Analysis of PUGNAc and NAG-thiazoline as transition state analogues for human O-GlcNAcase: mechanistic and structural insights into inhibitor selectivity and transition state poise

O-GlcNAcase catalyzes the cleavage of beta-O-linked 2-acetamido-2-deoxy-beta-d-glucopyranoside (O-GlcNAc) from serine and threonine residues of post-translationally modified proteins. Two potent inhibitors of this enzyme are O-(2-acetamido-2-deoxy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc) and 1,2-dideoxy-2'-methyl-alpha-d-glucopyranoso[2,1-d]-Delta2'-thiazoline (NAG-thiazoline). Derivatives of these inhibitors differ in their selectivity for human O-GlcNAcase over the functionally related human lysosomal beta-hexosamindases, with PUGNAc derivatives showing modest selectivities and NAG-thiazoline derivatives showing high selectivities. The molecular basis for this difference in selectivities is addressed as is how well these inhibitors mimic the O-GlcNAcase-stabilized transition state (TS). Using a series of substrates, ground state (GS) inhibitors, and transition state mimics having analogous structural variations, we describe linear free energy relationships of log(KM/kcat) versus log(KI) for PUGNAc and NAG-thiazoline. These relationships suggest that PUGNAc is a poor transition state analogue, while NAG-thiazoline is revealed as a transition state mimic. Comparative X-ray crystallographic analyses of enzyme-inhibitor complexes reveal subtle molecular differences accounting for the differences in selectivities between these two inhibitors and illustrate key molecular interactions. Computational modeling of species along the reaction coordinate, as well as PUGNAc and NAG-thiazoline, provide insight into the features of NAG-thiazoline that resemble the transition state and reveal where PUGNAc fails to capture significant binding energy. These studies also point to late transition state poise for the O-GlcNAcase catalyzed reaction with significant nucleophilic participation and little involvement of the leaving group. The potency of NAG-thiazoline, its transition state mimicry, and its lack of traditional transition state-like design features suggest that potent rationally designed glycosidase inhibitors can be developed that exploit variation in transition state poise.     

Development of transition state analogue inhibitors for <Emphasis Type="Italic">N</Emphasis>-acetylglycosyltransferases bearing <Emphasis Type="SmallCaps">d</Emphasis>psico- or <Emphasis Type="SmallCaps">d</Emphasis>tagatofuranose scaffolds

New potential transition state analogue inhibitors for N-acetylglucosyltransferases (GnTs) were synthesised. These compounds based on psico- and tagatofuranose (structure) scaffold contained a 2-thiophenyl-1-O-diethylphosphate moiety mimicking the proposed model of the transition state of the enzymatic reaction catalysed by N-acetylglucosyltransferases. The synthesised compounds as well as their precursors were fully characterised by NMR, optical rotation and mass techniques. Anomeric configuration of tagatofuranose derivatives was confirmed by X-ray crystallography. Two types of potential human glycosyltransferase (GnTs) inhibitors representing donor UDP-GlcNAc, assigned for biological assays on human GnTs, were prepared.     

Substrate and metal control of barrier heights for oxo transfer to Mo and W bis-dithiolene sites

Reaction coordinates for oxo transfer from the substrates Me(3)NO, Me(2)SO, and Me(3)PO to the biologically relevant Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)(2)](-) where mdt = 1,2-dimethyl-ethene-1,2-dithiolate(2-), and from Me(2)SO to the analogous W(IV) complex, have been calculated using density functional theory. In each case, the reaction first proceeds through a transition state (TS1) to an intermediate with substrate weakly bound, followed by a second transition state (TS2) around which breaking of the substrate X-O bond begins. By analyzing the energetic contributions to each barrier, it is shown that the nature of the substrate and metal determines which transition state controls the rate-determining step of the reaction.     

几种过渡态结构的有效优化方法

通过双桥反应机理、电环合反应和催化反应三个不同类型的过渡态优化，说明当标准方法难以给出结果时，对物理问题本身的分析有助于给出过渡态优化的线索．第一个例子根据化学问题给出限制条件，通过平衡几何构型优化方法优化得到过渡态；第二个例子是在使用标准过渡态优化方法失败后，根据物理问题从反应途径上用平衡几何构型优化方法选择过渡态优化的初始结构；第三个例子通过Gaussian 98程序中的标准方法QST2直接得到过渡态．     

Effects of entropy on the gas-phase pyrolysis of ethyl N,N-dimethylcarbamate

In this study, we examined the gas-phase pyrolysis of ethyl N,N-dimethylcarbamate theoretically at various theoretical levels. The reaction consists of a two-step mechanism, with N,N-dimethylcarbamic acid and ethylene as reaction intermediates. In the first step, the reaction proceeds via a six-membered cyclic transition state (TS), which is more favorable than that via a four-membered cyclic TS. Here, the contribution of entropy to the overall potential energy surface was found to play an important role in determining the rate-limiting step, which was found to be the second step when viewed in terms of the enthalpy of activation (DeltaH(not equal)), but the first step when entropy changes (-TDeltaS(not equal)) were considered. These results are consistent with experimental findings. Moreover, the experimental activation entropy can be reproduced by using the hindered rotor approximation, which converts some low vibration frequencies that correspond to internal rotational modes into hindered rotors.     

Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I

The Golgi glycosyltransferase, N-acetylglucosaminyltransferase I (GnT-I), catalyzes the transfer of a GlcNAc residue from the donor UDP-GlcNAc to the C2-hydroxyl group of a mannose residue in the trimannosyl core of the Man5GlcNAc2-Asn-X oligosaccharide. The catalytic mechanism of GnT-I was investigated using a hybrid quantum mechanical/molecular mechanical (QM/MM) method with a QM part containing 88 atoms treated with density functional theory (DFT) at the BP/TZP level. The remaining parts of a GnT-I complex, altogether 5633 atoms, were modeled using the AMBER molecular force field. A theoretical model of a Michaelis complex was built using the X-ray structure of GnT-I in complex with the donor having geometrical features consistent with kinetic studies. The QM(DFT)/MM model identified a concerted SN2-type of transition state with D291 as the catalytic base for the reaction in the enzyme active site. The TS model features nearly simultaneous nucleophilic addition and dissociation steps accompanied by the transfer of the nucleophile proton Hb2 to the catalytic base D291. The structure of the TS model is characterized by the Ob2-C1 and C1-O1 bond distances of 1.912 and 2.542 A, respectively. The activation energy for the proposed reaction mechanism was estimated to be approximately 19 kcal mol-1. The calculated alpha-deuterium kinetic isotope effect of 1.060 is consistent with the proposed reaction mechanism. Theoretical results also identified interactions between the Hb6 and beta-phosphate oxygen of the UDP and a low-barrier hydrogen bond between the nucleophile and the catalytic base D291. It is proposed that these interactions contribute to a stabilization of TS. This modeling study provided detailed insight into the mechanism of the GlcNAc transfer catalyzed by GnT-I, which is the first step in the conversion of high mannose oligosaccharides to complex and hybrid N-glycan structures.     

磷酰化丝氨酸形成六配位磷中间体的理论研究

用MNDO方法对磷酰化丝氨酸仿生化反应机理中六配位磷中间体的形成过程进行了研究.磷酰化丝氨酸(1)形成分子内磷酸-羧酸分子内混酐的五配位磷中间体(2)后,其酸性质子解离,分子经过具有氢桥键结构的过渡态,使氨基酸侧链羟基上的氢通过氢键作用向磷上的O₁进行转移,然后再经过构型由三角双锥向八面体的转变,形成六配位磷中间体(3).氢桥键的存在使反应过渡态能量降低,其相对能量为148.5kJ/mol.理论计算较成功的解释了六配位磷中间体的形成机理以及磷酰化丝氨酸仿生化反应中羧基和侧链羟基共同参与的实验结果.     

A strategy for the solution-phase parallel synthesis of N-(pyrrolidinylmethyl)hydroxamic acids

Both five- and six-membered iminocyclitols have proven to be useful transition-state analogue inhibitors of glycosidases. They also mimic the transition-state sugar moiety of the nucleoside phosphate sugar in glycosyltransferase-catalyzed reactions. Described here is the development of a general strategy toward the parallel synthesis of a five-membered iminocyclitol linked to a hydroxamic acid group designed to mimic the transition state of GDP-fucose complexed with Mn(II) in fucosyltransferase reactions. The iminocyclitol 8 containing a protected hydroxylamine unit was prepared from D-mannitol. The hydroxamic acid moiety was introduced via the reaction of 8 with various acid chlorides. The strategy is generally applicable to the construction of libraries for identification of glycosyltransferase inhibitors.     

Theoretical study of oxidation of cyclohexane diol to adipic anhydride by [Ru(IV)(O)(tpa)(H2O)]2+ complex (tpa ═ tris(2-pyridylmethyl)amine)

The catalytic conversion of 1,2-cyclohexanediol to adipic anhydride by Ru(IV)O(tpa) (tpa ═ tris(2-pyridylmethyl)amine) is discussed using density functional theory calculations. The whole reaction is divided into three steps: (1) formation of α-hydroxy cyclohexanone by dehydrogenation of cyclohexanediol, (2) formation of 1,2-cyclohexanedione by dehydrogenation of α-hydroxy cyclohexanone, and (3) formation of adipic anhydride by oxygenation of cyclohexanedione. In each step the two-electron oxidation is performed by Ru(IV)O(tpa) active species, which is reduced to bis-aqua Ru(II)(tpa) complex. The Ru(II) complex is reactivated using Ce(IV) and water as an oxygen source. There are two different pathways of the first two steps of the conversion depending on whether the direct H-atom abstraction occurs on a C-H bond or on its adjacent oxygen O-H. In the first step, the C-H (O-H) bond dissociation occurs in TS1 (TS2-1) with an activation barrier of 21.4 (21.6) kcal/mol, which is followed by abstraction of another hydrogen with the spin transition in both pathways. The second process also bifurcates into two reaction pathways. TS3 (TS4-1) is leading to dissociation of the C-H (O-H) bond, and the activation barrier of TS3 (TS4-1) is 20.2 (20.7) kcal/mol. In the third step, oxo ligand attack on the carbonyl carbon and hydrogen migration from the water ligand occur via TS5 with an activation barrier of 17.4 kcal/mol leading to a stable tetrahedral intermediate in a triplet state. However, the slightly higher energy singlet state of this tetrahedral intermediate is unstable; therefore, a spin crossover spontaneously transforms the tetrahedral intermediate into a dione complex by a hydrogen rebound and a C-C bond cleavage. Kinetic isotope effects (k(H)/k(D)) for the electronic processes of the C-H bond dissociations calculated to be 4.9-7.4 at 300 K are in good agreement with experiment values of 2.8-9.0.     

Insights into the mechanism of O₂ formation and release from the Mn₄O₄L₆ "cubane" cluster

To probe photoinduced water oxidation catalyzed by the Mn?O?L? cubane clusters, we have computationally studied the mechanism and controlling factors of the O? formation from the [Mn?O?L?] catalyst, 6. It was demonstrated that dissociation of an L = H?PO?? ligand from 6 facilitates the direct O-O bond formation that proceeds with a 28.3 (33.4) kcal/mol rate-determining energy barrier at the transition state TS1. This step (the O-O single bond formation) of the reaction is a two-electron oxidation/reduction process, during which two oxo ligands are transformed into to μ2:η2-O?2? unit, and two ("distal") Mn centers are reduced from the 4+ to the 3+ oxidation state. Next two-electron oxidation/reduction occurs by "dancing" of the resulted O?2? fragment between the Mn1 and Mn2/Mn(2')-centers, keeping its strong coordination to the Mn(1')-center. As a result of this four-electron oxidation/reduction process Mn centers of the Mn?-core of I transform from {Mn1(III)-Mn(1')(III)-Mn2(IV)-Mn(2')(IV)} to {Mn1(II)-Mn(1')(II)-Mn2(III)-Mn(2')(III)} in IV. In other words, upon O? formation in cationic complex [Mn?O?L?](+), I, all four Mn-centers are reduced by one electron each. The overall reaction I → TS1 → II → III → TS2 → IV → TS3 → V → VI + O? is found to be exothermic by 15.4 (10.5) kcal/mol. We analyze the lowest spin states and geometries of all reactants, intermediates, transition states, and products of the targeted reaction.     

Substitution effects on olefin epoxidation catalyzed by Oxoiron(IV) porphyrin π-cation radical complexes: A dft study

The effects of peripheral fluorine atoms on epoxidation reactions of ethylene by oxoiron(IV) porphyrin cation radical complex in the quartet and sextet spin multiplicities are systematically investigated using the DFT method. The overall reaction routes are determined using a model system of ethylene and Fe(IV)OCl-porphyrin with substituted fluorine atoms. By obtaining the energy diagrams and electron- and spin-density difference contour maps of the transition states and intermediate compounds, we confirm that the electron-withdrawing by peripheral fluorine atoms enhances the reactivity as the number of fluorine atoms increases, as is observed experimentally. The intersystem crossing between the quartet and sextet spin multiplicities is discussed by means of the intrinsic reaction coordinate method. We conclude that the rate-determining step is located at the first transition state (TS1) for the activation of CC and FeO bonds, and the ground electronic state changes from quartet to sextet around the TS1. © 2019 Wiley Periodicals, Inc.     

Theoretical study of mechanism of extraction reaction between silylene carbene and its derivatives and ethylene oxide

The mechanism of the oxide extraction reaction between singlet silylene carbene and its derivatives [X₂Si = C: (X = H, F, Cl, CH₃)] and ethylene oxide has been investigated with density functional theory, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated by B3LYP/6‐311G(d,p) method. From the potential energy profile, it can be predicted that the reaction pathway of this kind consists two steps, the first step is the two reactants firstly form an intermediate (INT) through a barrier‐free exothermic reaction; the second step is the INT then generates a product via a transition state (TS). This kind reaction has similar mechanism, when the silylene carbene and its derivatives [X₂Si = C: (X = H, F, Cl, CH₃)] and ethylene oxide close to each other, the shift of 2p lone electron pair of O in ethylene oxide to the 2p unoccupied orbital of C in X₂Si = C: gives a p → p donor–acceptor bond, thereby leading to the formation of INT. As the p → p donor–acceptor bond continues to strengthen (that is, the C? O bond continues to shorten), the INT generates product (P + C₂H₄) via TS. It is the substituent electronegativity, which mainly affects the extraction reactions. When the substituent electronegativity is greater, the energy barrier is lower, and the reaction rate is greater. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

The nature and function of the catalytic centres of the DMSO reductases

Density functional theory calculations have been performed to probe aspects of the function of the reaction centres of the DMSO reductase enzymes, in respect of catalysis of oxygen atom transfer (OAT). The first comparison between Mo and W at the active site of these enzymes has been accomplished by a consideration of the reaction profile for OAT from DMSO to [MoIV(OMe)(S2C2H2)2]1- versus that for the corresponding reaction with [WIV(OMe)(S2C2H2)2]1-. Both reaction profiles involve two transition states separated by a well-defined intermediate; however, whilst the second transition state (TS2) is clearly rate-limiting for the Mo system, the two transition states have a similar energy for the W system. The activation energy for OAT from DMSO to [WIV(OMe)(S2C2H2)2]1- is ca. 23 kJ mol-1 lower for the corresponding reaction with Mo, consistent with the significantly faster rate of reduction of DMSO by Rhodobacter capsulatus W-DMSO reductase than by its Mo counterpart. Consistent with the principle of the entatic state, the geometrical constraints imposed by the protein on the metal centre of the Mo- and W-DMSO reductases facilitate OAT by favouring a trigonal prismatic geometry for the transition state TS2 that is close to that observed for the metal in the oxidised form of each of these enzymes. The effects of different tautomers of a simplified form of the pyran ring-opened, dihydropterin state of the molybdopterin cofactor on the reaction profile for OAT have been considered. The major effect, a significant lowering of the activation barrier associated with TS2, is observed for a protonated form of a tautomer that involves conjugation between the pyrazine and metallodithiolene rings.     

单嘧磺隆除草剂水解机理的理论研究

用量子化学中密度泛函B3LYP方法在6-31G*水平上, 对单嘧磺隆的水解机理进行了理论研究. 优化了反应过程中反应物、中间体、过渡态及产物的几何构型, 并对各个过渡态和中间体进行了振动分析确认其真实性. 结果表明: 在碱性条件下, 水解反应主要经历一个五元环的过渡态TS1, 该反应速控步骤的能垒为25.7 kJ/mol; 在中性条件下, 水解反应涉及到一个三元环的过渡态和两个四元环的过渡态, 反应的速控步骤为M3'＋H₂O→TS2', 能垒为236.5 kJ/mol. 从能量上看, 碱性条件更有利于水解反应的进行, 与实验结果吻合. 同时, 我们还考虑了溶剂效应对水解反应的影响.     

The gas-phase reaction between O3 and HO radical: a theoretical study.

We report a theoretical study on the reaction of ozone with hydroxyl radical, which is important in the chemistry of the atmosphere and in particular participates in stratospheric ozone destruction. The reaction is a complex process that involves, in the first stage, a pre-reactive hydrogen-bonded complex (C1), which is formed previous to two transition states (TS1 and TS2) involving the addition of the hydroxyl radical to ozone, and leads to the formation of HO4 polyoxide radical before the release of the products HO2 and O2. The reaction is computed to be exothermic by 42.72 kcal mol(-1), which compares quite well with the experimental estimate, and the energy barriers of TS1 and TS2 with respect to C1 are computed to be 1.80 and 2.26 kcal mol(-1) at 0 K. A kinetic study based on the variational transition state theory (VTST) predicts a rate constant, at 298 K, of 7.37 x 10(-14) cm3 molecule(-1) s(-1), compared to the experimentally recommended value of 7.25 x 10(-14) cm3 molecule(-1) s(-1).     

Origins of enantioselectivity in the chiral diphosphine-ligated CuH-catalyzed asymmetric hydrosilylation of ketones

Computational investigations on the asymmetric hydrosilylation of acetophenone over ligated CuH catalysts were performed with the DFT method. The calculations predict that the catalytic reaction involves two steps: (1) CuH addition to the carbonyl group via a four-membered transition state (TS) with the formation of copper-alkoxide intermediates; (2) regeneration of the ligated CuH catalyst by an external SiH(4) through a metathesis process to yield the corresponding silyl ether. The calculations in the chiral diphosphine-ligated CuH systems suggest that the metathesis process is the rate-determining step (RDS). The CuH addition step is vital for the distribution of the racemic products and therefore represents the stereo-controlling step (SCT). In this step, the greater steric hindrance between the aromatic rings of the ligands and the substrate is identified as the major factor for enantioselectivity. The corresponding TS in the face-to-face mode, suffering less steric hindrance, is more stable than its analogue in the edge-to-face mode. The enantioselectivities are calculated to be related not only to the P-Cu-P bite angles in the stereo-controlling TSs, but also to the substituents at the P-aryl rings of the chiral ligands. In short, a larger P-Cu-P bite angle and suitably modified P-aryl rings together are necessary to achieve excellent ee values.     

Ab Initio Study on the Mechanism of the Atmospheric Reaction OH+O3→HO2+O2

The atmospheric reaction (1) OH + O₃→HO₂ + O₂ was investigated theoretically by using MP2, QCISD, QCISD(T), and CCSD(T) methods with various basis sets. At the highest level of theory, namely, QCISD, the reaction is direct, with only one transition state between reactants and products. However, at the MP2 level, the reaction proceeds through a two‐step mechanism and shows two transition states, TS1 and TS2 , separated by an intermediate, Int . The different methodologies employed in this paper consistently predict the barrier height of reaction (1) to be within the range 2.16–5.11 kcal mol^?1, somewhat higher than the experimental value of 2.0 kcal mol^?1.     

杂环反铂(Ⅱ)抗癌药物水解反应机理的DFT研究

用DFT-B3LYP方法和IEF-PCM溶剂化模型研究了反铂抗癌药物trans-[PtCl2(piperidine)(Am)](Am=2-picoline(1),3-picoline(2),4-picoline(3)),trans-[PtCl2(piperidine)(piperazine)](4),trans-[PtCl2(pipera-zine)2](5)and trans-[PtCl2(iminoether)2](6)的水解过程.水解反应是药物与DNA靶分子作用的关键活化步骤.全优化和表征了一水解和二水解反应经由一般的SN2路径过程所有物种的势能面稳定点.结果发现反应过程遵循已经建立的平面正方形配合物的配体取代反应理论,即取代反应通常通过一个三角双锥过渡态结构的铂配体交换反应发生.得到的过渡态结构与以前的相关工作一致,所有反应都是吸热反应;所有体系的二水解能垒都高于一水解.与顺铂相比,这些配合物都有更快的水解反应速率;并与以前类似的反铂配合物的研究做了比较.研究结果提供了这些配合物水解反应过程的详细能量变化,对理解药物与DNA靶分子的作用机理和新型反铂抗癌药物的设计有帮助.     

Experimental and Theoretical Insight into the Kinetics and Mechanism of the Synthesis Reaction of 2,3‐Dihydro‐2‐phenylquinazolin‐4(1H)‐one Catalyzed in Formic Acid

An efficient and simple method has been developed for the synthesis of 2,3‐dihydro‐2‐phenylquinazolin‐4(1H )‐one catalyzed in formic acid. Also, the synthesis reaction between benzaldehyde and 2‐aminobenzamid was monitored spectrally. On the basis of the kinetic data obtained by the UV–vis spectrophotometry, both the first and second steps of the speculative five steps mechanism were enabled to be a rate‐determining step and also reaction showed second‐order kinetics. Considering information obtained by the stopped‐flow technique indicated that the first step is certainly a fast step. Moreover, the reaction was energetically and thermodynamically evaluated using theoretical methods and results were profoundly compared with the experimental approaches. Herein, theoretical rate constants were obtained using potential energy surfaces and the transition state theory at the B3LYP/6–311+G** level of theory. The Winger method was also applied to describe the tunneling effects. Calculations showed that the second step was the rate‐determining step in accordance with the experimental data. It is also found that the oxidation step was the fastest step in the proposed mechanism. For all five steps, two possibilities were considered for generating the probable product by using the thermodynamic parameters and kinetic data. Thermodynamic parameters also showed an exothermic reaction.     

Pyrrolo[2,3-d]pyrimidine thymidylate synthase inhibitors: design and synthesis of one-carbon bridge derivatives

A series of novel pyrrolo[2,3-d]pyrimidine derivatives was designed and synthesized as thymidylate synthase (TS) inhibitors. Molecular design was performed on the human TS complex model built on the basis of the reported structure of TS-deoxyuridinemonophosphate (dUMP)-CB3717 ternary complex. From a docking study, we expected that a one-carbon bridge between pyrrolo[2,3-d]pyrimidine and an aromatic ring was suitable. Moreover, we found that the bridge carbon could be replaced with an alkyl group to fill out the unoccupied space. Based on this design, we synthesized five pyrrolo[2,3-d]pyrimidine derivatives with one-carbon bridge and evaluated their TS inhibitory activities. All synthesized compounds inhibited TS more potently than compound 2 (LY231514), and the C8-ethyl analogue (7) showed a remarkable inhibitory activity against TS (IC50=0.017 microM).