scholarly journals Modeling covalent-modifier drugs

2017 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
Andrew G Walsh ◽  
Christopher N Rowley
Keyword(s):  
Computer Modeling ◽  
Covalent Binding ◽  
Covalent Bond ◽  
Bioinformatic Analysis ◽  
Covalent Modification ◽  
Binding Affinities ◽  
Chemical Bonds ◽  
Irreversible Inhibition ◽  
Large Sets ◽  
Covalent Inhibitor

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein--ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent modifier drugs.

scholarly journals Modeling covalent-modifier drugs

2017 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
Andrew G Walsh ◽  
Christopher N Rowley
Keyword(s):  
Computer Modeling ◽  
Covalent Binding ◽  
Covalent Bond ◽  
Bioinformatic Analysis ◽  
Covalent Modification ◽  
Binding Affinities ◽  
Chemical Bonds ◽  
Irreversible Inhibition ◽  
Large Sets ◽  
Covalent Inhibitor

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein--ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent modifier drugs.

scholarly journals Modeling covalent-modifier drugs

2017 ◽  
Author(s):  
Ernest Awoonor-Williams ◽  
Andrew G Walsh ◽  
Christopher N Rowley
Keyword(s):  
Computer Modeling ◽  
Covalent Binding ◽  
Covalent Bond ◽  
Bioinformatic Analysis ◽  
Covalent Modification ◽  
Binding Affinities ◽  
Chemical Bonds ◽  
Irreversible Inhibition ◽  
Large Sets ◽  
Covalent Inhibitor

In this review, we present a summary of how computer modeling has been used in the development of covalent modifier drugs. Covalent modifier drugs bind by forming a chemical bond with their target. This covalent binding can improve the selectivity of the drug for a target with complementary reactivity and result in increased binding affinities due to the strength of the covalent bond formed. In some cases, this results in irreversible inhibition of the target, but some targeted covalent inhibitor (TCI) drugs bind covalently but reversibly. Computer modeling is widely used in drug discovery, but different computational methods must be used to model covalent modifiers because of the chemical bonds formed. Structural and bioinformatic analysis has identified sites of modification that could yield selectivity for a chosen target. Docking methods, which are used to rank binding poses of large sets of inhibitors, have been augmented to support the formation of protein--ligand bonds and are now capable of predicting the binding pose of covalent modifiers accurately. The pKa's of amino acids can be calculated in order to assess their reactivity towards electrophiles. QM/MM methods have been used to model the reaction mechanisms of covalent modification. The continued development of these tools will allow computation to aid in the development of new covalent modifier drugs.

scholarly journals Mechanism of Covalent Binding of Ibrutinib to Bruton’s Tyrosine Kinase revealed by QM/MM Calculations

2020 ◽  
Author(s):  
Angus Voice ◽  
Gary Tresadern ◽  
Rebecca Twidale ◽  
Herman Van Vlijmen ◽  
Adrian Mulholland
Keyword(s):  
Tyrosine Kinase ◽  
Covalent Binding ◽  
Bond Formation ◽  
Covalent Bond ◽  
Covalent Modification ◽  
Mechanistic Study ◽  
Bruton’S Tyrosine Kinase ◽  
Bruton's Tyrosine Kinase ◽  
Covalent Inhibitors ◽  
Covalent Bond Formation

<p>Ibrutinib is the first covalent inhibitor of Bruton’s tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition is crucial for the design of safer and more selective covalent inhibitors that target BTK. There are questions surrounding the precise mechanism of covalent bond formation in BTK as there is no appropriate active site residue that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. To address this, we have investigated several mechanistic pathways of covalent modification of C481 in BTK by ibrutinib using QM/MM reaction simulations. The lowest energy pathway we identified involves a direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (DG<sup>‡</sup>=10.5 kcal mol<sup>-1</sup>) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and related proteins. </p>

scholarly journals Mechanism of Covalent Binding of Ibrutinib to Bruton’s Tyrosine Kinase revealed by QM/MM Calculations

2020 ◽  
Author(s):  
Angus Voice ◽  
Gary Tresadern ◽  
Rebecca Twidale ◽  
Herman Van Vlijmen ◽  
Adrian Mulholland
Keyword(s):  
Tyrosine Kinase ◽  
Covalent Binding ◽  
Bond Formation ◽  
Covalent Bond ◽  
Covalent Modification ◽  
Mechanistic Study ◽  
Bruton’S Tyrosine Kinase ◽  
Bruton's Tyrosine Kinase ◽  
Covalent Inhibitors ◽  
Covalent Bond Formation

<p>Ibrutinib is the first covalent inhibitor of Bruton’s tyrosine kinase (BTK) to be used in the treatment of B-cell cancers. Understanding the mechanism of covalent inhibition is crucial for the design of safer and more selective covalent inhibitors that target BTK. There are questions surrounding the precise mechanism of covalent bond formation in BTK as there is no appropriate active site residue that can act as a base to deprotonate the cysteine thiol prior to covalent bond formation. To address this, we have investigated several mechanistic pathways of covalent modification of C481 in BTK by ibrutinib using QM/MM reaction simulations. The lowest energy pathway we identified involves a direct proton transfer from C481 to the acrylamide warhead in ibrutinib, followed by covalent bond formation to form an enol intermediate. There is a subsequent rate-limiting keto-enol tautomerisation step (DG<sup>‡</sup>=10.5 kcal mol<sup>-1</sup>) to reach the inactivated BTK/ibrutinib complex. Our results represent the first mechanistic study of BTK inactivation by ibrutinib to consider multiple mechanistic pathways. These findings should aid in the design of covalent drugs that target BTK and related proteins. </p>

scholarly journals A phage display approach to identify highly selective covalent binders

2019 ◽  
Author(s):  
Shiyu Chen ◽  
Matthew Bogyo
Keyword(s):  
Phage Display ◽  
Cyclic Peptides ◽  
Covalent Binding ◽  
Screening Method ◽  
Covalent Bond ◽  
Covalent Modification ◽  
Linear Peptide ◽  
Binding Inhibition ◽  
Covalent Bond Formation ◽  
Activity Of Enzymes

AbstractMolecules that bind macromolecular targets through direct covalent modification have found widespread applications as activity-based probes (ABPs) and as irreversible drugs. Covalent binders can be used to dynamically monitor the activity of enzymes in complex cellular environments, identify targets and induce permanent binding/inhibition of therapeutically important biomolecules. However, the general reactivity of the electrophiles needed for covalent bond formation makes control of selectivity difficult. There is currently no rapid, robust and unbiased screening method to identify new classes of covalent binding ligands from highly diverse pools of candidate molecules. Here we describe the development of a phage display method to screen for highly selective covalent binding ligands. This approach makes use of a reactive linker to form cyclic peptides on the phage surface while simultaneously introducing an electrophilic ‘warhead’ to covalently react with a nucleophile on the target. Using this approach, we identified cyclic peptides that selectively and irreversibly inhibited a cysteine protease with nanomolar potency, exceptional specificity and increased serum stability compared to a linear peptide containing the same electrophile. This approach should enable rapid, unbiased screening to identify new classes of highly selective covalent binding ligands for diverse molecular targets.

Irreversible inhibition of BoNT/A protease: proximity-driven reactivity contingent upon a bifunctional approach

2021 ◽  
Author(s):  
Lewis D. Turner ◽  
Alexander L. Nielsen ◽  
Lucy Lin ◽  
Sabine Pellett ◽  
Takashi Sugane ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Covalent Modification ◽  
Irreversible Inhibition ◽  
Metal Chelating

A proximity-driven covalent bond with intrinsically less reactive warheads has been made possible by using a metal-chelating anchor for directed targeted covalent modification of Cys165 within the BoNT/A protease.

scholarly journals Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Haixia Su ◽  
Sheng Yao ◽  
Wenfeng Zhao ◽  
Yumin Zhang ◽  
Jia Liu ◽  
...  
Keyword(s):  
Theoretical Calculations ◽  
Cysteine Proteinase ◽  
Covalent Binding ◽  
Food Sources ◽  
Binding Mechanism ◽  
Covalent Inhibitors ◽  
Catalytic Cysteine ◽  
3Cl Protease ◽  
Covalent Ligands ◽  
Covalent Inhibitor

AbstractThe ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CLpro) is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CLpro. Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CLpros, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.

scholarly journals Irreversible Inhibition of BoNT/A Protease: Unique Warhead Reactivity and Function Contingent upon a Bifunctional Approach

2021 ◽  
Author(s):  
Lewis Turner ◽  
Alexander Lund Nielsen ◽  
Lucy Lin ◽  
Sabine Pellett ◽  
Takashi Sugane ◽  
...  
Keyword(s):  
Enzyme Kinetics ◽  
Therapeutic Potential ◽  
Covalent Bond ◽  
Pharmacological Properties ◽  
Irreversible Inhibition ◽  
And Function ◽  
Chelating Compounds

We describe a comprehensive screening campaign of warheads, linked to a hydroxamate chelating anchor, for the modification of Cys165 within the BoNT/A protease. <div>Engaging thorough enzyme kinetics, we detail a remarkable proximity-driven covalent bond with an epoxide warhead, a weak electrophile; yet, one that possessed superior irreversible inhibition, and pharmacological properties, when compared to intrinsically higher reactive warheads. This directed, selective covalent bond was contingent upon the crucial hydroxamate-Zn<sup>2+ </sup>chelating interaction as exemplified by examining non-chelating compounds. </div><div>We discuss previous approaches using non-target selective cysteine-reactive warheads to modify the BoNT/A protease of which none present any therapeutic potential – our bifunctional strategy allows the use of intrinsically less reactive warheads to intercept the cysteine, which will allow for less off-target modifications of such inhibitors. Moreover, we also broach that this bifunctional approach is not a one-off strategy that we believe can be broadly translated to other metalloproteases that possess non-catalytic, yet, nucleophilic residues within the enzymes catalytic sphere. </div>

scholarly journals Effect of Doping on the Photoelectric Properties of Borophene

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Chunhong Zhang ◽  
Zhongzheng Zhang ◽  
Wanjun Yan ◽  
Xinmao Qin
Keyword(s):  
Optical Properties ◽  
Band Gap ◽  
Population Analysis ◽  
Covalent Bond ◽  
Infrared Light ◽  
Chemical Bonds ◽  
Mulliken Population Analysis ◽  
Mulliken Population ◽  
Photoelectric Properties ◽  
Effect Of Doping

Borophene is a new type of two-dimensional material with a series of unique and diversified properties. However, most of the research is still in its infancy and has not been studied in depth. Especially in the field of semiconductor optoelectronics, there is no related research on the modulation of photoelectric properties of borophene. In this work, we focus on the effect of doping on the photoelectric properties of borophene by using the first-principles pseudopotential plane wave method. We calculate the geometric structure, electronic structure, Mulliken population analysis, and optical properties of impurity (X = Al, Ga) doped α-sheet borophene. The results show that α-sheet borophene is an indirect band gap semiconductor with 1.396 eV. The band gap becomes wider after Al and Ga doping, and the band gap values are 1.437 eV and 1.422 eV, respectively. Due to the orbital hybridization between a small number of Al-3p electrons and Ga-4p state electrons and a large number of B 2p state electrons near the Fermi level, the band gap of borophene changes and the peak value of the electron density of states reduces after doping. Mulliken population analysis shows that the B0-B bond is mainly covalent bond, but there is also a small amount of ionic bond. However, when the impurity X is doped, the charge transfer between X and B atoms increases significantly, and the population of the corresponding X-B bonds decreases, indicating that the covalent bond strength of the chemical bonds in the doped system is weakened, and the chemical bonds have significant directionality. The calculation of optical properties shows that the static dielectric constant of the borophene material increases, and the appearance of a new dielectric peak indicates that the doping of Al and Ga can enhance the ability of borophene to store electromagnetic energy. After doping, the peak reflectivity decreases and the static refractive index n0 increases, which also fills the gap in the absorption of red light and infrared light by borophene materials. The research results provide a basis for the development of borophene materials in the field of infrared detection devices. The above results indicate that doping can modulate the photoelectric properties of α-sheet borophene.

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