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Human PAICS is a bifunctional enzyme that is involved in the

In this work, we elucidated some key aspects of the mechanism of action of the cisplatin anticancer drug, cis-[Pt(NH3)2Cl2], involving direct interactions with free nucleotides. A comprehensive in silico molecular modeling analysis was conducted to compare the interactions of Thermus aquaticus (Taq) DNA polymerase with three distinct N7-platinated deoxyguanosine triphosphates: [Pt(dien)(N7-dGTP)] (1), cis-[Pt(NH3)2Cl(N7-dGTP)] (2), and cis-[Pt(NH3)2(H2O)(N7-dGTP)] (3) {dien = diethylenetriamine; dGTP = 5′-(2′-deoxy)-guanosine-triphosphate}, using canonical dGTP as a reference, in the presence of DNA. The goal was to elucidate the binding site interactions between Taq DNA polymerase and the tested nucleotide derivatives, providing valuable atomistic insights. Unbiased molecular dynamics simulations (200 ns for each complex) with explicit water molecules were performed on the four ternary complexes, yielding significant findings that contribute to a better understanding of experimental results. The molecular modeling highlighted the crucial role of a specific α-helix (O-helix) within the fingers subdomain, which facilitates the proper geometry for functional contacts between the incoming nucleotide and the DNA template needed for incorporation into the polymerase. The analysis revealed that complex 1 exhibits a much lower affinity for Taq DNA polymerase than complexes 2–3. The affinities of cisplatin metabolites 2–3 for Taq DNA polymerase were found to be quite similar to those of natural dGTP, resulting in a lower incorporation rate for complex 1 compared to complexes 2–3. These findings could have significant implications for the cisplatin mechanism of action, as the high intracellular availability of free nucleobases might promote the competitive incorporation of platinated nucleotides over direct cisplatin attachment to DNA. The study’s insights into the incorporation of platinated nucleotides into the Taq DNA polymerase active site suggest that the role of platinated nucleotides in the cisplatin mechanism of action may have been previously underestimated.

A DFT and TDDFT study has been carried out on Red Nile dye (RN) and on two chalcogens-derivatives in which the carbonyl-oxygen was replaced by Sulphur- (SNR) and Selenium-(SeNR) in order to evaluate the effect of such substitution on their photophysical properties. Inspection of Type I and Type II photoreactions have been achieved exploring the absorption properties, computing spin-orbit coupling, proposing the most plausible deactivation channels leading to the population of excited triplet states and through the analysis of vertical electron affinities and ionization potentials. Our data show a useful bathochromic shift of the lowest energy 1ππ* absorption band as the size of the substituted atom increases combined with an enhancement of the SOC values for the main nπ*→ ππ* S1→T1 deactivation pathways, suggesting a more efficient ISC mechanism for the thio- and seleno-dye. Moreover, the introduction of selenium in the NR dye has the intriguing effect to promote also the electron transfer reaction producing the O2(−)• species through the TypeI mechanism, allowing us to propose that designed dye as a dual TypeI/II PS. Our study supports the strategy to afford heavy-atom effect by using chalcogens showing as it could be successfully exploited to achieve metal-free PSs with desirable properties.

The L-type amino acid transporter LAT1, involved in many biological processes including the overexpression of some tumors, is considered a potential pharmacological target. The 1,2,3-Dithiazole scaffold was predicted to inhibit LAT1 by the formation of an intermolecular disulfide bond with the thiolate group of cysteine(s). As a result of the identification of these irreversible covalent inhibitors, we decided to deeply investigate the recognition stage and the covalent interaction, characterizing the chemical structures of the selected ligands. With the aim to provide new insights into the access of the ligands to the binding pocket and to reveal the residues involved in the inhibition, we performed docking, molecular dynamics simulations, and density functional theory-based investigation of three 1,2,3-dithiazoles against LAT1. Our computational analysis further highlighted the crucial role played by water molecules in the inhibition mechanism. The results here presented are consistent with experimental observations and provide insights that can be helpful for the rational design of new-to-come LAT1’s inhibitors.

In this study, the scavenging activity against OOH radicals and the copper-chelating ability of two new synthesized molecules (L1 and L2) that can act as multiple target agents against Alzheimer's disease have been investigated at the DFT level.

Both toxic and physiological effects of CO are mostly caused by well described interactions with heme-groups of proteins. Interactions of CO with non-heme proteins have also been unveiled. Besides interaction of CO with mitochondrial heme containing respiratory complexes, a BK channel and the phosphate carrier which do not contain metal cofactors, have been identified as CO targets. However, the molecular mechanisms of interaction with non-metal-containing proteins are not understood. We show in this work the effect of CO on the mitochondrial carnitine carrier (SLC25A20) using CORM-3, a widely recognized CO releasing compound. CO exerts an inhibitory effect at the micromolar concentration on the transport function of the transporter extracted from treated mitochondria. The effect is due to a single Cys residue, C136 as revealed by mass spectrometry analysis. A computational approach predicted the need for vicinal Asp and Lys residues for the C136 carbonylation to occur. These data demonstrate a novel mechanism of interaction of CO with a protein not containing metal atoms and will enable the prediction of CO targets.

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 dip...

The histone deacetylase 6 enzyme, HDAC6, is a metalloprotein with multiple pathophysiological roles and, as such, is the subject of intense research and drug discovery efforts. Different from the H...

The nitrile hydration reaction mechanism catalyzed by a MnI(NH)-OH complex has been elucidated by means of DFT computations, first exploring three mechanistic hypotheses experimentally suggested in...

The recently discovered methanol dehydrogenase, XoxF, is a widespread enzyme used by methylotrophic bacteria to oxidize methanol for carbon and energy, and requires lanthanide ions for its activity. This enzyme represents an essential component of methanol utilization by both methanol- and methane-utilizing bacteria. The present investigation looks on the electronic, energetic and geometrical behavior of the methanol dehydrogenase from Methylacidiphilum fumariolicum SolV, which is strictly dependent on early lanthanide metals with +3 oxidation states, by examining enzyme-substrate complexes of all the lanthanides. We focus on the catalytic reaction mechanism of two methanol dehydrogenases having as cofactor europium and ytterbium belonging to the mid- and later- series of lanthanides, in comparison with the methanol dehydrogenase containing the cerium, one early lanthanide. Our results provide evidence for the influence of the lanthanide contraction effect in all the elementary steps of the catalytic reaction mechanism. This indication may prove useful for developing new catalytic machineries of enzymes that adopt new-to-nature transformations.

Atomic resolution X-ray crystallography has shown that an intermediate (the X5P-ThDP adduct) of the catalytic cycle of transketolase (TK) displays a significant, putatively highly energetic, out-of-plane distortion in a sp2 carbon adjacent to a lytic bond, suggested to lower the barrier of the subsequent step, and thus was postulated to embody a clear-cut demonstration of the intermediate destabilization effect. The lytic bond of the subsequent rate-limiting step was very elongated in the X-ray structure (1.61 Å), which was proposed to be a consequence of the out-of-plane distortion. Here we use high-level QM and QM/MM calculations to study the intermediate destabilization effect. We show that the intrinsic energy penalty for the observed distortion is small (0.2 kcal·mol–1) and that the establishment of a favorable hydrogen bond within X5P-ThDP, instead of enzyme steric strain, was found to be the main cause for the distortion. As the net energetic effect of the distortion is small, the establishment of the internal hydrogen bond (−0.6 kcal·mol–1) offsets the associated penalty. This makes the distorted structure more stable than the nondistorted one. Even though the energy contributions determined here are close to the accuracy of the computational methods in estimating penalties for geometric distortions, our data show that the intermediate destabilization effect provides a small contribution to the observed reaction rate and does not represent a catalytic effect that justifies the many orders of magnitude which enzymes accelerate reaction rates. The results help to understand the intrinsic enzymatic machinery behind enzyme’s amazing proficiency.

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., Reaction mechanism and enantioselectivity of Ao IRED (Amycolatopsis orientalis imine reductase) were investigated by density functional theory calculations. Two different substrates were considered, namely 1‐methyl‐3,4‐dihydroisoquinoline and 2‐propyl‐piperideine. Detailed analyses of the optimized geometries of enzyme‐substrate complexes and transition states for both wild‐type and mutant enzymes shed light on the origins of the stereoinduction.

Nature exploits different strategies for enhancing the catalytic activity of enzymes, often resorting to producing beneficial mutations. The case of post-translational proline hydroxylation mutation in the active site of polysaccharide deacetylase (PDA) Bc1960 from Bacillus cereus is an interesting example of how small chemical modifications can cause significant improvements in enzymatic activity. In the present study the deacetylation mechanism promoted by both OH-proline (2Hyp) and standard proline (Pro) containing PDA is investigated using density functional theory. Although the mechanism presented for the two examined enzymes is in agreement with protease catalysis in metalloenzymes, the analysis along the potential energy surface (PES) reveals that the intermediate and product benefit energetically from the presence of the hydroxyl group on the proline. Our calculations provide evidence that for PDA-2Hyp, the hydrogen bond network established by the -OH group on the Cα of the proline with its closest neighbors stabilizes the transition states and, consequently, the reaction takes advantage of this. These results further contribute towards explaining the different catalytic activity experimentally observed for the polysaccharide deacetylase enzymes.

Sulfonated Polysulfone (sPSU) is emerging as a concrete alternative to Nafion ionomer for the development of proton exchange electrolytic membranes for low cost, environmentally friendly and high-performance PEM fuel cells. This ionomer has recently gained great consideration since it can effectively combine large availability on the market, excellent film-forming ability and remarkable thermo-mechanical resistance with interesting proton conductive properties. Despite the great potential, however, the morphological architecture of hydrated sPSU is still unknown. In this study, computational and experimental advanced tools are combined to preliminary describe the relationship between the microstructure of highly sulfonated sPSU (DS = 80%) and its physico-chemical, mechanical and electrochemical features. Computer simulations allowed for describing the architecture and to estimate the structural parameters of the sPSU membrane. Molecular dynamics revealed an interconnected lamellar-like structure for hydrated sPSU, with ionic clusters of about 14–18 Å in diameter corresponding to the hydrophilic sulfonic-acid-containing phase. Water dynamics were investigated by 1H Pulsed Field Gradient (PFG) NMR spectroscopy in a wide temperature range (20–120 °C) and the self-diffusion coefficients data were analyzed by a “two-sites” model. It allows to estimate the hydration number in excellent agreement with the theoretical simulation (e.g., about 8 mol H2O/mol SO3= @ 80 °C). The PEM performance was assessed in terms of dimensional, thermo-mechanical and electrochemical properties by swelling tests, DMA and EIS, respectively. The peculiar microstructure of sPSU provides a wider thermo-mechanical stability in comparison to Nafion, but lower dimensional and conductive features. Nonetheless, the single H2/O2 fuel cell assembled with sPSU exhibited better features than any earlier published hydrocarbon ionomers, thus opening interesting perspectives toward the design and preparation of high-performing sPSU-based PEMs.

This contribution aims for a brief, but as comprehensive as possible, overview of computational enzymology examining all the steps necessary for an enzyme (enzyme–substrate complex formation, chemical reaction, product release and catalytic cycle restoration) to exert its catalytic action. Due to its great importance in pharmacology, covalent inhibition is also considered. Examples of how to extract valuable information from the combined use of classical molecular dynamics with pure and hybrid quantum chemical tools (QM and QM/MM) are also reported.

Oxidative conditions are frequently enhanced by the presence of redox metal ions. In this study, the role of capsaicin (8-methyl-N-vanillyl-6-nonenamide, CAP) in copper-induced oxidative stress was investigated using density functional theory simulations. It was found that CAP has the capability to chelate Cu(II), leading to complexes that are harder to reduce than free Cu(II). CAP fully turns off the Cu(II) reduction by Asc−, and slows down the reduction in this cation by O2•−. Therefore, CAP is proposed as an •OH-inactivating ligand by impeding the reduction in metal ions (OIL-1), hindering the production of •OH via Fenton-like reactions, at physiological pH. CAP is also predicted to be an excellent antioxidant as a scavenger of •OH, yielded through Fenton-like reactions (OIL-2). The reactions between CAP-Cu(II) chelates and •OH were estimated to be diffusion-limited. Thus, these chelates are capable of deactivating this dangerous radical immediately after being formed by Fenton-like reactions.

The exact chemical structure of non-crystallising natural products is still one of the main challenges in Natural Sciences. Despite tremendous advances in total synthesis, the absolute structural determination of a myriad of natural products with very sensitive chemical functionalities remains undone. Here, we show that a metal-organic framework (MOF) with alcohol-containing arms and adsorbed water, enables selective hydrolysis of glycosyl bonds, supramolecular order with the so-formed chiral fragments and absolute determination of the organic structure by single-crystal X-ray crystallography in a single operation. This combined strategy based on a biomimetic, cheap, robust and multigram available solid catalyst opens the door to determine the absolute configuration of ketal compounds regardless degradation sensitiveness, and also to design extremely-mild metal-free solid-catalysed processes without formal acid protons.

[EN] The exact chemical structure of non-crystallising natural products is still one of the main challenges in Natural Sciences. Despite tremendous advances in total synthesis, the absolute structural determination of a myriad of natural products with very sensitive chemical functionalities remains undone. Here, we show that a metal-organic framework (MOF) with alcohol-containing arms and adsorbed water, enables selective hydrolysis of glycosyl bonds, supramolecular order with the so-formed chiral fragments and absolute determination of the organic structure by single-crystal X-ray crystallography in a single operation. This combined strategy based on a biomimetic, cheap, robust and multigram available solid catalyst opens the door to determine the absolute configuration of ketal compounds regardless degradation sensitiveness, and also to design extremely-mild metal-free solid-catalysed processes without formal acid protons. Elucidation of the chemical structure of natural products constitutes one of the main challenges in Natural Sciences. Here, the authors show that an amino acid-based metal-organic framework exhibits hydrolase-like catalytic activity and crystallographic determination of the resulting products, This work was supported by the Ministero dell'Istruzione, dell'Universita e della Ricerca (Italy) and the MINECO (Spain) (Projects CTQ2016-75671-P, CTQ 2017-86735-P, RTC-2017-6331-5, Severo Ochoa program SEV-2016-0683 and Excellence Unit "Maria de Maeztu" MDM-2015-0538). R.B. thanks the MIUR (Project PON R&I FSE-FESR 2014-2020) for grant. L.B wishes to thank Italian MIUR for grant n. AIM1899391-1 in the framework of the project "Azione I.2, Mobilita dei Ricercatori, PON R&I 2014-2020". Thanks are also extended to the "2019 Post-doctoral Junior Leader-Retaining Fellowship, la Caixa Foundation (ID100010434 and fellowship code LCF/BQ/PR19/11700011" (J. F.-S.). S. S.-N. thanks ITQ for the concession of a contract. D.A. acknowledges the financial support of the Fondazione CARIPLO/"Economia Circolare: ricerca per un futuro sostenibile" 2019, Project code: 2019-2090, MOCA. E.P. acknowledges the financial support of the European Research Council under the European Union's Horizon 2020 research and innovation program/ERC Grant Agreement No. 814804, MOF-reactors.

The antioxidant capability of scutellarein, a flavonoid extracted from different plants of the Scutellaria family, was computationally predicted by considering its reaction with the OOH radical in both lipid-like and water environments. The pKa and equilibrium behavior in the aqueous phase were also calculated. Different reaction mechanisms involving the most populated species were considered. The work was performed by using the density functional level of theory. The individual, total, and fraction-corrected total rate constants were obtained. The results show that scutellarein has scavenging power against the hydroperoxyl radical similar to that of Trolox, which is generally used as a reference antioxidant.

To elucidate the catalytic mechanism of cobalt(III)-benzonitrile and iron(III)--pivalonitrile hydratases, we have performed at density functional level a study using the cluster model approach. Computations were made in a protein framework. Following the suggestions given in a recent work on the analogous enzyme Fe(III)-NHase, we have explored the feasibility of a new working mechanism of examined enzymes. According to our results, after the formation of enzyme substrate complex, the reaction evolves toward product in only three steps. The first one is the nucleophilic attack, led by the -OH group of the αCys113-S-OH on the nitrile carbon atom, followed by the amide formation and by the enzyme restoring phase that our computations indicate as the most expensive step from the energetic point of view in both catalytic processes.

Lanthanides are an example of nonbiogenic metal species and have been widely used in crystallographic and spectroscopic studies to probe Mg2+/Ca2+ binding sites in metalloproteins by replacing the native cofactor. Recently, a methanol dehydrogenase (MDH) enzyme containing cerium ion in the active site has been isolated from Methylacidiphilum Fumariolicum bacterium. With the aim to highlight as metal ion substitution can be reflected in catalytic mechanism, a comparative DFT study between Ca- and Ce-MDH has been undertaken. The obtained potential energy surfaces (PES), for two considered reaction mechanisms (named A and B), indicate mechanism A (addition-elimination and protonation processes) as the favored for both the enzymes and show as the barrier for the rate-determining step of Ce-MDH requires 19.4 kcal/mol.

We have computationally determined the catalytic mechanism of human transketolase (hTK) using a cluster model approach and density functional theory calculations. We were able to determine all the relevant structures, bringing solid evidences to the proposed experimental mechanism, and to add important detail to the structure of the transition states and the energy profile associated with catalysis. Furthermore, we have established the existence of a crucial intermediate of the catalytic cycle, in agreement with experiments. The calculated data brought new insights to hTK's catalytic mechanism, providing free-energy values for the chemical reaction, as well as adding atomistic detail to the experimental mechanism.

Methanol dehydrogenase (MDH) enzymes are quinoproteins that require calcium or magnesium ion as well as pyrroloquinoline quinone as a cofactor for activity in the oxidation of methanol to formaldehyde. Lately, MDH enzymes containing lanthanide ions in the active site have been isolated in drastic conditions from Methylacidiphilum fumariolicum bacterium. The present theoretical study performed in the framework of the density functional theory employing the quantum mechanical cluster approach mainly focused on the catalytic mechanism of cerium containing MDH enzyme. In order to rationalize the effect of the metal ion substitution on the catalytic activity, geometrical and electronic properties of the “Michaelis–Menten” enzyme–methanol complexes of Ce-MDH and Eu-MDH are also discussed as well as the substrate’s activation mediated by the metal ion. With the aim to better describe the Lewis acidity of metal ions in the methanol oxidation, the comparison of the catalytic performance between Ce-MDH and Ca-MDH was also made.

Piperlongumine (PL) is an anticancer compound whose activity is related to the inhibition of human glutathione transferase of pi class (GSTP1) overexpressed in cancerous tumors and implicated in the metabolism of electrophilic compounds. In the present work, the inhibition mechanism of hydrolyzed piperlongumine (hPL) has been investigated employing QM and QM/MM levels of theory. The potential energy surfaces (PESs) underline the contributions of Tyr residue close to G site in the catalytic pocket of the enzyme. The proposed mechanism occurs through a one-step process represented by the nucleophilic addition of the glutathione thiol to electrophilic species giving rise to the simultaneous C-S and H-C bonds formation. Both the used methods give barrier heights (19.8 and 21.5 kcal mol−1 at QM/MM and QM, respectively) close to that experimentally measured for the C-S bond formations (23.8 kcal mol−1).

Oxidative conditions are frequently enhanced by the presence of redox metal ions. In this study, the role of capsaicin (8-methyl-N-vanillyl-6-nonenamide, CAP) in copper-induced oxidative stress was investigated using density functional theory simulations. It was found that CAP has the capability to chelate Cu(II), leading to complexes that are harder to reduce than free Cu(II). CAP fully turns off the Cu(II) reduction by Asc-, and slows down the reduction in this cation by O2&bull, Therefore, CAP is proposed as an &bull, OH-inactivating ligand by impeding the reduction in metal ions (OIL-1), hindering the production of &bull, OH via Fenton-like reactions, at physiological pH. CAP is also predicted to be an excellent antioxidant as a scavenger of &bull, OH, yielded through Fenton-like reactions (OIL-2). The reactions between CAP-Cu(II) chelates and &bull, OH were estimated to be diffusion-limited. Thus, these chelates are capable of deactivating this dangerous radical immediately after being formed by Fenton-like reactions.