering challenges.
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Affiliation(s)
- Uwe Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Greifswald, Germany
| | - Romas J Kazlauskas
- Department of Biochemistry, Molecular Biology and Biophysics and the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota
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Baker PJ, Montclare JK. Enhanced Refoldability and Thermoactivity of Fluorinated Phosphotriesterase. Chembiochem 2011; 12:1845-8. [DOI: 10.1002/cbic.201100221] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Indexed: 12/13/2022]
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Kim K, Tsay OG, Atwood DA, Churchill DG. Destruction and detection of chemical warfare agents. Chem Rev 2011; 111:5345-403. [PMID: 21667946 DOI: 10.1021/cr100193y] [Citation(s) in RCA: 563] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kibong Kim
- Molecular Logic Gate Laboratory, Department of Chemistry, KAIST, Daejeon, 305-701, Republic of Korea
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Briseño-Roa L, Timperley CM, Griffiths AD, Fersht AR. Phosphotriesterase variants with high methylphosphonatase activity and strong negative trade-off against phosphotriesters. Protein Eng Des Sel 2010; 24:151-9. [PMID: 21037279 DOI: 10.1093/protein/gzq076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The most lethal organophosphorus nerve agents (NA), like sarin, soman, agent-VX and Russian-VX, share a methylphosphonate moiety. Pseudomonas diminuta phosphotriesterase (PTE) catalyses the hydrolysis of methylphosphonate NA analogues with a catalytic efficiency orders of magnitude lower than that towards the pesticide paraoxon. With a view to obtaining PTE variants that more readily accept methylphosphonate NA, ~75,000 PTE variants of the substrate-binding residues Gly-60, Ile-106, Leu-303 and Ser-308 were screened with fluorogenic analogues of the NA Russian-VX and cyclosarin. Seven new PTE variants were isolated, purified and their k(cat)/K(M) determined against five phosphotriesters and five methylphosphonate analogues of sarin, cyclosarin, soman, agent-VX and Russian-VX. The novel PTE variants exhibited as much as a 10-fold increase in activity towards the methylphosphonate compounds--many reaching a k(cat)/K(M) of 10⁶ M⁻¹ s⁻¹--and as much as a 29,000-fold decrease in their phosphotriesterase activity. The mutations found in two of the variants, SS0.5 (G60V/I106L/S308G) and SS4.5 (G60V/I106A/S308G), were modelled into a high-resolution structure of PTE-wild type and docked with analogues of cyclosarin and Russian-VX using Autodock 4.2. The kinetic data and docking simulations suggest that the increase in activity towards the methylphosphonates and the loss of function against the phosphotriesters were due to an alteration of the shape and hydrophobicity of the binding pocket that hinders the productive binding of non-chiral racemic phosphotriesters, yet allows the binding of the highly asymmetric methylphosphonates.
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Affiliation(s)
- Luis Briseño-Roa
- MRC Centre for Protein Engineering, Hills Road, Cambridge CB20QH, UK.
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41
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Tsai PC, Bigley A, Li Y, Ghanem E, Cadieux CL, Kasten SA, Reeves TE, Cerasoli DM, Raushel FM. Stereoselective hydrolysis of organophosphate nerve agents by the bacterial phosphotriesterase. Biochemistry 2010; 49:7978-87. [PMID: 20701311 DOI: 10.1021/bi101056m] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organophosphorus compounds include many synthetic, neurotoxic substances that are commonly used as insecticides. The toxicity of these compounds is due to their ability to inhibit the enzyme acetylcholine esterase. Some of the most toxic organophosphates have been adapted for use as chemical warfare agents; the most well-known are GA, GB, GD, GF, VX, and VR. All of these compounds contain a chiral phosphorus center, with the S(P) enantiomers being significantly more toxic than the R(P) enantiomers. Phosphotriesterase (PTE) is an enzyme capable of detoxifying these agents, but the stereochemical preference of the wild-type enzyme is for the R(P) enantiomers. A series of enantiomerically pure chiral nerve agent analogues containing the relevant phosphoryl centers found in GB, GD, GF, VX, and VR has been developed. Wild-type and mutant forms of PTE have been tested for their ability to hydrolyze this series of compounds. Mutant forms of PTE with significantly enhanced, as well as relaxed or reversed, stereoselectivity have been identified. A number of variants exhibited dramatically improved kinetic constants for the catalytic hydrolysis of the more toxic S(P) enantiomers. Improvements of up to 3 orders of magnitude relative to the value of the wild-type enzyme were observed. Some of these mutants were tested against racemic mixtures of GB and GD. The kinetic constants obtained with the chiral nerve agent analogues accurately predict the improved activity and stereoselectivity against the authentic nerve agents used in this study.
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Affiliation(s)
- Ping-Chuan Tsai
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, Texas 77842, USA
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Tsai PC, Fan Y, Kim J, Yang L, Almo SC, Gao YQ, Raushel FM. Structural determinants for the stereoselective hydrolysis of chiral substrates by phosphotriesterase. Biochemistry 2010; 49:7988-97. [PMID: 20695627 DOI: 10.1021/bi101058z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wild-type phosphotriesterase (PTE) preferentially hydrolyzes the R(P) enantiomers of the nerve agents sarin (GB) and cyclosarin (GF) and their chromophoric analogues. The active site of PTE can be subdivided into three binding pockets that have been denoted as the small, large, and leaving group pockets based on high-resolution crystal structures. The sizes and shapes of these pockets dictate the substrate specificity and stereoselectivity for catalysis. Mutants of PTE that exhibit substantial changes in substrate specificity and the ability to differentiate between chiral substrates have been prepared. For example, the G60A mutant is stereoselective for the hydrolysis of the R(P) enantiomer of the chromophoric analogues of sarin and cyclosarin, whereas the H254G/H257W/L303T (GWT) mutant reverses the stereoselectivity for the enantiomers of these two compounds. Molecular dynamics simulations and high-resolution X-ray structures identified the correlations between structural changes in the active site and the experimentally determined kinetic parameters for substrate hydrolysis. New high-resolution structures were determined for the H257Y/L303T (YT), I106G/F132G/H257Y (GGY), and H254Q/H257F (QF) mutants of PTE. Molecular dynamics calculations were conducted using the S(P) and R(P) enantiomers of the analogues for sarin and cyclosarin for the wild-type PTE and the G60A, YT, GGY, QF, and GWT mutants. The experimental stereoselectivity correlated nicely with the difference in the computed angle of attack for the nucleophilic hydroxide relative to the phenolic leaving group of the substrate.
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Affiliation(s)
- Ping-Chuan Tsai
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, USA
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Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme. Biochem J 2010; 429:313-21. [DOI: 10.1042/bj20100233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The metal ion co-ordination sites of many metalloproteins have been characterized by a variety of spectroscopic techniques and small-molecule model systems, revealing many important insights into the structural determinants of metal ion co-ordination. However, our understanding of this fundamentally and practically important phenomenon remains frustratingly simplistic; in many proteins it is essentially impossible to predict metal ion specificity and the effects of remote ‘outer-shell’ residues on metal ion co-ordination strength are also poorly defined. This is exemplified by our inability to explain why metalloenzymes with identical metal ion co-ordination spheres, such as the closely related orthologues of bacterial PTE (phosphotriesterase) from Agrobacterium radiobacter and Pseudomonas diminuta, display different metal ion specificity and co-ordination strength. In the present study, we present a series of PTE variants that all possess identical metal ion co-ordination spheres, yet display large differences in their metal ion co-ordination strength. Using measurement of the rates of metal ion dissociation from the active site alongside analysis of structural data obtained through X-ray crystallography, we show that ‘outer-shell’ residues provide essential support for the metal ion ligands, in effect buttressing them in their optimal orientation. Remote mutations appear to modulate metal ion interactions by increasing or decreasing the stabilizing effects of these networks. The present study therefore provides a description of how the greater protein fold can be modified to ‘tune’ the strength of metal ion co-ordination and metal ion specificity, as well as reinforcing the concept of proteins as ensembles of conformational states with unique structures and biochemical properties.
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Melzer M, Chen JCH, Heidenreich A, Gäb J, Koller M, Kehe K, Blum MM. Reversed enantioselectivity of diisopropyl fluorophosphatase against organophosphorus nerve agents by rational design. J Am Chem Soc 2010; 131:17226-32. [PMID: 19894712 DOI: 10.1021/ja905444g] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diisopropyl fluorophosphatase (DFPase) from Loligo vulgaris is an efficient and robust biocatalyst for the hydrolysis of a range of highly toxic organophosphorus compounds including the nerve agents sarin, soman, and cyclosarin. In contrast to the substrate diisopropyl fluorophosphate (DFP) the nerve agents possess an asymmetric phosphorus atom, which leads to pairs of enantiomers that display markedly different toxicities. Wild-type DFPase prefers the less toxic stereoisomers of the substrates which leads to slower detoxification despite rapid hydrolysis. Enzyme engineering efforts based on rational design yielded two quadruple enzyme mutants with reversed enantioselectivity and overall enhanced activity against tested nerve agents. The reversed stereochemical preference is explained through modeling studies and the crystal structures of the two mutants. Using the engineered mutants in combination with wild-type DFPase leads to significantly enhanced activity and detoxification, which is especially important for personal decontamination. Our findings may also be of relevance for the structurally related enzyme human paraoxonase (PON), which is of considerable interest as a potential catalytic in vivo scavenger in case of organophosphorus poisoning.
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Affiliation(s)
- Marco Melzer
- Blum-Scientific Services, Ledererstrasse 23, 80331 Munich, Germany
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Gomes DE, Lins RD, Pascutti PG, Lei C, Soares TA. The role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized mesoporous silica surfaces. J Phys Chem B 2010; 114:531-40. [PMID: 19938866 PMCID: PMC2818561 DOI: 10.1021/jp9083635] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme organophosphorous hydrolase (OPH) catalyzes the hydrolysis of a wide variety of organophosphorous compounds with high catalytic efficiency and broad substrate specificity. The immobilization of OPH in functionalized mesoporous silica (FMS) surfaces increases significantly its catalytic specific activity, as compared to the enzyme in solution, with important applications for the detection and decontamination of insecticides and chemical warfare agents. Experimental measurements of immobilization efficiency as a function of the charge and coverage percentage of different functional groups have been interpreted as electrostatic forces being the predominant interactions underlying the adsorption of OPH onto FMS surfaces. Explicit solvent molecular dynamics simulations have been performed for OPH in bulk solution and adsorbed onto two distinct interaction potential models of the FMS functional groups to investigate the relative contributions of nonbonded interactions to the conformational dynamics and adsorption of the protein. Our results support the conclusion that electrostatic interactions are responsible for the binding of OPH to the FMS surface. However, these results also show that van der Waals forces are detrimental for interfacial adhesion. In addition, it is found that OPH adsorption onto the FMS models favors a protein conformation whose active site is fully accessible to the substrate, in contrast to the unconfined protein.
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Affiliation(s)
- Diego E.B. Gomes
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
| | - Roberto D. Lins
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Departamento de Química Fundamental, CCEN, UFPE, 50590-470, Recife PE, Brazil
| | - Pedro G. Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21949-900, Brazil
| | - Chenghong Lei
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
| | - Thereza A. Soares
- Pacific Northwest National Laboratory, P.O. Box 999, MSIN K7-90, Richland, WA 99352, USA
- Departamento de Química Fundamental, CCEN, UFPE, 50590-470, Recife PE, Brazil
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Zhang X, Wu R, Song L, Lin Y, Lin M, Cao Z, Wu W, Mo Y. Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase. J Comput Chem 2009; 30:2388-401. [PMID: 19353598 PMCID: PMC2754597 DOI: 10.1002/jcc.21238] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent-exposed metal ion Zn(beta), but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Zn(beta). The subsequent SN2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Zn(alpha) or the micro-hydroxo bridge between the alpha- and beta-metals. Our simulations supported the latter and showed that the rate-limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates.
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Affiliation(s)
- Xin Zhang
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Ruibo Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Lingchun Song
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yuchun Lin
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Menghai Lin
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Zexing Cao
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Wei Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
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Affiliation(s)
- Romas J Kazlauskas
- Biotechnology Institute and Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, St. Paul, Minnesota, USA.
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Carletti E, Jacquamet L, Loiodice M, Rochu D, Masson P, Nachon F. Update on biochemical properties of recombinant Pseudomonas diminuta phosphotriesterase. J Enzyme Inhib Med Chem 2009; 24:1045-55. [DOI: 10.1080/14756360802608518] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Eugénie Carletti
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 24 av des Maquis du Grésivaudan, 38700 La Tronche, France
| | - Lilian Jacquamet
- Laboratoire de Cristallogenèse et Cristallographie des Protéines. Institut de Biologie Structurale (CEA-CNRS-UJF), 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Mélanie Loiodice
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 24 av des Maquis du Grésivaudan, 38700 La Tronche, France
| | - Daniel Rochu
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 24 av des Maquis du Grésivaudan, 38700 La Tronche, France
| | - Patrick Masson
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 24 av des Maquis du Grésivaudan, 38700 La Tronche, France
| | - Florian Nachon
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées (CRSSA), 24 av des Maquis du Grésivaudan, 38700 La Tronche, France
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Mugford P, Wagner UG, Jiang Y, Faber K, Kazlauskas R. Enantiocomplementary Enzymes: Classification, Molecular Basis for Their Enantiopreference, and Prospects for Mirror-Image Biotransformations. Angew Chem Int Ed Engl 2008; 47:8782-93. [DOI: 10.1002/anie.200705159] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mugford P, Wagner U, Jiang Y, Faber K, Kazlauskas R. Enantiokomplementäre Enzyme: Klassifizierung, molekulare Grundlage der Enantiopräferenz und Prognosen für spiegelbildliche Biotransformationen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705159] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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