ArticleBiochemistry2009
Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 65 citations in OpenAlex.
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- Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method.Molecules (Basel, Switzerland) · 2021Article
- Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies.International journal of molecular sciences · 2021Review
- Exploitation of Conformational Dynamics in Imparting Selective Inhibition for Related Matrix Metalloproteinases.ACS medicinal chemistry letters · 2017Article
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- Metastasis review: from bench to bedside.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Review
- Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.Biochemistry · 2012Article
- Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.The Journal of chemical physics · 2012Article
- Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.Journal of chemical theory and computation · 2012Article
- Matrix metalloproteinases in tumorigenesis: an evolving paradigm.Cellular and molecular life sciences : CMLS · 2011Review
- Sulfonate-containing thiiranes as selective gelatinase inhibitors.ACS medicinal chemistry letters · 2011Article
- QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue.Journal of chemical theory and computation · 2010Article
- Matrix metalloproteinase 2 (MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT.The journal of physical chemistry. B · 2010Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The inhibition mechanism of matrix metalloproteinase 2 (MMP2) by the selective inhibitor (4-phenoxyphenylsulfonyl)methylthiirane (SB-3CT) and its oxirane analogue is investigated computationally. The inhibition mechanism involves C-H deprotonation with concomitant opening of the three-membered heterocycle. SB-3CT was docked into the active site of MMP2, followed by molecular dynamics simulation to prepare the complex for combined quantum mechanics and molecular mechanics (QM/MM) calculations. QM/MM calculations with B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine the reaction of these two inhibitors in the active site of MMP2. The calculations show that the reaction barrier for transformation of SB-3CT is 1.6 kcal/mol lower than its oxirane analogue, and the ring-opening reaction energy of SB-3CT is 8.0 kcal/mol more exothermic than that of its oxirane analogue. Calculations also show that protonation of the ring-opened product by water is thermodynamically much more favorable for the alkoxide obtained from the oxirane than for the thiolate obtained from the thiirane. A six-step partial charge fitting procedure is introduced for the QM/MM calculations to update atomic partial charges of the quantum mechanics region and to ensure consistent electrostatic energies for reactants, transition states, and products.
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