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Oyewusi HA, Adedamola Akinyede K, Wahab RA, Susanti E, Syed Yaacob SN, Huyop F. Biological and molecular approaches of the degradation or decolorization potential of the hypersaline Lake Tuz Bacillus megaterium H2 isolate. J Biomol Struct Dyn 2024; 42:6228-6244. [PMID: 37455463 DOI: 10.1080/07391102.2023.2234040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
The presence of synthetic dyes in water bodies and soil is one of the major issues affecting the global ecology, possibly impacting societal well-being adversely due to the colorants' recalcitrance and toxicity. Herein, the study spectrophotometrically monitored the ability of the Bacillus megaterium H2 azoreductase (AzrBmH2) to degrade four synthetic dyes, reactive blue 4, remazol brilliant red, thymol blue, and methyl red, followed by in-silico assessment using GROMACS. We found that the bacterium degraded as much as 60% of all four synthetic dyes at various tested concentrations. The genome analysis revealed five different azoreductase genes, which were then modeled into the AzrBmH21, AzrBmH22/3, and AzrBmH24/5 templates. The AzrBmH2-substrate complexes showed binding energies with all the dyes of between -10.6 to -6.9 kcal/mol and formed 4-6 hydrogen bonds with the predicted catalytic binding residues (His10, Glu 14, Ser 58, Met 99, Val 107, His 183, Asn184 and Gln 191). In contrast, the lowest binding energies were observed for the AzrBmH21-substrates (-10.6 to -7.9). Molecular dynamic simulations revealed that the AzrBmH21-substrate complexes were more stable (RMSD 0.2-0.25 nm, RMSF 0.05 - 0.3 nm) and implied strong bonding with the dyes. The Molecular Mechanics Poisson-Boltzmann Surface Area results also mirrored this outcome, showing the lowest azoreductase-dye binding energy in the order of AzrBmH21-RB4 (-78.18 ± 8.92 kcal/mol), AzrBmH21-RBR (-67.51 ± 7.74 kcal/mol), AzrBmH21-TB (-46.62 ± 5.23 kcal/mol) and AzrBmH21-MR (-40.78 ± 7.87 kcal/mol). In short, the study demonstrated the ability of the B. megaterium H2 to efficiently decolorize the above-said synthetic dyes, conveying the bacterium's promising use for large-scale dye remediation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Science Technology, Biochemistry Unit, The Federal Polytechnic, Ado Ekiti, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry Unit, The Federal Polytechnic, Ado Ekiti, Nigeria
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Department of Applied Science, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Malang, Indonesia
| | - Evi Susanti
- Department of Applied Science, Faculty of Mathematics and Natural Sciences, Universitas Negeri Malang, Malang, Indonesia
| | - Syariffah Nuratiqah Syed Yaacob
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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2
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Dudas B, Miteva MA. Computational and artificial intelligence-based approaches for drug metabolism and transport prediction. Trends Pharmacol Sci 2024; 45:39-55. [PMID: 38072723 DOI: 10.1016/j.tips.2023.11.001] [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: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 01/07/2024]
Abstract
Drug metabolism and transport, orchestrated by drug-metabolizing enzymes (DMEs) and drug transporters (DTs), are implicated in drug-drug interactions (DDIs) and adverse drug reactions (ADRs). Reliable and precise predictions of DDIs and ADRs are critical in the early stages of drug development to reduce the rate of drug candidate failure. A variety of experimental and computational technologies have been developed to predict DDIs and ADRs. Recent artificial intelligence (AI) approaches offer new opportunities for better predicting and understanding the complex processes related to drug metabolism and transport. We summarize the role of major DMEs and DTs, and provide an overview of current progress in computational approaches for the prediction of drug metabolism, transport, and DDIs, with an emphasis on AI including machine learning (ML) and deep learning (DL) modeling.
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Affiliation(s)
- Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Maria A Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France.
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3
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Toth D, Dudas B, Miteva MA, Balog E. Role of Conformational Dynamics of Sulfotransferases SULT1A1 and SULT1A3 in Substrate Specificity. Int J Mol Sci 2023; 24:16900. [PMID: 38069221 PMCID: PMC10706399 DOI: 10.3390/ijms242316900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Sulfotransferases (SULTs) are phase II metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3'-Phosphoadenosine 5'-Phosphosulfate (PAPS) to a wide variety of endogenous compounds, drugs and natural products. Although SULT1A1 and SULT1A3 share 93% identity, SULT1A1, the most abundant SULT isoform in humans, exhibits a broad substrate range with specificity for small phenolic compounds, while SULT1A3 displays a high affinity toward monoamine neurotransmitters like dopamine. To elucidate the factors determining the substrate specificity of the SULT1 isoenzymes, we studied the dynamic behavior and structural specificities of SULT1A1 and SULT1A3 by using molecular dynamics (MD) simulations and ensemble docking of common and specific substrates of the two isoforms. Our results demonstrated that while SULT1A1 exhibits a relatively rigid structure by showing lower conformational flexibility except for the lip (loop L1), the loop L2 and the cap (L3) of SULT1A3 are extremely flexible. We identified protein residues strongly involved in the recognition of different substrates for the two isoforms. Our analyses indicated that being more specific and highly flexible, the structure of SULT1A3 has particularities in the binding site, which are crucial for its substrate selectivity.
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Affiliation(s)
- Daniel Toth
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
| | - Balint Dudas
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Maria A. Miteva
- CiTCoM UMR 8038 CNRS, INSERM U1268 MCTR, Université Paris Cité, 75006 Paris, France; (D.T.); (B.D.)
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
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Oyewusi HA, Akinyede KA, Abdul Wahab R, Huyop F. In silico analysis of a putative dehalogenase from the genome of halophilic bacterium Halomonas smyrnensis AAD6T. J Biomol Struct Dyn 2023; 41:319-335. [PMID: 34854349 DOI: 10.1080/07391102.2021.2006085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Microbial-assisted removal of natural or synthetic pollutants is the prevailing green, low-cost technology to treat polluted environments. However, the challenge with enzyme-assisted bioremediation is the laborious nature of dehalogenase-producing microorganisms' bioprospecting. This bottleneck could be circumvented by in-silico analysis of certain microorganisms' whole-genome sequences to predict their protein functions and enzyme versatility for improved biotechnological applications. Herein, this study performed structural analysis on a dehalogenase (DehHsAAD6) from the genome of Halomonas smyrnensis AAD6 by molecular docking and molecular dynamic (MD) simulations. Other bioinformatics tools were also employed to identify substrate preference (haloacids and haloacetates) of the DehHsAAD6. The DehHsAAD6 preferentially degraded haloacids and haloacetates (-3.2-4.8 kcal/mol) and which formed three hydrogen bonds with Tyr12, Lys46, and Asp182. MD simulations data revealed the higher stability of DehHsAAD6-haloacid- (RMSD 0.22-0.3 nm) and DehHsAAD6-haloacetates (RMSF 0.05-0.14 nm) complexes, with the DehHsAAD6-L-2CP complex being the most stable. The detail of molecular docking calculations ranked complexes with the lowest binding free energies as: DehHsAAD6-L-2CP complex (-4.8 kcal/mol) = DehHsAAD6-MCA (-4.8 kcal/mol) < DehHsAAD6-TCA (-4.5 kcal/mol) < DehHsAAD6-2,3-DCP (-4.1 kcal/mol) < DehHsAAD6-D-2CP (-3.9 kcal/mol) < DehHsAAD6-2,2-DCP (-3.5 kcal/mol) < DehHsAAD6-3CP (-3.2 kcal/mol). In a nutshell, the study findings offer valuable perceptions into the elucidation of possible reaction mechanisms of dehalogenases for extended substrate specificity and higher catalytic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria
| | - Kolajo Adedamola Akinyede
- Department of Science Technology, Biochemistry unit, The Federal Polytechnic P.M.B, Ado Ekiti, Ekiti State, Nigeria.,Department of Medical Bioscience, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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5
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Isvoran A, Peng Y, Ceauranu S, Schmidt L, Nicot AB, Miteva MA. Pharmacogenetics of human sulfotransferases and impact of amino acid exchange on Phase II drug metabolism. Drug Discov Today 2022; 27:103349. [PMID: 36096358 DOI: 10.1016/j.drudis.2022.103349] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022]
Abstract
Sulfotransferases (SULTs) are Phase II drug-metabolizing enzymes (DMEs) catalyzing the sulfation of a variety of endogenous compounds, natural products, and drugs. Various drugs, such as nonsteroidal anti-inflammatory drugs (NSAIDS) can inhibit SULTs, affecting drug-drug interactions. Several polymorphisms have been identified for SULTs that might be crucial for interindividual variability in drug response and toxicity or for increased disease risk. Here, we review current knowledge on non-synonymous single nucleotide polymorphisms (nsSNPs) of human SULTs, focusing on the coded SULT allozymes and molecular mechanisms explaining their variable activity, which is essential for personalized medicine. We discuss the structural and dynamic bases of key amino acid (AA) variants implicated in the impacts on drug metabolism in the case of SULT1A1, as revealed by molecular modeling approaches.
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Affiliation(s)
- Adriana Isvoran
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Yunhui Peng
- INSERM U1268 Medicinal Chemistry and Translational Research, CiTCoM UMR 8038 CNRS - Université Paris Cité, 75006 Paris, France
| | - Silvana Ceauranu
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Leon Schmidt
- Department of Biology-Chemistry and Advanced Environmental Research Laboratories, West University of Timisoara, 16 Pestalozzi, 300115 Timisoara, Romania
| | - Arnaud B Nicot
- INSERM, Nantes Université, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000 Nantes, France.
| | - Maria A Miteva
- INSERM U1268 Medicinal Chemistry and Translational Research, CiTCoM UMR 8038 CNRS - Université Paris Cité, 75006 Paris, France.
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Oyewusi HA, Wu YS, Safi SZ, Wahab RA, Hatta MHM, Batumalaie K. Molecular dynamics simulations reveal the inhibitory mechanism of Withanolide A against α-glucosidase and α-amylase. J Biomol Struct Dyn 2022:1-16. [PMID: 35904027 DOI: 10.1080/07391102.2022.2104375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Diabetes mellitus (DM) is a global chronic disease characterized by hyperglycemia and insulin resistance. The unsavory severe gastrointestinal side-effects of synthetic drugs to regulate hyperglycemia have warranted the search for alternative treatments to inhibit the carbohydrate digestive enzymes (e.g. α-amylase and α-glucosidase). Certain phytochemicals recently captured the scientific community's attention as carbohydrate digestive enzyme inhibitors due to their low toxicity and high efficacy, specifically the Withanolides-loaded extract of Withania somnifera. That said, the present study evaluated in silico the efficacy of Withanolide A in targeting both α-amylase and α-glucosidase in comparison to the synthetic drug Acarbose. Protein-ligand interactions, binding affinity, and stability were characterized using pharmacological profiling, high-end molecular docking, and molecular-dynamic simulation. Withanolide A inhibited the activity of α-glucosidase and α-amylase better, exhibiting good pharmacokinetic properties, absorption, and metabolism. Also, Withanolide A was minimally toxic, with higher bioavailability. Interestingly, Withanolide A bonded well to the active site of α-amylase and α-glucosidase, yielding the lowest binding free energy of -82.144 ± 10.671 kcal/mol and -102.1043 ± 11.231 kcal/mol compared to the Acarbose-enzyme complexes (-63.220 ± 13.283 kcal/mol and -82.148 ± 10.671 kcal/mol). Hence, the findings supported the therapeutic potential of Withanolide A as α-amylase and α-glucosidase inhibitor for DM treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Science Technology, Biochemistry unit, The Federal Polytechnic, Ado Ekiti, Ekiti State, Nigeria
| | - Yuan-Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia.,Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Sher Zaman Safi
- IRCBM, COMSATS University Islamabad, Lahore Campus, Punjab, Pakistan
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Kalaivani Batumalaie
- Department of Biomedical Science, Faculty of Health Sciences, Asia Metropolitan University, Johor Bahru, Johor, Malaysia
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Pedersen LC, Yi M, Pedersen LG, Kaminski AM. From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function. Drug Metab Dispos 2022; 50:1027-1041. [PMID: 35197313 PMCID: PMC10753775 DOI: 10.1124/dmd.121.000478] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.
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Affiliation(s)
- Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - MyeongJin Yi
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Lee G Pedersen
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
| | - Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory (L.C.P., L.G.P., A.M.K.) and Reproductive and Developmental Biology Laboratory (M.Y.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina; and Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (L.G.P.)
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8
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Bril’kov MS, Dobrovolska O, Ødegård-Fougner Ø, Turcu DC, Strømland Ø, Underhaug J, Aasland R, Halskau Ø. Binding Specificity of ASHH2 CW Domain Toward H3K4me1 Ligand Is Coupled to Its Structural Stability Through Its α1-Helix. Front Mol Biosci 2022; 9:763750. [PMID: 35495628 PMCID: PMC9043364 DOI: 10.3389/fmolb.2022.763750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/25/2022] [Indexed: 11/14/2022] Open
Abstract
The CW domain binds to histone tail modifications found in different protein families involved in epigenetic regulation and chromatin remodeling. CW domains recognize the methylation state of the fourth lysine on histone 3 and could, therefore, be viewed as a reader of epigenetic information. The specificity toward different methylation states such as me1, me2, or me3 depends on the particular CW subtype. For example, the CW domain of ASHH2 methyltransferase binds preferentially to H3K4me1, and MORC3 binds to both H3K4me2 and me3 modifications, while ZCWPW1 is more specific to H3K4me3. The structural basis for these preferential bindings is not well understood, and recent research suggests that a more complete picture will emerge if dynamical and energetic assessments are included in the analysis of interactions. This study uses fold assessment by NMR in combination with mutagenesis, ITC affinity measurements, and thermal denaturation studies to investigate possible couplings between ASHH2 CW selectivity toward H3K4me1 and the stabilization of the domain and loops implicated in binding. The key elements of the binding site—the two tryptophans and the α1-helix form and maintain the binding pocket— were perturbed by mutagenesis and investigated. Results show that the α1-helix maintains the overall stability of the fold via the I915 and L919 residues and that the correct binding consolidates the loops designated as η1 and η3, as well as the C-terminal. This consolidation is incomplete for H3K4me3 binding to CW, which experiences a decrease in overall thermal stability on binding. Loop mutations not directly involved in the binding site, nonetheless, affect the equilibrium positions of the key residues.
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Affiliation(s)
- Maxim S. Bril’kov
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Pharmacy, University of Tromsø, Tromsø, Norway
| | - Olena Dobrovolska
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Øyvind Ødegård-Fougner
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Diana C. Turcu
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Jarl Underhaug
- Department of Chemistry, University of Bergen, Bergen, Norway
| | - Rein Aasland
- Department of Biosciences, University of Oslo, Oslo, Norway
- *Correspondence: Rein Aasland, ; Øyvind Halskau,
| | - Øyvind Halskau
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- *Correspondence: Rein Aasland, ; Øyvind Halskau,
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Huang H, Lan BD, Zhang YJ, Fan XJ, Hu MC, Qin GQ, Wang FG, Wu Y, Zheng T, Liu JH. Inhibition of Human Sulfotransferases by Phthalate Monoesters. Front Endocrinol (Lausanne) 2022; 13:868105. [PMID: 35528018 PMCID: PMC9072656 DOI: 10.3389/fendo.2022.868105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE This study aimed to investigate the inhibition of human important phase II metabolic enzyme sulfotransferases (SULTs) by phthalate monoesters, which are important metabolites of phthalate esters (PAEs). METHOD Recombinant SULT-catalyzed metabolism of p-nitrophenol (PNP) was employed as the probe reactions of SULTs to investigate the inhibition of 8 kinds of phthalate monoesters towards SULT isoforms. An in vitro incubation system was utilized for preliminary screening, and 100 μM of phthalate monoesters was used. Inhibition kinetics were carried out to determine the inhibition of SULTs by phthalate monoesters. RESULT Multiple phthalate monoesters have been demonstrated to exert strong inhibition potential towards SULT1A1, SULT1B1, and SULT1E1, and no significant inhibition of phthalate monoesters towards SULT1A3 was found. The activity of SULT1A1 was strongly inhibited by mono-hexyl phthalate (MHP), mono-octyl phthalate (MOP), mono-benzyl phthalate (MBZP), and mono-ethylhexyl phthalate (MEHP). Monobutyl phthalate (MBP), MHP, MOP, mono-cyclohexyl phthalate (MCHP), and MEHP significantly inhibited the activity of SULT1B1. MHP, MOP, and MEHP significantly inhibited the activity of SULT1E1. MOP was chosen as the representative phthalate monoester to determine the inhibition kinetic parameters (Ki) towards SULT1B1 and SULT1E1. The inhibition kinetic parameters (Ki) were calculated to be 2.23 μM for MOP-SULT1B1 and 5.54 μM for MOP-SULT1E1. In silico docking method was utilized to understand the inhibition mechanism of SULT1B1 by phthalate monoesters. CONCLUSIONS All these information will be beneficial for understanding the risk of phthalate monoester exposure from a new perspective.
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Affiliation(s)
- Hui Huang
- Department of Cardiology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Bei-Di Lan
- Department of CardioMetabolic Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yu-Jing Zhang
- Department of Cardiology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Xiao-Juan Fan
- Department of CardioMetabolic Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Min-Cui Hu
- Tianjin Life Science Research Center, Department of Microbiology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Guo-Qiang Qin
- Human Resources Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Fei-Ge Wang
- Human Resources Department, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yue Wu
- Department of CardioMetabolic Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tao Zheng
- Department of CardioMetabolic Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Tao Zheng, ; Jun-Hui Liu,
| | - Jun-Hui Liu
- Department of CardioMetabolic Center, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Tao Zheng, ; Jun-Hui Liu,
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Lessigiarska I, Peng Y, Tsakovska I, Alov P, Lagarde N, Jereva D, Villoutreix BO, Nicot AB, Pajeva I, Pencheva T, Miteva MA. Computational Analysis of Chemical Space of Natural Compounds Interacting with Sulfotransferases. Molecules 2021; 26:molecules26216360. [PMID: 34770768 PMCID: PMC8588419 DOI: 10.3390/molecules26216360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to investigate the chemical space and interactions of natural compounds with sulfotransferases (SULTs) using ligand- and structure-based in silico methods. An in-house library of natural ligands (hormones, neurotransmitters, plant-derived compounds and their metabolites) reported to interact with SULTs was created. Their chemical structures and properties were compared to those of compounds of non-natural (synthetic) origin, known to interact with SULTs. The natural ligands interacting with SULTs were further compared to other natural products for which interactions with SULTs were not known. Various descriptors of the molecular structures were calculated and analyzed. Statistical methods (ANOVA, PCA, and clustering) were used to explore the chemical space of the studied compounds. Similarity search between the compounds in the different groups was performed with the ROCS software. The interactions with SULTs were additionally analyzed by docking into different experimental and modeled conformations of SULT1A1. Natural products with potentially strong interactions with SULTs were outlined. Our results contribute to a better understanding of chemical space and interactions of natural compounds with SULT enzymes and help to outline new potential ligands of these enzymes.
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Affiliation(s)
- Iglika Lessigiarska
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
| | - Yunhui Peng
- INSERM U1268 “Medicinal Chemistry and Translational Research”, CiTCoM UMR 8038 CNRS—Université de Paris, 75006 Paris, France;
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Ivanka Tsakovska
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
| | - Petko Alov
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
| | - Nathalie Lagarde
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, 2 Rue Conté, Hésam Université, 75003 Paris, France;
| | - Dessislava Jereva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
| | | | - Arnaud B. Nicot
- INSERM, Nantes Université, Center for Research in Transplantation and Translational Immunology, UMR 1064, ITUN, F-44000 Nantes, France;
| | - Ilza Pajeva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
| | - Tania Pencheva
- Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (I.L.); (I.T.); (P.A.); (D.J.); (I.P.)
- Correspondence: (T.P.); (M.A.M.)
| | - Maria A. Miteva
- INSERM U1268 “Medicinal Chemistry and Translational Research”, CiTCoM UMR 8038 CNRS—Université de Paris, 75006 Paris, France;
- Correspondence: (T.P.); (M.A.M.)
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11
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Zhang S, Wang Y, Han L, Fu X, Wang S, Li W, Han W. Targeting N-Terminal Human Maltase-Glucoamylase to Unravel Possible Inhibitors Using Molecular Docking, Molecular Dynamics Simulations, and Adaptive Steered Molecular Dynamics Simulations. Front Chem 2021; 9:711242. [PMID: 34527658 PMCID: PMC8435576 DOI: 10.3389/fchem.2021.711242] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/26/2021] [Indexed: 02/04/2023] Open
Abstract
There are multiple drugs for the treatment of type 2 diabetes, including traditional sulfonylureas biguanides, glinides, thiazolidinediones, α-glucosidase inhibitors, glucagon-like peptide-1 (GLP-1) receptor agonists, dipeptidyl peptidase IV (DPP-4) inhibitors, and sodium-glucose cotransporter 2 (SGLT2) inhibitors. α-Glucosidase inhibitors have been used to control postprandial glucose levels caused by type 2 diabetes since 1990. α-Glucosidases are rather crucial in the human metabolic system and are principally found in families 13 and 31. Maltase-glucoamylase (MGAM) belongs to glycoside hydrolase family 31. The main function of MGAM is to digest terminal starch products left after the enzymatic action of α-amylase; hence, MGAM becomes an efficient drug target for insulin resistance. In order to explore the conformational changes in the active pocket and unbinding pathway for NtMGAM, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed for two NtMGAM-inhibitor [de-O-sulfonated kotalanol (DSK) and acarbose] complexes. MD simulations indicated that DSK bound to NtMGAM may influence two domains (inserted loop 1 and inserted loop 2) by interfering with the spiralization of residue 497–499. The flexibility of inserted loop 1 and inserted loop 2 can influence the volume of the active pocket of NtMGAM, which can affect the binding progress for DSK to NtMGAM. ASMD simulations showed that compared to acarbose, DSK escaped from NtMGAM easily with lower energy. Asp542 is an important residue on the bottleneck of the active pocket of NtMGAM and could generate hydrogen bonds with DSK continuously. Our theoretical results may provide some useful clues for designing new α-glucosidase inhibitors to treat type 2 diabetes.
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Affiliation(s)
- Shitao Zhang
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
| | - Yi Wang
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
| | - Lu Han
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
| | - Xueqi Fu
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China
| | - Wannan Li
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
| | - Weiwei Han
- School of Life Science, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, National Engineering Laboratory for AIDS Vaccine, Jilin University, Changchun, China
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12
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Dudas B, Toth D, Perahia D, Nicot AB, Balog E, Miteva MA. Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations. Sci Rep 2021; 11:13129. [PMID: 34162941 PMCID: PMC8222352 DOI: 10.1038/s41598-021-92480-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/10/2021] [Indexed: 11/14/2022] Open
Abstract
Sulfotransferases (SULTs) are phase II drug-metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to a substrate. It has been previously suggested that a considerable shift of SULT structure caused by PAPS binding could control the capability of SULT to bind large substrates. We employed molecular dynamics (MD) simulations and the recently developed approach of MD with excited normal modes (MDeNM) to elucidate molecular mechanisms guiding the recognition of diverse substrates and inhibitors by SULT1A1. MDeNM allowed exploring an extended conformational space of PAPS-bound SULT1A1, which has not been achieved up to now by using classical MD. The generated ensembles combined with docking of 132 SULT1A1 ligands shed new light on substrate and inhibitor binding mechanisms. Unexpectedly, our simulations and analyses on binding of the substrates estradiol and fulvestrant demonstrated that large conformational changes of the PAPS-bound SULT1A1 could occur independently of the co-factor movements that could be sufficient to accommodate large substrates as fulvestrant. Such structural displacements detected by the MDeNM simulations in the presence of the co-factor suggest that a wider range of drugs could be recognized by PAPS-bound SULT1A1 and highlight the utility of including MDeNM in protein–ligand interactions studies where major rearrangements are expected.
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Affiliation(s)
- Balint Dudas
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS - University of Paris, Pharmacy Faculty of Paris, Paris, France.,Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Gif-sur-Yvette, France
| | - Daniel Toth
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Gif-sur-Yvette, France
| | - Arnaud B Nicot
- Inserm, Université de Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000, Nantes, France
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
| | - Maria A Miteva
- Inserm U1268 MCTR, CiTCoM UMR 8038 CNRS - University of Paris, Pharmacy Faculty of Paris, Paris, France.
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13
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Wang K, Chan YC, So PK, Liu X, Feng L, Cheung WT, Lee SST, Au SWN. Structure of mouse cytosolic sulfotransferase SULT2A8 provides insight into sulfonation of 7α-hydroxyl bile acids. J Lipid Res 2021; 62:100074. [PMID: 33872606 PMCID: PMC8134075 DOI: 10.1016/j.jlr.2021.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/09/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022] Open
Abstract
Cytosolic sulfotransferases (SULTs) catalyze the transfer of a sulfonate group from the cofactor 3'-phosphoadenosine 5'-phosphosulfate to a hydroxyl (OH) containing substrate and play a critical role in the homeostasis of endogenous compounds, including hormones, neurotransmitters, and bile acids. In human, SULT2A1 sulfonates the 3-OH of bile acids; however, bile acid metabolism in mouse is dependent on a 7α-OH sulfonating SULT2A8 via unknown molecular mechanisms. In this study, the crystal structure of SULT2A8 in complex with adenosine 3',5'-diphosphate and cholic acid was resolved at a resolution of 2.5 Å. Structural comparison with human SULT2A1 reveals different conformations of substrate binding loops. In addition, SULT2A8 possesses a unique substrate binding mode that positions the target 7α-OH of the bile acid close to the catalytic site. Furthermore, mapping of the critical residues by mutagenesis and enzyme activity assays further highlighted the importance of Lys44 and His48 for enzyme catalysis and Glu237 in loop 3 on substrate binding and stabilization. In addition, limited proteolysis and thermal shift assays suggested that the cofactor and substrates have protective roles in stabilizing SULT2A8 protein. Together, the findings unveil the structural basis of bile acid sulfonation targeting 7α-OH and shed light on the functional diversity of bile acid metabolism across species.
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Affiliation(s)
- Kai Wang
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Yan-Chun Chan
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Xing Liu
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Lu Feng
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wing-Tai Cheung
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Susanna Sau-Tuen Lee
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Shannon Wing-Ngor Au
- Faculty of Science, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong; Center for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.
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14
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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