scholarly journals Application of the quantum theory of atoms in molecules (QTAIM) to the study of the enzymatic kinetic resolution of propranolol, an amino alcohol with pharmaceutical applications

2020 ◽  
Author(s):  
D.A. Rincón ◽  
M.C. Daza ◽  
M. Doerr
Keyword(s):  
Quantum Theory ◽  
Hydrogen Bonds ◽  
Active Site ◽  
Kinetic Resolution ◽  
Catalytic Triad ◽  
Enantiomeric Purity ◽  
Atoms In Molecules ◽  
Racemic Mixture ◽  
Oxyanion Hole ◽  
Adrenergic Antagonist

Propranolol, ((R,S)-1-iso-propylamino-3-(1-naphthoxy)-2-propanol), is a β-adrenergic antagonist and is commercially available as a racemic mixture. Only the S-enantiomer has the desired therapeutic effect. Therefore, many researchers have been working on strategies to obtain S-propranolol with high enantiomeric purity. One approach to carry out the acetylation of (R,S)-Propranolol using Candida antarctica lipase B, CalB. This reaction leads to an enantiomeric purity of 96% at a relatively low conversion rate of 30 %. In our research group, we have been studying this reaction. The CalB active site is composed by the triad catalytic (ASP 187, HIS 224 and SER 105) and oxyanion hole (GLN 106 and THR 40). In a previous work, a QM/MM (Quantum Mechanics / Molecular Mechanics) study was carried out, using a QM region consisting only of the catalytic triad of CalB and (R,S)-propranolol [1]. In the present study, we investigate the effect of expanding the quantum region to include the oxyanion hole and to comprehend the effect of intermolecular hydrogen bonds present between the (R,S)-propranolol and the CalB active site. The electronic structure was analyzed using the Quantum Theory of Atoms In Molecules, QTAIM. Our results show that: 1. the studied reactions are more exothermic with the inclusion of the oxyanion hole than with only the catalytic triad. 2. the intermolecular interactions between (R,S)-propranolol and the CalB active site are dominated by hydrogen bonds (HB). Among those HBs, only one between propranolol and HIS 224, and another one between THR 40 and the carbonyl oxygen of acetylated SER 105 play an important role.

scholarly journals Analysis of the Strength of Interfacial Hydrogen Bonds between Tubulin Dimers Using Quantum Theory of Atoms in Molecules

2014 ◽  
Vol 107 (3) ◽  
pp. 740-750 ◽  
Author(s):  
Ahmed T. Ayoub ◽  
Travis J.A. Craddock ◽  
Mariusz Klobukowski ◽  
Jack Tuszynski
Keyword(s):  
Quantum Theory ◽  
Hydrogen Bonds ◽  
Atoms In Molecules

scholarly journals A multifunctional surfactant catalyst inspired by hydrolases

2020 ◽  
Vol 6 (14) ◽  
pp. eaaz0404 ◽  
Author(s):  
Mitchell D. Nothling ◽  
Zeyun Xiao ◽  
Nicholas S. Hill ◽  
Mitchell T. Blyth ◽  
Ayana Bhaskaran ◽  
...  
Keyword(s):  
Active Site ◽  
Self Assembly ◽  
Md Simulation ◽  
Hydrolytic Enzymes ◽  
Surfactant Molecule ◽  
Catalytic Triad ◽  
Oxyanion Hole ◽  
Enzyme Active Site ◽  
Close Proximity ◽  
Hydrolysis Of

The remarkable power of enzymes to undertake catalysis frequently stems from their grouping of multiple, complementary chemical units within close proximity around the enzyme active site. Motivated by this, we report here a bioinspired surfactant catalyst that incorporates a variety of chemical functionalities common to hydrolytic enzymes. The textbook hydrolase active site, the catalytic triad, is modeled by positioning the three groups of the triad (-OH, -imidazole, and -CO2H) on a single, trifunctional surfactant molecule. To support this, we recreate the hydrogen bond donating arrangement of the oxyanion hole by imparting surfactant functionality to a guanidinium headgroup. Self-assembly of these amphiphiles in solution drives the collection of functional headgroups into close proximity around a hydrophobic nano-environment, affording hydrolysis of a model ester at rates that challenge α-chymotrypsin. Structural assessment via NMR and XRD, paired with MD simulation and QM calculation, reveals marked similarities of the co-micelle catalyst to native enzymes.

C—Br...S halogen bonds in novel thiourea N-oxide cocrystals: analysis of energetic and QTAIM parameters

2020 ◽  
Vol 76 (2) ◽  
pp. 170-176 ◽  
Author(s):  
Kinga Wzgarda-Raj ◽  
Agnieszka J. Rybarczyk-Pirek ◽  
Sławomir Wojtulewski ◽  
Marcin Palusiak
Keyword(s):  
Quantum Theory ◽  
Hydrogen Bonds ◽  
Quantum Chemistry ◽  
Halogen Bonding ◽  
Atoms In Molecules ◽  
Monoclinic Space Group ◽  
Halogen Bonds ◽  
Space Group ◽  
Oxide Component ◽  
Bonding Interaction

Cocrystals of thiourea with 4-nitropyridine N-oxide, C5H4N2O3·2CH4N2S, (I), and 3-bromopyridine N-oxide, C5H4BrNO·CH4N2S, (II), crystallize in the monoclinic space group P21/c. In the crystals, molecules of both components are linked by N—H...O hydrogen bonds, creating R 2 1(6) synthons. The bromine substituent of the N-oxide component in (II) is a centre for C—Br...S halogen bonding to the thiourea molecule. Computations based on quantum chemistry methods (quantum theory of atoms in molecules, QTAIM) and atoms in molecules (AIM) theory were performed for a more detailed description of the observed type of halogen-bonding interaction.

scholarly journals Tetrahydroberberine, a pharmacologically active naturally occurring alkaloid

2015 ◽  
Vol 71 (4) ◽  
pp. 262-265 ◽  
Author(s):  
Subramanya Pingali ◽  
James P. Donahue ◽  
Florastina Payton-Stewart
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Racemic Mixture ◽  
Inversion Center ◽  
Intermolecular Hydrogen Bonds ◽  
Naturally Occurring ◽  
Pharmacologically Active

Tetrahydroberberine (systematic name: 9,10-dimethoxy-5,8,13,13a-tetrahydro-6H-benzo[g][1,3]benzodioxolo[5,6-a]quinolizine), C20H21NO4, a widely distributed naturally occurring alkaloid, has been crystallized as a racemic mixture about an inversion center. A bent conformation of the molecule is observed, with an angle of 24.72 (5)° between the arene rings at the two ends of the reduced quinolizinium core. The intermolecular hydrogen bonds that play an apparent role in crystal packing are 1,3-benzodioxole –CH2...OCH3and –OCH3...OCH3interactions between neighboring molecules.

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.

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

2013 ◽  
Vol 454 (3) ◽  
pp. 387-399 ◽  
Author(s):  
Patrick Masson ◽  
Sofya Lushchekina ◽  
Lawrence M. Schopfer ◽  
Oksana Lockridge
Keyword(s):  
Osmotic Stress ◽  
Osmotic Pressure ◽  
Active Site ◽  
Md Simulations ◽  
Catalytic Triad ◽  
Wild Type ◽  
Irreversible Inhibitor ◽  
Enzyme Active Site ◽  
Diffusion Controlled ◽  
Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

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