Revealing the Roles of Subdomains in the Catalytic Behavior of Lipases/Acyltransferases Homologous to CpLIP2 through Rational Design of Chimeric Enzymes

Anne-Hélène Jan; Éric Dubreucq; Maeva Subileau

doi:10.1002/cbic.201600672

Comparative Experimental and Theoretical Study of Mg, Al and Zn Aryloxy Complexes in Copolymerization of Cyclic Esters: The Role of the Metal Coordination in Formation of Random Copolymers

Polymers ◽

10.3390/polym12102273 ◽

2020 ◽

Vol 12 (10) ◽

pp. 2273

Author(s):

Ilya Nifant’ev ◽

Pavel Komarov ◽

Valeriya Ovchinnikova ◽

Artem Kiselev ◽

Mikhail Minyaev ◽

...

Keyword(s):

Density Functional ◽

Rational Design ◽

Qualitative Difference ◽

Random Copolymers ◽

Coordination Polymerization ◽

Polymer Backbone ◽

Catalytic Behavior ◽

Cyclic Esters ◽

Dft Modeling ◽

The Density Functional Theory

Homogeneity of copolymers is a general problem of catalytic coordination polymerization. In ring-opening polymerization of cyclic esters, the rational design of the catalyst is generally applied to solve this problem by the equalization of the reactivities of comonomers—however, it often leads to a reduction of catalytic activity. In the present paper, we studied the catalytic behavior of BnOH-activated complexes (BHT)Mg(THF)2nBu (1), (BHT)2AlMe (2) and [(BHT)ZnEt]2 (3), based on 2,6-di-tert-butyl-4-methylphenol (BHT-H) in homo- and copolymerization of L-lactide (lLA) and ε-caprolactone (εCL). Even at 1:5 lLA/εCL ratio Mg complex 1 catalyzed homopolymerization of lLA without involving εCL to the formation of the polymer backbone. On the contrary, Zn complex 3 efficiently catalyzed random lLA/εCL copolymerization; the presence of mono-lactate subunits in the copolymer chain clearly pointed to the transesterification mechanism of copolymer formation. Both epimerization and transesterification side processes were analyzed using the density functional theory (DFT) modeling that confirmed the qualitative difference in catalytic behavior of 1 and 3: Mg and Zn complexes demonstrated different types of preferable coordination on the PLA chain (k2 and k3, respectively) with the result that complex 3 catalyzed controlled εCL ROP/PLA transesterification, providing the formation of lLA/εCL copolymers that contain mono-lactate fragments separated by short oligo(εCL) chains. The best results in the synthesis of random lLA/εCL copolymers were obtained during experiments on transesterification of commercially available PLLA, the applicability of 3/BnOH catalyst in the synthesis of random copolymers of εCL with methyl glycolide, ethyl ethylene phosphonate and ethyl ethylene phosphate was also demonstrated.

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Substrate Specificity of Chimeric Enzymes Formed by Interchange of the Catalytic and Specificity Domains of the 5′-Nucleotidase UshA and the 3′-Nucleotidase CpdB

Molecules ◽

10.3390/molecules26082307 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2307

Author(s):

Alicia Cabezas ◽

Iralis López-Villamizar ◽

María Jesús Costas ◽

José Carlos Cameselle ◽

João Meireles Ribeiro

Keyword(s):

Catalytic Domain ◽

Nucleotidase Activity ◽

Catalytic Behavior ◽

Substrate Specificities ◽

Chimeric Enzymes ◽

Domain Structures ◽

The Common ◽

Partial Overlap ◽

Specificity Domain ◽

Terminal Domains

The 5′-nucleotidase UshA and the 3′-nucleotidase CpdB from Escherichia coli are broad-specificity phosphohydrolases with similar two-domain structures. Their N-terminal domains (UshA_Ndom and CpdB_Ndom) contain the catalytic site, and their C-terminal domains (UshA_Cdom and CpdB_Cdom) contain a substrate-binding site responsible for specificity. Both enzymes show only partial overlap in their substrate specificities. So, it was decided to investigate the catalytic behavior of chimeras bearing the UshA catalytic domain and the CpdB specificity domain, or vice versa. UshA_Ndom–CpdB_Cdom and CpdB_Ndom–UshA_Cdom were constructed and tested on substrates specific to UshA (5′-AMP, CDP-choline, UDP-glucose) or to CpdB (3′-AMP), as well as on 2′,3′-cAMP and on the common phosphodiester substrate bis-4-NPP (bis-4-nitrophenylphosphate). The chimeras did show neither 5′-nucleotidase nor 3′-nucleotidase activity. When compared to UshA, UshA_Ndom–CpdB_Cdom conserved high activity on bis-4-NPP, some on CDP-choline and UDP-glucose, and displayed activity on 2′,3′-cAMP. When compared to CpdB, CpdB_Ndom–UshA_Cdom conserved phosphodiesterase activities on 2′,3′-cAMP and bis-4-NPP, and gained activity on the phosphoanhydride CDP-choline. Therefore, the non-nucleotidase activities of UshA and CpdB are not fully dependent on the interplay between domains. The specificity domains may confer the chimeras some of the phosphodiester or phosphoanhydride selectivity displayed when associated with their native partners. Contrarily, the nucleotidase activity of UshA and CpdB depends strictly on the interplay between their native catalytic and specificity domains.

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Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Physical Chemistry Chemical Physics ◽

10.1039/d0cp05759b ◽

2021 ◽

Vol 23 (1) ◽

pp. 219-228

Author(s):

Nabanita Saikia ◽

Mohamed Taha ◽

Ravindra Pandey

Keyword(s):

Nucleic Acid ◽

Boron Nitride ◽

Nucleic Acids ◽

Dynamic Stability ◽

Peptide Nucleic Acid ◽

Rational Design ◽

Peptide Nucleic Acids ◽

Boron Nitride Nanotubes ◽

Molecular Hybrids ◽

Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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Optimizing electron density of nickel sulfide electrocatalysts through sulfur vacancy engineering for alkaline hydrogen evolution

Journal of Materials Chemistry A ◽

10.1039/d0ta05594h ◽

2020 ◽

Vol 8 (35) ◽

pp. 18207-18214

Author(s):

Dongbo Jia ◽

Lili Han ◽

Ying Li ◽

Wenjun He ◽

Caichi Liu ◽

...

Keyword(s):

Hydrogen Evolution ◽

Electron Density ◽

Rational Design ◽

Nickel Sulfide ◽

Catalytic Performance ◽

Sulfide Catalysts ◽

Sulfur Vacancy

A novel, rational design for porous S-vacancy nickel sulfide catalysts with remarkable catalytic performance for alkaline HER.

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Rational design & continuous evolution of minimalist proteins that target the E-box DNA site

10.1021/scimeetings.0c07226 ◽

2020 ◽

Author(s):

Jumi Shin

Keyword(s):

Rational Design ◽

Continuous Evolution ◽

E Box

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Rational design of annotine analogues with increased inhibitory activity towards acetylcholinesterase

Planta Medica ◽

10.1055/s-0036-1596773 ◽

2016 ◽

Vol 81 (S 01) ◽

pp. S1-S381

Author(s):

ES Halldorsdottir ◽

S Oddsson ◽

AM Einarsdottir ◽

B Eiriksdottir ◽

NM Kowal ◽

...

Keyword(s):

Inhibitory Activity ◽

Rational Design

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Anticoagulant Activity of Hirulog™, a Direct Thrombin Inhibitor, in Humans

Thrombosis and Haemostasis ◽

10.1055/s-0038-1651573 ◽

1993 ◽

Vol 69 (02) ◽

pp. 157-163 ◽

Cited By ~ 137

Author(s):

Irving Fox ◽

Adrian Dawson ◽

Peter Loynds ◽

Jane Eisner ◽

Kathleen Findlen ◽

...

Keyword(s):

Rational Design ◽

Therapeutic Potential ◽

Anticoagulant Activity ◽

Subcutaneous Administration ◽

Direct Thrombin Inhibitor ◽

Controlled Study ◽

Thrombin Inhibitor ◽

Thrombin Time ◽

Thrombotic Disease ◽

Dose Dependent

SummaryHirulog™ (BG8967) is a direct thrombin inhibitor built by rational design using the protein hirudin as a model (Maraganore et al. [1990]; Biochemistry 29: 7095–101). In order to evaluate the therapeutic potential for hirulog in the management of thrombotic disease, the tolerability and anticoagulant activity of the agent were examined in a study of human volunteers.In a randomized, placebo-controlled study (n = 54), the intravenous infusion of hirulog over 15 min showed a rapid, dose-dependent prolongation of activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT). There was a corresponding dose-dependent increase in plasma hirulog levels. The peptide was rapidly cleared with a half-life of 36 min and a total body clearance rate for the peptide of 0.43 1 kg−1 h−1. Similar activity was observed following subcutaneous injection but with sustained pharmacodynamic and pharmacokinetic behavior. There was a significant correlation between pharmacokinetic and pharmacodynamic variables for both intravenous (r = 0.8, p <0.001) and subcutaneous administration (r = 0.7, p = 0.002).To evaluate the possible interactions of aspirin on the tolerability and anticoagulant activity of intravenous hirulog, a cross-over design was employed in eight subjects. Aspirin administration did not modify the peptide’s activity. At the administered dose of 0.6 mg kg−1 h−1 for 2 h, hirulog infusion prolonged APTT from 230 to 260% baseline. The infusion of hirulog in subjects who had received aspirin was not associated with any significant changes in the template bleeding time.The final phase of the study examined the activity and tolerability of hirulog in ten subjects during prolonged intravenous infusions for up to 24 h. The peptide (0.3 mg kg−1 h−1) exhibited sustained anticoagulant activity with no evidence for a cumulative effect. During hirulog infusion, APTT was prolonged from 210 to 250% baseline.In all phases of the study, hirulog administration was generally well-tolerated.Our observations show that hirulog is an active antithrombin agent with excellent tolerability in humans. As a direct thrombin inhibitor, hirulog provides a novel approach for the management of thrombotic disease.

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