scholarly journals Deciding Between One-Step and Two-Step Irreversible Inhibition Mechanisms on the Basis of “Kobs” Data: A Statistical Approach

2020 ◽  
Author(s):  
Petr Kuzmic
Keyword(s):  
Drug Discovery ◽  
Statistical Approach ◽  
Enzyme Inhibitors ◽  
Chemical Reactivity ◽  
Kinetic Mechanism ◽  
Irreversible Inhibitor ◽  
Experimental Drugs ◽  
Covalent Inhibitors ◽  
Kinetic Mechanisms ◽  
One Step

Covalent (irreversible) enzyme inhibitors are an important group of actual or potential therapeutics. For example, Aspirin is an irreversible inhibitor of the cyclooxygenase enzyme. Evaluating covalent inhibitors in the drug discovery is exceptionally challenging, because their overall inhibitory potency consists of two separate but intertwined contributions: (1) initial binding affinity and (2) chemical reactivity. It is especially difficult to reliably asses the kinetic mechanism of inhibition. This paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition, from kinetic experiments based on the standard "kobs" method [Copeland (2013) "Evaluation of Enzyme Inhibitors in Drug Discovery", section 9.1]. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. The proposed statistical toolkit uses four independent methods to arrive at a reliable mechanistic conclusion. The results are illustrated by using recently published experimental data on the inhibition of two different protein kinases by the experimental drugs ibrutinib (PCI-32765) and acalabrutinib [Hopper <i>et al.</i> (2020) <i>J. Pharm. Exp. Therap.</i> <b>372</b>, 331–338].

scholarly journals Deciding Between One-Step and Two-Step Irreversible Inhibition Mechanisms on the Basis of “Kobs” Data: A Statistical Approach

2020 ◽  
Author(s):  
Petr Kuzmic
Keyword(s):  
Drug Discovery ◽  
Statistical Approach ◽  
Enzyme Inhibitors ◽  
Chemical Reactivity ◽  
Kinetic Mechanism ◽  
Irreversible Inhibitor ◽  
Experimental Drugs ◽  
Covalent Inhibitors ◽  
Kinetic Mechanisms ◽  
One Step

Covalent (irreversible) enzyme inhibitors are an important group of actual or potential therapeutics. For example, Aspirin is an irreversible inhibitor of the cyclooxygenase enzyme. Evaluating covalent inhibitors in the drug discovery is exceptionally challenging, because their overall inhibitory potency consists of two separate but intertwined contributions: (1) initial binding affinity and (2) chemical reactivity. It is especially difficult to reliably asses the kinetic mechanism of inhibition. This paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition, from kinetic experiments based on the standard "kobs" method [Copeland (2013) "Evaluation of Enzyme Inhibitors in Drug Discovery", section 9.1]. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. The proposed statistical toolkit uses four independent methods to arrive at a reliable mechanistic conclusion. The results are illustrated by using recently published experimental data on the inhibition of two different protein kinases by the experimental drugs ibrutinib (PCI-32765) and acalabrutinib [Hopper <i>et al.</i> (2020) <i>J. Pharm. Exp. Therap.</i> <b>372</b>, 331–338].

scholarly journals Deciding Between One-Step and Two-Step Irreversible Inhibition Mechanisms on the Basis of “Kobs” Data: A Statistical Approach

2020 ◽  
Author(s):  
Petr Kuzmic
Keyword(s):  
Drug Discovery ◽  
Statistical Approach ◽  
Enzyme Inhibitors ◽  
Chemical Reactivity ◽  
Kinetic Mechanism ◽  
Irreversible Inhibitor ◽  
Experimental Drugs ◽  
Covalent Inhibitors ◽  
Kinetic Mechanisms ◽  
One Step

Covalent (irreversible) enzyme inhibitors are an important group of actual or potential therapeutics. For example, Aspirin is an irreversible inhibitor of the cyclooxygenase enzyme. Evaluating covalent inhibitors in the drug discovery is exceptionally challenging, because their overall inhibitory potency consists of two separate but intertwined contributions: (1) initial binding affinity and (2) chemical reactivity. It is especially difficult to reliably asses the kinetic mechanism of inhibition. This paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition, from kinetic experiments based on the standard "kobs" method [Copeland (2013) "Evaluation of Enzyme Inhibitors in Drug Discovery", section 9.1]. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. The proposed statistical toolkit uses four independent methods to arrive at a reliable mechanistic conclusion. The results are illustrated by using recently published experimental data on the inhibition of two different protein kinases by the experimental drugs ibrutinib (PCI-32765) and acalabrutinib [Hopper <i>et al.</i> (2020) <i>J. Pharm. Exp. Therap.</i> <b>372</b>, 331–338].

scholarly journals Deciding between one-step and two-step irreversible inhibition mechanisms on the basis of “kobs” data: A statistical approach

2020 ◽  
Author(s):  
Petr Kuzmič
Keyword(s):  
Tyrosine Kinase ◽  
Statistical Approach ◽  
Enzyme Inhibitor ◽  
Kinetic Mechanism ◽  
Irreversible Inhibition ◽  
Inactivation Rate Constant ◽  
Mechanism Of Inhibition ◽  
Bruton Tyrosine Kinase ◽  
Kinetic Mechanisms ◽  
One Step

AbstractThis paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition from kinetic experiments based on the standard “kobs” method. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. Recently published experimental data [Hopper et al. (2020) J. Pharm. Exp. Therap.372, 331–338] on the irreversible inhibition of Bruton tyrosine kinase (BTK) and tyrosine kinase expressed in hepatocellular carcinoma (TEC) by ibrutinib (PCI-32765) and acalabrutinib are used as an illustrative example. The results show that the kinetic mechanism of inhibition was misdiagnosed in the original publication for at least one of the four enzyme/inhibitor combinations. In particular, based on the available kobs data, ibrutinib behaves effectively as a one-step inhibitor of the TEC enzyme, which means that it is not possible to reliably determine either the inhibition constant Ki or the inactivation rate constant kinact, but only the covalent efficiency constant keff = kinact/Ki. Thus, the published values of Ki and kinact for this system are not statistically valid.

scholarly journals A two-point IC50 method for evaluating the biochemical potency of irreversible enzyme inhibitors

2020 ◽  
Author(s):  
Petr Kuzmič
Keyword(s):  
Binding Affinity ◽  
Enzyme Inhibitors ◽  
Chemical Reactivity ◽  
Single Point ◽  
Reaction Times ◽  
Kinetic Mechanism ◽  
Enzyme Concentration ◽  
Inactivation Rate Constant ◽  
Covalent Inhibitors ◽  
Simplifying Assumptions

AbstractIrreversible (covalent) enzyme inhibitors cannot be unambiguously ranked for biochemical potency by using IC50 values determined at a single point in time, because the same IC50 value could originate either from relatively low initial binding affinity accompanied by high chemical reactivity, or the other way around. To disambiguate the potency ranking of covalent inhibitors, here we describe a data-analytic procedure relying on two separate IC50 values, determined at two different reaction times. In the case of covalent inhibitors following the two-step kinetic mechanism E + I ⇌ E I → EI, the two IC50 values alone can be used to estimate both the inhibition constant (Ki) as a measure of binding affinity and the inactivation rate constant (kinact) as a measure of chemical reactivity. In the case of covalent inhibitors following the one-step kinetic mechanism E + I → EI, a simple algebraic formula can be used to estimate the covalent efficiency constant (kinact/Ki) from a single experimental value of IC50. The two simplifying assumptions underlying the method are (1) zero inhibitor depletion, which implies that the inhibitor concentrations are always significantly higher than the enzyme concentration; and (2) constant reaction rate in the uninhibited control assay. The newly proposed method is validated by using a simulation study involving 64 irreversible inhibitors with covalent efficiency constants spanning seven orders of magnitude.

Structure Revision of Protoaculeine B, a Posttranslationally Modified N-Terminal Residue in the Peptide Toxin Aculeine B

2020 ◽  
Author(s):  
Raku Irie ◽  
Kei Miyako ◽  
Satoko Matsunaga ◽  
Ryuichi Sakai ◽  
Masato Oikawa
Keyword(s):  
Mass Spectra ◽  
Chemical Reactivity ◽  
Model Compounds ◽  
Structural Revision ◽  
Structure Revision ◽  
Peptide Toxin ◽  
One Step ◽  
Marine Peptide ◽  
Synthetic Models ◽  
Long Chain

<div>Here, we newly propose the structure of protoaculeine B, an N-terminal moiety of the marine peptide toxin aculeine B, as possessing the cis-disubstituted tetrahydro-beta-carboline framework. We prepared two truncated model compounds that lack long-chain polyamine by one-step Pictet-Spengler reaction of tryptophan, and compared the NMR and mass spectra and chemical reactivity with those of natural protoaculeine B. The synthetic models reproduced the profiles of the natural product well, which was conclusive for the structural revision.</div>

Triazol: a privileged scaffold for proteolysis targeting chimeras

2019 ◽  
Vol 11 (22) ◽  
pp. 2919-2973 ◽  
Author(s):  
Li-Wen Xia ◽  
Meng-Yu Ba ◽  
Wei Liu ◽  
Weyland Cheng ◽  
Chao-Ping Hu ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Anticancer Activity ◽  
Mode Of Action ◽  
Critical Analysis ◽  
Enzyme Inhibitors ◽  
Structure Activity Relationship ◽  
Target Protein ◽  
Activity Relationship ◽  
Structure Activity ◽  
Privileged Scaffold

Current traditional drugs such as enzyme inhibitors and receptor agonists/antagonists present inherent limitations due to occupancy-driven pharmacology as the mode of action. Proteolysis targeting chimeras (PROTACs) are composed of an E3 ligand, a connecting linker and a target protein ligand, and are an attractive approach to specifically knockdown-targeted proteins utilizing an event-driven mode of action. The length, hydrophilicity and rigidity of connecting linkers play important role in creating a successful PROTAC. Some PROTACs with a triazole linker have displayed promising anticancer activity. This review provides an overview of PROTACs with a triazole scaffold and discusses its structure–activity relationship. Important milestones in the development of PROTACs are addressed and a critical analysis of this drug discovery strategy is also presented.

ChemInform Abstract: Drug Discovery Considerations in the Development of Covalent Inhibitors

ChemInform ◽  
2014 ◽  
Vol 45 (10) ◽  
pp. no-no
Author(s):  
Robert Mah ◽  
Jason R. Thomas ◽  
Cynthia M. Shafer
Keyword(s):  
Drug Discovery ◽  
Covalent Inhibitors

scholarly journals Estimating kinetic mechanisms with prior knowledge II: Behavioral constraints and numerical tests

2018 ◽  
Vol 150 (2) ◽  
pp. 339-354 ◽  
Author(s):  
Marco A. Navarro ◽  
Autoosa Salari ◽  
Mirela Milescu ◽  
Lorin S. Milescu
Keyword(s):  
Prior Knowledge ◽  
Estimation Procedure ◽  
Kinetic Mechanism ◽  
Arbitrary Parameter ◽  
Linear Parameter ◽  
Open Probability ◽  
Behavioral Constraints ◽  
Kinetic Mechanisms ◽  
Mathematical Relationships ◽  
Optimization Mechanism

Kinetic mechanisms predict how ion channels and other proteins function at the molecular and cellular levels. Ideally, a kinetic model should explain new data but also be consistent with existing knowledge. In this two-part study, we present a mathematical and computational formalism that can be used to enforce prior knowledge into kinetic models using constraints. Here, we focus on constraints that quantify the behavior of the model under certain conditions, and on constraints that enforce arbitrary parameter relationships. The penalty-based optimization mechanism described here can be used to enforce virtually any model property or behavior, including those that cannot be easily expressed through mathematical relationships. Examples include maximum open probability, use-dependent availability, and nonlinear parameter relationships. We use a simple kinetic mechanism to test multiple sets of constraints that implement linear parameter relationships and arbitrary model properties and behaviors, and we provide numerical examples. This work complements and extends the companion article, where we show how to enforce explicit linear parameter relationships. By incorporating more knowledge into the parameter estimation procedure, it is possible to obtain more realistic and robust models with greater predictive power.

Targeting histidine for developing a new generation of covalent enzyme inhibitors

2021 ◽  
Vol 17 ◽  
Author(s):  
Donald Poirier
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Drug Development ◽  
Chemical Bond ◽  
Amino Acid Residue ◽  
Enzyme Inhibitors ◽  
Irreversible Inhibitors ◽  
Covalent Inhibitors ◽  
Targeted Inhibitors ◽  
New Generation

: Despite the significant number of irreversible inhibitors developed over the years, strong prejudices remain for this type of therapeutic molecule, particularly in the area of drug development. New generations of covalent targeted inhibitors are, however, in development, and interest is increasingly growing. In fact, the new generation of covalent inhibitors has a weakly reactive species (warhead) that is able, in a particular context, to selectively form a chemical bond with a given amino acid residue, which can be irreversible or reversible. In addition to new selective warheads, new amino acids are also targeted. In the following text, we will focus on covalent targeted inhibitors that selectively alkylate histidine.

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