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Rodríguez-Salarichs J, García de Lacoba M, Prieto A, Martínez MJ, Barriuso J. Versatile Lipases from the Candida rugosa-like Family: A Mechanistic Insight Using Computational Approaches. J Chem Inf Model 2021; 61:913-920. [PMID: 33555857 PMCID: PMC8479805 DOI: 10.1021/acs.jcim.0c01151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Lipases
are enzymes able to catalyze the hydrolysis or synthesis
of triglycerides, depending on the reaction conditions, whereas sterol
esterases show the same ability on sterol esters. Structurally, both
kinds of enzymes display an α/β-hydrolase fold, with a
substrate-binding pocket formed by a hydrophobic cavity covered by
a mobile lid. However, it has been reported that some lipases from
the Candida rugosa-like family display
wide substrate specificity on both triglycerides and sterol esters.
Among them, enzymes with different biotechnological applications,
such as the lipase isoenzymes produced by C. rugosa and the sterol esterase from Ophiostoma piceae, have been exhaustively characterized and their crystal structures
are available. Differences in substrate affinity among these proteins
have been attributed to changes in their hydrophobicity. In this work,
we analyzed the full catalytic mechanisms of these proteins using
molecular dynamics tools, gaining insight into their mechanistic properties.
In addition, we developed an in silico protocol to
predict the substrate specificity using C. rugosa and O. piceae lipases as model enzymes
and triglycerides and cholesterol esters with different fatty acid
chain lengths as model substrates. The protocol was validated by comparing
the in silico results with those described in the
literature. These results would be useful to perform virtual screening
of substrates for enzymes of the C. rugosa-like family with unknown catalytic properties.
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Affiliation(s)
- Javier Rodríguez-Salarichs
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mario García de Lacoba
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Murugan A, Prathiviraj R, Mothay D, Chellapandi P. Substrate-imprinted docking of Agrobacterium tumefaciens uronate dehydrogenase for increased substrate selectivity. Int J Biol Macromol 2019; 140:1214-1225. [PMID: 31472210 DOI: 10.1016/j.ijbiomac.2019.08.194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/15/2019] [Accepted: 08/22/2019] [Indexed: 11/18/2022]
Abstract
Agrobacterium tumefaciens uronate dehydrogenase (AtuUdh) belongs to the short-chain dehydrogenase superfamily, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. It is apparently required for the production of D-glucaric acid. AtuUdh-catalyzed reaction is reversible with dual substrate-specific activity (D-galacturonic acid and D-glucuronic acid) in nature. In our study, 34 mutants were pre-screened from 155 mutants generated from AtuUdh (wild-type) and selected 10 structurally stable mutants with increased substrate selectivity. The specificity, efficiency, and selectivity of these mutants for different substrates and cofactors were predicted from 121 docked models using a substrate-imprinted docking approach. Q14F, S36L, and S75T mutants have shown a high binding affinity to D-glucuronic acid and its substrate intermediates such as D-glucaro-1,4-lactone and D-glucaro-1,5-lactone. These mutants exhibited a low binding affinity to the substrate and cofactor required for D-galactaric acid. D34S, N112E and S165E mutants found to show a high selectivity of D-galacturonic acid and its substrate intermediates for D-galactaric acid production. Ser75, Ser165, and Arg174 are active residues playing an imperative role in the substrate selectivity and also contributed in the conjecture the mechanism of transition state stabilization catalyzed by AtuUdh mutants. The present approach was used to reveal the substrate binding mechanism of AtuUdh mutants for a better understanding of the structural basis for selectivity and function.
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Affiliation(s)
- A Murugan
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - R Prathiviraj
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Dipti Mothay
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
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3
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Paul M, Kumar Panda M, Thatoi H. Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. J Biomol Struct Dyn 2018; 37:3947-3967. [PMID: 30295165 DOI: 10.1080/07391102.2018.1532321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hispolon is a polyphenolic compound derived from black hoof mushroom (Phellinus linteus) or shaggy bracket mushroom (Inonotus hispidus) which induces the inhibition of cancer-promoting nuclear factor-kappa beta (NF-κβ) complex. To develop more potent lead molecules with enhanced anticancer efficiency, the mechanism of hispolon-mediated nuclear factor-κβ inhibition has been investigated by molecular modelling and docking. Ten derivatives of hispolon (DRG1-10) have been developed by pharmacophore-based design with a view to enhance the anticancer efficacy. Hispolon and its derivatives were further screened for different pharmacological parameters like binding free energy, drug likeliness, absorption-digestion-metabolism-excretion (ADME), permeability, mutagenicity, toxicity and inhibitory concentration 50 (IC50) to find a potent lead molecule. Based on pharmacological validation, comparative molecular dynamics (MD) simulations have been performed for three lead molecules: Hispolon, DRG2 and DRG7 complexed with human NF-κβ up to 50 ns. By analysing different factors like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA) and principal component analysis (PCA), Gibb's free energy plots DRG2 have more binding efficiency compared to hispolon and DRG7. In RMSD plot, hispolon-bound NF-κβ has the most deviation within a range between 0.125 and 0.45 nm, and DRG2-bound complex showed the range between 0.125 and 0.25 nm. The residues of NF-κβ responsible for hydrophobic interactions with ligand, e.g. Met469, Leu522 and Cys533, have the lowest fluctuation values in DRG2-bound complex. The average Rg fluctuation for DRG2-bound NF-κβ has been recorded under 2.025 nm for most of the simulation time which is much less compared to hispolon and DRG7. Gibb's free energy plots also define the highest stability of DRG2-bound NF-κβ. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Paul
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
| | | | - Hrudayanath Thatoi
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
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Yao Z, Jiang S, Zhang L, Gao B, He X, Zhang JZH, Wei D. Crius: A novel fragment-based algorithm of de novo substrate prediction for enzymes. Protein Sci 2018; 27:1526-1534. [PMID: 29722450 DOI: 10.1002/pro.3437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 11/07/2022]
Abstract
The study of enzyme substrate specificity is vital for developing potential applications of enzymes. However, the routine experimental procedures require lot of resources in the discovery of novel substrates. This article reports an in silico structure-based algorithm called Crius, which predicts substrates for enzyme. The results of this fragment-based algorithm show good agreements between the simulated and experimental substrate specificities, using a lipase from Candida antarctica (CALB), a nitrilase from Cyanobacterium syechocystis sp. PCC6803 (Nit6803), and an aldo-keto reductase from Gluconobacter oxydans (Gox0644). This opens new prospects of developing computer algorithms that can effectively predict substrates for an enzyme.
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Affiliation(s)
- Zhiqiang Yao
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Lujia Zhang
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Molecular Engineering, East China Normal University, Shanghai, 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, East China university of Science and Technology, Meilong Road 130th, Shanghai, People's Republic of China
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