CPMD Simulation of a Bimolecular Chemical Reaction: Nucleophilic Attack of a Disulfide Bond under Mechanical Stress

2012 ◽  
Vol 18 (51) ◽  
pp. 16332-16338 ◽  
Author(s):  
Florian Hofbauer ◽  
Irmgard Frank
Keyword(s):  
Mechanical Stress ◽  
Chemical Reaction ◽  
Disulfide Bond ◽  
Nucleophilic Attack ◽  
Bimolecular Chemical Reaction

Force-activated reactivity switch in a bimolecular chemical reaction

2009 ◽  
Vol 1 (3) ◽  
pp. 236-242 ◽  
Author(s):  
Sergi Garcia-Manyes ◽  
Jian Liang ◽  
Robert Szoszkiewicz ◽  
Tzu-Ling Kuo ◽  
Julio M. Fernández
Keyword(s):  
Chemical Reaction ◽  
Bimolecular Chemical Reaction

Relaxation of stored mechanical stress along chemical reaction pathways

Nature ◽  
1984 ◽  
Vol 312 (5996) ◽  
pp. 746-748 ◽  
Author(s):  
A. Silberberg ◽  
M. Hennenberg
Keyword(s):  
Mechanical Stress ◽  
Chemical Reaction ◽  
Reaction Pathways

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.

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