scholarly journals Boronic Acids as Prospective Inhibitors of Metallo-β-Lactamases: Efficient Chemical Reaction in the Enzymatic Active Site Revealed by Molecular Modeling

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 2026
Author(s):  
Alexandra V. Krivitskaya ◽  
Maria G. Khrenova
Keyword(s):  
Chemical Reaction ◽  
Active Site ◽  
Boronic Acid ◽  
Boronic Acids ◽  
Nucleophilic Attack ◽  
Carbonyl Carbon Atom ◽  
Antibacterial Drug ◽  
Acid Inhibitor ◽  
Fukui Indices ◽  
Ic50 Values

Boronic acids are prospective compounds in inhibition of metallo-β-lactamases as they form covalent adducts with the catalytic hydroxide anion in the enzymatic active site upon binding. We compare this chemical reaction in the active site of the New Delhi metallo-β-lactamase (NDM-1) with the hydrolysis of the antibacterial drug imipenem. The nucleophilic attack occurs with the energy barrier of 14 kcal/mol for imipenem and simultaneously upon binding a boronic acid inhibitor. A boron atom of an inhibitor exhibits stronger electrophilic properties than the carbonyl carbon atom of imipenem in a solution that is quantified by atomic Fukui indices. Upon forming the prereaction complex between NDM-1 and inhibitor, the lone electron pair of the nucleophile interacts with the vacant p-orbital of boron that facilitates the chemical reaction. We analyze a set of boronic acid compounds with the benzo[b]thiophene core complexed with the NDM-1 and propose quantitative structure-sroperty relationship (QSPR) equations that can predict IC50 values from the calculated descriptors of electron density. These relations are applied to classify other boronic acids with the same core found in the database of chemical compounds, PubChem, and proposed ourselves. We demonstrate that the IC50 values for all considered benzo[b]thiophene-containing boronic acid inhibitors are 30–70 μM.

scholarly journals Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

2021 ◽  
Author(s):  
Carlos A. Ramos-Guzmán ◽  
J. Javier Ruiz-Pernía ◽  
Iñaki Tuñón
Keyword(s):  
Proton Transfer ◽  
Active Site ◽  
Noncovalent Complex ◽  
Carbonyl Oxygen ◽  
Nucleophilic Attack ◽  
Hydroxyl Group ◽  
Inhibition Mechanism ◽  
Carbonyl Carbon Atom ◽  
Main Protease ◽  
3Cl Protease

<p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p>

scholarly journals Characterization of peptidyl boronic acid inhibitors of mammalian 20 S and 26 S proteasomes and their inhibition of proteasomes in cultured cells

2000 ◽  
Vol 346 (2) ◽  
pp. 447-454 ◽  
Author(s):  
Robert C. GARDNER ◽  
Stephen J. ASSINDER ◽  
Gary CHRISTIE ◽  
Grant G. F. MASON ◽  
Roger MARKWELL ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Boronic Acid ◽  
Cultured Cells ◽  
Gel Filtration ◽  
Boronic Acids ◽  
Cell Extracts ◽  
Catalytic Sites ◽  
Ic50 Values ◽  
In Cells

Proteasomes are large multisubunit proteinases which have several distinct catalytic sites. In this study a series of di- and tri-peptidyl boronic acids have been tested on the chymotrypsin-like activity of purified mammalian 20 S and 26 S proteasomes assayed with succinyl-Leu-Leu-Val-Tyr-amidomethylcoumarin (suc-Leu-Leu-Val-Tyr-AMC) as substrate. The inhibition of 20 S proteasomes is competitive but only slowly reversible. The Ki values for the best inhibitors were in the range 10-100 nM with suc-Leu-Leu-Val-Tyr-AMC as substrate, but the compounds tested were much less effective on other proteasome activities measured with other substrates. Free boronic acid inhibitors exhibited equivalent potency to their pinacol esters. Both benzoyl (Bz)-Phe-boroLeu and benzyloxycarbonyl (Cbz)-Leu-Leu-boroLeu pinacol ester inhibited 20 S and 26 S proteasomes with non-ideal behaviour, differences in inhibition of the two forms of proteasomes becoming apparent at high inhibitor concentrations (above 3×Ki). Both of these compounds were also potent inhibitors of 20 S and 26 S proteasomes in cultured cells. However, gel filtration of cell extracts prepared from cells treated with radiolabelled phenacetyl-Leu-Leu-boroLeu showed that only 20 S proteasomes were strongly labelled, demonstrating differences in the characteristics of inhibition of 20 S and 26 S proteasomes. The usefulness of peptidyl boronic acid inhibitors for investigations of proteasome-mediated protein degradation was confirmed by the observation that Bz-Phe-boroLeu and Cbz-Leu-Leu-boroLeu pinacol ester inhibited NFĸB activation with IC50 values comparable to their Ki values for purified proteasomes. The latter result supports the view that the chymotrypsin-like activity of proteasomes assayed with suc-Leu-Leu-Val-Tyr-AMC is a critical one for protein degradation in cells.

scholarly journals Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations

2021 ◽  
Author(s):  
Carlos A. Ramos-Guzmán ◽  
J. Javier Ruiz-Pernía ◽  
Iñaki Tuñón
Keyword(s):  
Proton Transfer ◽  
Active Site ◽  
Noncovalent Complex ◽  
Carbonyl Oxygen ◽  
Nucleophilic Attack ◽  
Hydroxyl Group ◽  
Inhibition Mechanism ◽  
Carbonyl Carbon Atom ◽  
Main Protease ◽  
3Cl Protease

<p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p>

The Effect of Active Site-inhibited Factor VIIa on Tissue Factor-initiated Coagulation Using Platelets before and after Aspirin Administration

1997 ◽  
Vol 78 (04) ◽  
pp. 1202-1208 ◽  
Author(s):  
Marianne Kjalke ◽  
Julie A Oliver ◽  
Dougald M Monroe ◽  
Maureane Hoffman ◽  
Mirella Ezban ◽  
...  
Keyword(s):  
Tissue Factor ◽  
Active Site ◽  
Large Scale ◽  
Thrombin Generation ◽  
Factor Viia ◽  
Dependent Manner ◽  
Antithrombotic Agent ◽  
Before And After ◽  
Ic50 Values

SummaryActive site-inactivated factor VIIa has potential as an antithrombotic agent. The effects of D-Phe-L-Phe-L-Arg-chloromethyl ketone-treated factor VIla (FFR-FVIIa) were evaluated in a cell-based system mimicking in vivo initiation of coagulation. FFR-FVIIa inhibited platelet activation (as measured by expression of P-selectin) and subsequent large-scale thrombin generation in a dose-dependent manner with IC50 values of 1.4 ± 0.8 nM (n = 8) and 0.9 ± 0.7 nM (n = 7), respectively. Kd for factor VIIa binding to monocytes ki for FFR-FVIIa competing with factor VIIa were similar (11.4 ± 0.8 pM and 10.6 ± 1.1 pM, respectively), showing that FFR-FVIIa binds to tissue factor in the tenase complex with the same affinity as factor VIIa. Using platelets from volunteers before and after ingestion of aspirin (1.3 g), there were no significant differences in the IC50 values of FFR-FVIIa [after aspirin ingestion, the IC50 values were 1.7 ± 0.9 nM (n = 8) for P-selectin expression, p = 0.37, and 1.4 ± 1.3 nM (n = 7) for thrombin generation, p = 0.38]. This shows that aspirin treatment of platelets does not influence the inhibition of tissue factor-initiated coagulation by FFR-FVIIa, probably because thrombin activation of platelets is not entirely dependent upon expression of thromboxane A2.

Theoretical Studies of the Acid-Base Equilibria in a Model Active Site of the Human 20S Proteasome

2020 ◽  
Author(s):  
Jon Uranga ◽  
Lukas Hasecke ◽  
Jonny Proppe ◽  
Jan Fingerhut ◽  
Ricardo A. Mata
Keyword(s):  
Active Site ◽  
Boronic Acid ◽  
Computational Study ◽  
Ubiquitin Proteasome System ◽  
Bayesian Optimization ◽  
Inhibition Mechanism ◽  
20S Proteasome ◽  
Acid Base ◽  
Ubiquitin Proteasome ◽  
Infection Cycles

The 20S Proteasome is a macromolecule responsible for the chemical step in the ubiquitin-proteasome system of degrading unnecessary and unused proteins of the cell. It plays a central role both in the rapid growth of cancer cells as well as in viral infection cycles. Herein, we present a computational study of the acid-base equilibria in an active site of the human proteasome, an aspect which is often neglected despite the crucial role protons play in the catalysis. As example substrates, we take the inhibition by epoxy and boronic acid containing warheads. We have combined cluster quantum mechanical calculations, replica exchange molecular dynamics and Bayesian optimization of non-bonded potential terms in the inhibitors. In relation to the latter, we propose an easily scalable approach to the reevaluation of non-bonded potentials making use of QM/MM dynamics information. Our results show that coupled acid-base equilibria need to be considered when modeling the inhibition mechanism. The coupling between a neighboring lysine and the reacting threonine is not affected by the presence of the inhibitor.

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

scholarly journals Inhibition of pancreatic lipase in vitro by the covalent inhibitor tetrahydrolipstatin

1988 ◽  
Vol 256 (2) ◽  
pp. 357-361 ◽  
Author(s):  
P Hadváry ◽  
H Lengsfeld ◽  
H Wolfer
Keyword(s):  
Transition State ◽  
Acid Derivative ◽  
Pancreatic Lipase ◽  
Active Site ◽  
Boronic Acid ◽  
Selective Inhibitor ◽  
Covalent Intermediate ◽  
State Form ◽  
Covalent Inhibitor

Tetrahydrolipstatin inhibits pancreatic lipase from several species, including man, with comparable potency. The lipase is progressively inactivated through the formation of a long-lived covalent intermediate, probably with a 1:1 stoichiometry. The lipase substrate triolein and also a boronic acid derivative, which is presumed to be a transition-state-form inhibitor, retard the rate of inactivation. Therefore, in all probability, tetrahydrolipstatin reacts with pancreatic lipase at, or near, the substrate binding or active site. Tetrahydrolipstatin is a selective inhibitor of lipase; other hydrolases tested were at least a thousand times less potently inhibited.

scholarly journals A Theoretical Model to Study the Interaction Between Boronic Acids and Insulin

2020 ◽  
Author(s):  
Durgesh Kumar ◽  
Kamlesh Kumari ◽  
PRASHANT SINGH
Keyword(s):  
Amino Acids ◽  
Theoretical Model ◽  
Boronic Acid ◽  
Significant Interaction ◽  
Biological Activities ◽  
Boronic Acids ◽  
Biological Molecules ◽  
Computational Tools ◽  
Medical Expertise ◽  
Stabilizing Agents

Boronic acids are widely used in various applications in view of their ability to recognize and bind at specific sites of the biological molecules to mimic several processes. Therefore, this has attracted the researchers, academician and medical expertise to explore them. In the present work, the authors have designed a theoretical approach to study the interaction of boronic acid with insulin using computational tools. A library of boronic acids (114 compounds) are designed, optimized and interacted with insulin using computational tools i.e. iGEMDOCK. Further, their different biological activities and toxicity are determined. Results indicates the promising potential of the boronic acids on interaction with the insulin. Amongst, 114 molecules of boronic acids, 3-Benzyloxyphenylboronic acid (71) showed the best interaction with amino-acids of insulin and significant interaction was shown with the Glu21 and His5 residues. Further, these results were compared with the stabilizing agents and found to be more potent.

scholarly journals Modeling and synthesis of antiplasmodial chromones, chromanones and chalcones based on natural products of Kenya

2018 ◽  
Vol 16 (1) ◽  
pp. 8-21
Author(s):  
MANYIM SCOLASTICA ◽  
ALBERT J. NDAKALA ◽  
SOLOMON DERESE
Keyword(s):  
Natural Products ◽  
Drug Design ◽  
Active Site ◽  
Docking Studies ◽  
Moderate Activity ◽  
Vigorous Activity ◽  
Structure Based Drug Design ◽  
Web Based ◽  
Ic50 Values ◽  
Accessible Form

Scolastica M, Ndakala AJ, Derese S. 2018. Modeling and synthesis of antiplasmodial chromones, chromanones and chalcones based on natural products of Kenya. Biofarmasi J Nat Prod Biochem 16: 8-21. Despite numerous research that has been done on plants of Kenya resulting in the isolation of thousands of natural products, data on these natural products are not systematically organized in a readily accessible form. This has urged the construction of a web-based database of natural products of Kenya. The database is named Mitishamba and is hosted at http://mitishamba.uonbi.ac.ke. The Mitishamba database was queried for chromones, chromanones, and chalcones that were subjected to structure-based drug design using Fred (OpenEye) docking utility program with 1TV5 PDB structure of the PfDHODH receptor to identify complex of ligands that bind with the active site. Ligand-based drug design (Shape and electrostatics comparison) was also done on the ligands against query A77 1726 (38) (the ligand that co-crystallized with PfDHODH receptor) using ROCS and EON programs, respectively, of OpenEye suite. There was a substantial similarity among the top performing ligands in the docking studies with shape and electrostatic comparison that led to the identification of compounds of interest which were targeted for synthesis and antiplasmodial assay. In this study, a chromanone (7-hydroxy-2-(4-methoxyphenyl) chroman-4-one (48)) and two intermediate chalcones (2',4'-dihydroxy-4-methoxychalcone (45) and 2’,4’-dihydroxy-4-chlorochalcone (47)), were synthesized and subjected to antiplasmodial assay. Among these substances, 45 showed vigorous activity, whereas 47 and 48 had moderate activity against the chloroquine resistant K1 strain of P. falciparum with IC50 values of 4.56±1.66, 17.62 ± 5.94 and 18.01 ±1.66 µg/ml, respectively. Since the synthesized compounds showed antiplasmodial potential, there is a need for further computational refinement of these compounds to optimize their antiplasmodial activity.

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