| 1. |
- Medina, Fabiola E., et al.
(författare)
-
Water Molecules Allow the Intramolecular Activation of the Thiamine Di-Phosphate Cofactor in Human Transketolase : Mechanistic Insights into a Famous Proposal
- 2021
-
Ingår i: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 11:7, s. 4136-4145
-
Tidskriftsartikel (refereegranskat)abstract
- Thiamine diphosphate-dependent enzymes are central to a wide range of technological areas and fields of science. The activity of these enzymes is closely related to the presence of the thiamine diphosphate cofactor (ThDP), which carries out catalysis in its activated form. In this state, the ThDP species has an unusual carbanion in the C2 position of the hetero thiazolium ring. For the ThDP-dependent transketolase (TK) enzyme in particular, this step plays a crucial role in the control of physiological routes, with implications on health/ill conditions for living organisms and the enantioselective synthesis of chemicals at the industrial level. For these reasons, a detailed knowledge on the activation mechanism of ThDP is fundamental. In this work, we present a theoretical study on the water-assisted activation of the ThDP cofactor in Homo sapiens transketolase (hTK). We explore the cofactor activation in the hTK with classical molecular dynamics and hybrid quantum mechanics/molecular mechanics calculations, using three layers, two of them described by high-level ab initio methods at the DLPNO-CCSD(T)/CBS plus B3LYP-D3/6-311 + G(2d,2p):AMBER. The activation of ThDP occurs in one asynchronous, water-mediated proton transfer from C2 to the N4' atoms and exhibits an activation energy of 5.1 kcal.mol(-1). The Gibbs activation energy for the ThDP activation was -10.3 kcal.mol(-1). Finally, by estimating the electrostatic effect per residue, we rationally identify those that can be mutated to design a much more competent TK enzyme.
|
|
| 2. |
- Prejanò, Mario, et al.
(författare)
-
Computational Study of Mechanism and Enantioselectivity of Imine Reductase from Amycolatopsis orientalis
- 2022
-
Ingår i: ChemistryOpen. - : Wiley. - 2191-1363. ; 11:1
-
Tidskriftsartikel (refereegranskat)abstract
- Imine reductases (IREDs) are NADPH-dependent enzymes (NADPH=nicotinamide adenine dinucleotide phosphate) that catalyze the reduction of imines to amines. They exhibit high enantioselectivity for a broad range of substrates, making them of interest for biocatalytic applications. In this work, we have employed density functional theory (DFT) calculations to elucidate the reaction mechanism and the origins of enantioselectivity of IRED from Amycolatopsis orientalis. Two substrates are considered, namely 1-methyl-3,4-dihydroisoquinoline and 2-propyl-piperideine. A model of the active site is built on the basis of the available crystal structure. For both substrates, different binding modes are first evaluated, followed by calculation of the hydride transfer transition states from each complex. We have also investigated the effect of mutations of certain important active site residues (Tyr179Ala and Asn241Ala) on the enantioselectivity. The calculated energies are consistent with the experimental observations and the analysis of transition states geometries provides insights into the origins of enantioselectivity of this enzyme.
|
|
| 3. |
- Prejanò, Mario, et al.
(författare)
-
Reaction Mechanism of Human PAICS Elucidated by Quantum Chemical Calculations
- 2022
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 144:31, s. 14258-14268
-
Tidskriftsartikel (refereegranskat)abstract
- Human PAICS is a bifunctional enzyme that is involved in the de novo purine biosynthesis, catalyzing the conversion of aminoimidazole ribonucleotide (AIR) into N-succinylcarboxamide-5-aminoimidazole ribonucleo-tide (SAICAR). It comprises two distinct active sites, AIR carboxylase (AIRc) where the AIR is initially converted to carboxyaminoimidazole ribonucleotide (CAIR) by reaction with CO2 and SAICAR synthetase (SAICARs) in which CAIR then reacts with an aspartate to form SAICAR, in an ATP-dependent reaction. Human PAICS is a promising target for the treatment of various types of cancer, and it is therefore of high interest to develop a detailed understanding of its reaction mechanism. In the present work, density functional theory calculations are employed to investigate the PAICS reaction mechanism. Starting from the available crystal structures, two large models of the AIRc and SAICARs active sites are built and different mechanistic proposals for the carboxylation and phosphorylation-condensation mechanisms are examined. For the carboxylation reaction, it is demonstrated that it takes place in a two-step mechanism, involving a C-C bond formation followed by a deprotonation of the formed tetrahedral intermediate (known as isoCAIR) assisted by an active site histidine residue. For the phosphorylation-condensation reaction, it is shown that the phosphorylation of CAIR takes place before the condensation reaction with the aspartate. It is further demonstrated that the three active site magnesium ions are involved in binding the substrates and stabilizing the transition states and intermediates of the reaction. The calculated barriers are in good agreement with available experimental data.
|
|
| 4. |
- Spiegel, Maciej, et al.
(författare)
-
Antioxidant and copper-chelating power of new molecules suggested as multiple target agents against Alzheimer's disease. A theoretical comparative study
- 2022
-
Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:26, s. 16353-16359
-
Tidskriftsartikel (refereegranskat)abstract
- In this study, the scavenging activity against OOH radicals and the copper-chelating ability of two new synthesized molecules (named L1 and L2) that can act as multiple target agents against Alzheimer's disease have been investigated at the density functional theory level. The pKa and molar fractions at physiological pH have been predicted. The main antioxidant reaction mechanisms in lipid-like and water environments have been considered and the relative rate constants determined. The copper-chelating ability of the two compounds has also been explored at different coordination sites and computing the complexation kinetic constants. Results show the L1 compound is a more effective radical scavenging and copper-chelating agent than L2.
|
|
| 5. |
- Spiegel, Maciej, et al.
(författare)
-
Primary and secondary antioxidant properties of scutellarin and scutellarein in water and lipid-like environments : A theoretical investigation
- 2022
-
Ingår i: Journal of Molecular Liquids. - : Elsevier BV. - 0167-7322 .- 1873-3166. ; 366
-
Tidskriftsartikel (refereegranskat)abstract
- The scavenging capability of scutellarin flavonoid against the OOH radical has been studied, at Density Functional level of theory, by considering different reaction mechanisms in both lipid-like and water media. In water phase, the neutral and charged species present in solution, identified from the computed pKa equilibria, have been determined. Furthermore, the complexation ability of Scutellarin and its metabolite scutellarein with respect to the Cu2+ and Fe3+ ions has been determined at the same level of theory. From the obtained rate constants results that scutellarin is a better Fe(III) ligand while scutellarein show a revers behavior. The glucuronidation process affect both the primar and secondary antiox-idant properties of the systems.
|
|
