Estimating kinetic constants in the Michaelis–Menten model from one enzymatic assay using Approximate Bayesian Computation

Tomczak, Jakub M.; Węglarz-Tomczak, Ewelina

doi:10.1002/1873-3468.13531

Cited by 25 publications

(22 citation statements)

References 29 publications

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“…We estimated kinetic parameters of hydrolysis of Ub-AMC ( Fig. 3f) using the recently published novel Approximate Bayesian Computation (ABC) computational tool for calculating kinetic constants in the Michaelis-Menten equation 38 ( Fig. 3c-e), see the Supplementary Data for more details.…”

Section: Kinetic Analysis Of the Ub-amc Hydrolysis By Pl Pro From Sarmentioning

confidence: 99%

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Węglarz-Tomczak

Tomczak

Talma

et al. 2021

Sci Rep

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114

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An efficient treatment against a COVID-19 disease, caused by the novel coronavirus SARS-CoV-2 (CoV2), remains a challenge. The papain-like protease (PLpro) from the human coronavirus is a protease that plays a critical role in virus replication. Moreover, CoV2 uses this enzyme to modulate the host’s immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. We used Approximate Bayesian Computation tools, molecular modelling and enzyme activity studies to identify highly active inhibitors of the PLpro. We discovered organoselenium compounds, ebselen and its structural analogues, as a novel approach for inhibiting the activity of PLproCoV2. Furthermore, we identified, for the first time, inhibitors of PLproCoV2 showing potency in the nanomolar range. Moreover, we found a difference between PLpro from SARS and CoV2 that can be correlated with the diverse dynamics of their replication, and, putatively to disease progression.

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Section: Kinetic Analysis Of the Ub-amc Hydrolysis By Pl Pro From Sarmentioning

confidence: 99%

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Węglarz-Tomczak

Tomczak

Talma

et al. 2021

Sci Rep

Self Cite

114

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“…PL Pro SARS catalyzed the reaction faster and achieved saturation. We estimated kinetic parameters of hydrolysis of Ub-AMC (Table 1) using the recently published novel Approximate Bayesian Computation (ABC) computational tool for calculating kinetic constants in the Michaelis-Menten equation [28]. This extremely useful framework gives us the opportunity to find the turnover number ( k cat ), the Michaelis Menten constant ( K M ) and, as a consequence, the catalytic efficiency of the enzyme ( k cat / K M ) without using high concentrations of Ub-AMC ( Figures 2B and 2D).…”

Section: Figurementioning

confidence: 99%

Ebselen as a highly active inhibitor of PL^ProCoV2

Węglarz-Tomczak

Talma

et al. 2020

Preprint

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Since December 2019 a novel a coronavirus identified as SARS-CoV-2 or COV2 has been spreading around the world. On the 16th of May around 4.5 million people got infected and over 300,000 died due to the infection of COV2. The effective treatment remains a challenge. Targeted therapeutics are still under investigation. The papain-like protease (PL Pro ) from the human SARS-CoV-2 coronavirus is a cysteine protease that plays a critical role in virus replication. Its activity is required to process the viral polyprotein into functional, mature subunits. Moreover, COV2 uses this enzyme to modulate the host's immune system to its own benefit. Therefore, it represents a highly promising target for the development of antiviral drugs. In this work, we discovered that ebselen, a synthetic organoselenium drug molecule with anti-inflammatory, anti-oxidant and cytoprotective activity in mammalian cells and cytotoxicity in lower organisms, is a highly active inhibitor of PL Pro CoV2. We proved that ebselen is a covalent, fast-binding inhibitor of PL Pro CoV2 exhibiting a low micromolar potency. Furthermore, we identified a difference between PL Pro from SARS-CoV-1 (the corona virus which caused the 2002-2004 outbreak, SARS) and SARS-CoV-2 that allows to explain the difference in dynamics of the replication, and, thus, the disease progression. Namely, we present that they show differences in the binding affinity of substrates that we observed through kinetics and molecular docking studies. Using a novel Approximate Bayesian Computation method we were able to find kinetic constants for both enzymes. Molecular modeling study on the structure of the active site and binding mode of the ebselen with SARS and COV2 showed also significant differences that could explain our observation that ebselen is less active and slower bounding with SARS than COV2. In conclusion, we show that ebselen inhibits the activity of the essential viral enzyme papain-like protease (PLpro) from SARS-COV-2 in low micromolar range.

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“…The relation between substrate concentration and dose rate reduces to a linear system [ 95 ]. Kinetic constants in the Michelis-Menten metabolism from one enzymatic assay could be approximated using Bayesian computation [ 96 ]. Also pharmacokinetics of thymidine, thymine, and fluorouracil is nonlinear in dose [ 11 ].…”

Section: Discussionmentioning

confidence: 99%

Application of modified Michaelis – Menten equations for determination of enzyme inducing and inhibiting drugs

Saganuwan

2021

BMC Pharmacol Toxicol

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Background Pharmacokinetics (PK) is the process of absorption, distribution, metabolism and elimination (ADME) of drugs. Some drugs undergo zero-order kinetics (ethyl alcohol), first order kinetics (piroxicam) and mixed order kinetics (ascorbic acid). Drugs that undergo Michaelis-Menten metabolism are characterized by either increased or decreased metabolism constant (Km) and maximum velocity (Vmax) of enzyme reaction. Hence literatures were searched with a view to translating in vitro-in vivo enzyme kinetics to pharmacokinetic/pharmacodynamic parameters for determination of enzyme inducing and inhibiting drugs, in order to achieve optimal clinical efficacy and safety. Methods A narrative review of retrospective secondary data on drugs, their metabolites, Vmax and Km, generated in the laboratory and clinical environments was adopted, using inclusion and exclusion criteria. Key word search strategy was applied, to assess databases of published articles on enzyme inducing and inhibiting drugs, that obey Michaelis-Menten kinetics. In vitro and in vivo kinetic parameters, such as concentration of substrate, rate of endogenous substrate production, cellular metabolic rate, initial velocity of metabolism, intrinsic clearance, percent saturation and unsaturation of the enzyme substrate, were calculated using original and modified formulas. Years and numbers of searched publications, types of equations and their applications were recorded. Results A total of fifty-six formulas both established and modified were applied in the present study. Findings have shown that theophylline, voriconazole, phenytoin, thiopental, fluorouracil, thyamine and thymidine are enzyme inducers whereas, mibefradil, metronidazole, isoniazid and puromicin are enzyme inhibitors. They are metabolized and eliminated according to Michaelis-Menten principle. The order could be mixed but may change to zero or first order, depending on drug concentration, frequency and route of drug administration. Conclusion Hence, pharmacokinetic-pharmacodynamic translation can be optimally achieved by incorporating, newly modified Michaelis-Menten equations into pharmacokinetic formulas for clinical efficacy and safety of the enzyme inducing and inhibiting therapeutic agents used in laboratory and clinical settings.

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Estimating kinetic constants in the Michaelis–Menten model from one enzymatic assay using Approximate Bayesian Computation

Cited by 25 publications

References 29 publications

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Ebselen as a highly active inhibitor of PL^ProCoV2

Application of modified Michaelis – Menten equations for determination of enzyme inducing and inhibiting drugs

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Estimating kinetic constants in the Michaelis–Menten model from one enzymatic assay using Approximate Bayesian Computation

Cited by 25 publications

References 29 publications

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Identification of ebselen and its analogues as potent covalent inhibitors of papain-like protease from SARS-CoV-2

Ebselen as a highly active inhibitor of PLProCoV2

Application of modified Michaelis – Menten equations for determination of enzyme inducing and inhibiting drugs

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Product

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Ebselen as a highly active inhibitor of PL^ProCoV2