Mechanism Of Stereoselectivity Research Articles

Mechanistic Insights into a Chiral Phosphoric Acid-Catalyzed Asymmetric Pinacol Rearrangement.

The first catalytic enantioselective pinacol rearrangement was reported by Antilla and co-workers in 2010. The reaction was catalyzed by a chiral phosphoric acid and resulted in high levels of enantioselectivity (up to 96% ee). The present study uses density functional theory to investigate the mechanism and origins of stereoselectivity of this important reaction and to explain the difference in selectivity between different catalysts. An OH···O hydrogen bond between the intermediate indolyl alcohol and the phosphate group from the catalyst together with a CH···O hydrogen bond between the indole and the phosphate group were observed in the preferred activation mode for the stereodetermining [1,2]-aryl shift. A stronger CH···O interaction in the major transition state was found to contribute to the high levels of enantioselectivity. A more bulky catalyst (TRIP) was found to impede the formation of the key CH···O interaction, leading to lower levels of enantioselectivity.

Asymmetric phosphoric acid-catalyzed four-component Ugi reaction.

The Ugi reaction constructs α-acylaminoamide compounds by combining an aldehyde or ketone, an amine, a carboxylic acid, and an isocyanide in a single flask. Its appealing features include inherent atom and step economy together with the potential to generate products of broad structural diversity. However, control of the stereochemistry in this reaction has proven to be a formidable challenge. We describe an efficient enantioselective four-component Ugi reaction catalyzed by a chiral phosphoric acid derivative that delivers more than 80 α-acylaminoamides in good to excellent enantiomeric excess. Experimental and computational studies establish the reaction mechanism and origins of stereoselectivity.

Enantioselective, Noncovalent, Substrate-Directable Heck-Matsuda and Oxidative Heck Arylations of Unactivated Five-Membered Carbocyclic Olefins.

Highly diastereo- and enantioselective, noncovalent, substrate-directable Heck desymmetrizations of cyclopentenyl olefins containing hydroxymethyl and carboxylate functional groups are presented. These conformationally unbiased cyclic olefins underwent effective arylations in yields of up to 97 %, diastereoselectivity up to >20:1, and enantiomeric excesses of up to 99 %. Noncovalent directing effects were shown to be prevalent in both Heck-Matsuda and oxidative Heck reactions, allowing the preferential formation of cis-substituted aryl cyclopentenes containing two stereocenters, including quaternary stereocenters. These results further validate the internal out-of-coordination-sphere ion-dipole interaction concept directing the reaction diastereoselectivity to the cis-Heck product. This approach is complementary to existing methods using bis-phosphine monoxide ligands to give the opposite trans-diastereoisomer. The applicability of the method is showcased by the straightforward synthesis of a potent phosphodiesterase 4 inhibitor in a diastereo- and enantioselective manner. The reaction is operationally simple and has broad scope with regard to the nature of the arenediazonium salt and boronic acid employed. The mechanism and origin of stereoselectivity were investigated with control experiments and DFT calculations that fully supported the stabilizing internal out-of-coordination-sphere ion-dipole interaction between the resident functional group and cationic palladium.

Evidence for a Stereoselective Mechanism of Action for Non‐competitive Antagonism of the D3 Dopamine Receptor by Extended‐Length Bitopic Ligands

Dopamine receptors (DRs) are comprised of two subfamilies based on structure and pharmacology: D1‐like (D1R and D5R) and D2‐like (D2R, D3R, and D4R). The D3R expression is more restricted to the limbic system, as compared to the D2R, suggesting that modulation of the D3R may be useful for treating substance abuse or psychosis‐related disorders without the motor side effects associated with D2R blockade. Extensive structure‐activity relationship investigations indicate that D3R‐selective antagonists with extended‐length structures engage two distinct sites on the receptor. The extended‐length ligand's primary pharmacophore (PP) binds to the orthosteric site whereas the ligand's secondary pharmacophore (SP) interacts with a unique secondary binding pocket (SBP). Bivalent compounds that concurrently engage both the orthosteric site and a SBP that has allosteric properties, have been termed “bitopic”. We previously synthesized and characterized several extended‐length compounds with a conformationally restricted trans‐cyclopropyl linking chain based on the structure of SB269,652, a potent D3R‐preferring bitopic antagonist that acts in a noncompetitive/allosteric manner at both the D3R and the D2R. We found that relatively subtle changes in both the linker and the SP can affect the competitive/noncompetitive nature of the compounds, and identified two novel ligands that behave as noncompetitive antagonists at the D3R. We resolved the optical isomers of one of these compounds (VK04‐87) to gain a better understanding of the molecular basis of their allosteric activity. We found that the (+)‐isomer has higher affinity and is more D3R>D2R selective than the (−)‐isomer. Strikingly, using beta‐arrestin recruitment assays as a functional output, we found that (+)‐VK04‐87 inhibits the D3R in a non‐competitive manner, while (−)‐VK04‐87 behaves as a competitive antagonist. These data suggest that the bitopic interactions of VK04‐87 with the D3R are stereoselective in nature with the allosteric properties residing with the (+)‐isomer. To further investigate, we made a mutation (E90A) in the secondary binding pocket of the D3R that was previously found to decrease the affinity and negative cooperativity of SB269,652 for the D2R. We found that this mutation decreased the affinity of extended‐length ligands, including SB269,652, for the D3R, but had no effect on the affinities of smaller, competitive antagonists consisting of PPs. Further analyses of the interactions of the extended‐length ligands with the D3R E90A mutant are ongoing. These studies could help to determine how ligand interactions with the SBP can be utilized to engender allosterism, potentially producing compounds with unique pharmacological effects.Support or Funding InformationNINDS IRPThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

How membrane lipids control the 3D structure and function of receptors

The cohabitation of lipids and proteins in the plasma membrane of mammalian cells is controlled by specific biochemical and biophysical rules. Lipids may be either constitutively tightly bound to cell-surface receptors (non-annular lipids) or less tightly attached to the external surface of the protein (annular lipids). The latter are exchangeable with surrounding bulk membrane lipids on a faster time scale than that of non-annular lipids. Not only do non-annular lipids bind to membrane proteins through stereoselective mechanisms, they can also help membrane receptors acquire (or maintain) a functional 3D structure. Cholesterol is the prototype of membrane lipids that finely controls the 3D structure and function of receptors. However, several other lipids such as sphingolipids may also modulate the function of membrane proteins though conformational adjustments. All these concepts are discussed in this review in the light of representative examples taken from the literature.

Insights into the NHC-catalyzed cascade Michael/aldol/lactamization reaction: mechanism and origin of stereoselectivity

A DFT study of the NHC-catalyzed cascade Michael/aldol/lactamization reaction has been performed for the first time.

Mechanism and Origins of Ligand-Controlled Stereoselectivity of Ni-Catalyzed Suzuki-Miyaura Coupling with Benzylic Esters: AComputational Study.

Nickel catalysts have shown unique ligand control of stereoselectivity in the Suzuki-Miyaura cross-coupling of boronates with benzylic pivalates and derivatives involving C(sp3)-O cleavage. The SIMes ligand (1,3-dimesityl-4,5-dihydroimidazol-2-ylidene) produces the stereochemically inverted C-C coupling product, while the tricyclohexylphosphine (PCy3) ligand delivers the retained stereochemistry. We have explored the mechanism and origins of the ligand-controlled stereoselectivity with density functional theory (DFT) calculations. The oxidative addition determines the stereoselectivity with two competing transition states, an SN2 back-side attack type transition state that inverts the benzylic stereogenic center and a concerted oxidative addition through a cyclic transition state, which provides stereoretention. The key difference between the two transition states is the substrate-nickel-ligand angle distortion; the ligand controls the selectivity by differentiating the ease of this angle distortion. For the PCy3 ligand, the nickel-ligand interaction involves mainly σ-donation, which does not require a significant energy penalty for the angle distortion. The facile angle distortion with PCy3 ligand allows the favorable cyclic oxidative addition transition state, leading to the stereoretention. For the SIMes ligand, the extra d-p back-donation from nickel to the coordinating carbene increases the rigidity of the nickel-ligand bond, and the corresponding angle distortion is more difficult. This makes the concerted cyclic oxidative addition unfavorable with SIMes ligand, and the back-side SN2-type oxidative addition delivers the stereoinversion.

Isospecific, Chain Shuttling Polymerization of Propylene Oxide Using a Bimetallic Chromium Catalyst: A New Route to Semicrystalline Polyols.

Hydroxy-telechelic poly(propylene oxide) (PPO) is widely used industrially as a midsegment in polyurethane synthesis. These atactic polymers are produced from racemic propylene oxide using chain shuttling agents and double-metal cyanide catalysts. Unlike atactic PPO, isotactic PPO is semicrystalline with a melting temperature of approximately 67 °C. Currently there is no practical route to hydroxy-telechelic isotactic PPO using racemic propylene oxide as the monomer. In this paper, hydroxy-telechelic isotactic PPO is synthesized from racemic propylene oxide with control of molecular weight using enantioselective and isoselective bimetallic catalysts in conjunction with chain shuttling agents. The discovery of an easily accessible bimetallic chromium catalyst is reported for this transformation. Diol, triol, and polymeric chain shuttling agents are used to give hydroxy-telechelic isotactic PPO of varying functionality and structure. Detailed quantum chemical studies are used to reveal the polymerization mechanism and origin of stereoselectivity.

Hypercoordinate Iodine Catalysts in Enantioselective Transformation: The Role of Catalyst Folding in Stereoselectivity

The need for metal-free environmentally benign catalysts has provided a strong impetus toward the emergence of hypercoordinate iodine reagents. At this stage of development, molecular insights on the mechanism and origin of stereoselectivity are quite timely. In this study, the origin of stereoinduction in a class of iodoresorcinol-based chiral hypercoordinate iodine-catalyzed synthesis of biologically important spirocyclic bisoxindoles from aryl dianilides has been established by using density functional computations. Formation of an interesting helical fold by the 2,6-chiral amide arms on the resorcinol framework is found to be facilitated by a network of noncovalent interactions. In the chiral environment provided by the helical fold, enantioselectivity is surprisingly controlled in a mechanistic event prior to the ring closure to the final spirocyclic product, unlike that commonly found in spirocyclic ring formation. A vital 1,3-migration of the chiral aryl iodonium (Ar*-I(CF3COO)) in an O-iodonium en...

Mechanism and Origins of Stereoselectivity in the Cinchona Thiourea- and Squaramide-Catalyzed Asymmetric Michael Addition of Nitroalkanes to Enones.

We report density functional theory calculations that examine the mechanism and origins of stereoselectivity of Soós' landmark discovery from 2005 that cinchona thioureas catalyze the asymmetric Michael addition of nitroalkanes to enones. We show that the electrophile is activated by the catalyst's protonated amine and that the nucleophile binds to the thiourea moiety by hydrogen bonding. These results lead to the correction of published mechanistic work which did not consider this activation mode. We have also investigated the corresponding cinchona squaramide-catalyzed reaction and found that it proceeds by the same mechanism despite the differences in the geometry of the two catalysts' hydrogen-bond-donating groups, which demonstrates the generality of this mechanistic model.

Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed by (+)-Limonene Synthase from Citrus sinensis Using Fluorinated Substrate Analogues.

The stereochemical course of monoterpene synthase reactions is thought to be determined early in the reaction sequence by selective binding of distinct conformations of the geranyl diphosphate (GPP) substrate. We explore here formation of early Michaelis complexes of the (+)-limonene synthase [(+)-LS] from Citrus sinensis using monofluorinated substrate analogues 2-fluoro-GPP (FGPP) and 2-fluoroneryl diphosphate (FNPP). Both are competitive inhibitors for (+)-LS with KI values of 2.4 ± 0.5 and 39.5 ± 5.2 μM, respectively. The KI values are similar to the KM for the respective nonfluorinated substrates, indicating that fluorine does not significantly perturb binding of the ligand to the enzyme. FGPP and FNPP are also substrates, but with dramatically reduced rates (kcat values of 0.00054 ± 0.00005 and 0.00024 ± 0.00002 s-1, respectively). These data are consistent with a stepwise mechanism for (+)-LS involving ionization of the allylic GPP substrate to generate a resonance-stabilized carbenium ion in the rate-limiting step. Crystals of apo-(+)-LS were soaked with FGPP and FNPP to obtain X-ray structures at 2.4 and 2.2 Å resolution, respectively. The fluorinated analogues are found anchored in the active site through extensive interactions involving the diphosphate, three metal ions, and three active-site Asp residues. Electron density for the carbon chains extends deep into a hydrophobic pocket, while the enzyme remains mostly in the open conformation observed for the apoprotein. While FNPP was found in multiple conformations, FGPP, importantly, was in a single, relatively well-defined, left-handed screw conformation, consistent with predictions for the mechanism of stereoselectivity in the monoterpene synthases.

Computational Studies on Reaction Mechanism and Origins of Selectivities in Nickel-Catalyzed (2 + 2 + 2) Cycloadditions and Alkenylative Cyclizations of 1,6-Ene-Allenes and Alkenes.

The reaction mechanism and origins of ligand-controlled selectivity, regioselectivity, and stereoselectivity of Ni-catalyzed (2 + 2 + 2) cycloadditions and alkenylative cyclizations of 1,6-ene-allenes and alkenes were studied by using density functional theory. The catalytic cycle involves intermolecular oxidative coupling and an intramolecular concerted 1,4-addition step to afford a stable metallacycloheptane intermediate; these steps determine both the regioselectivity and stereoselectivity. Subsequent C-C reductive elimination leads to the cyclohexane product, whereas the β-hydride elimination leads to the trans-diene product. The selectivity between (2 + 2 + 2) cycloadditions and alkenylative cyclizations is controlled by the ligand. Irrespective of the nature of the terminal substituents on the ene-allene and alkene, the P(o-tol)3 ligand always favors the C-C reductive elimination, resulting in the cyclohexane product. On the other hand, the flexibility of the PBu3 ligand means that electronic and steric factors play important roles. Electron-withdrawing groups such as CO2Me in the ene-allene terminal substituent induce obvious substrate-ligand repulsion and destabilize the C-C reductive elimination, giving rise to the trans-diene product.

Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity.

Plants produce an enormous array of biologically active metabolites, often with stereochemical variations on the same molecular scaffold. These changes in stereochemistry dramatically impact biological activity. Notably, the stereoisomers of the heteroyohimbine alkaloids show diverse pharmacological activities. We reported a medium chain dehydrogenase/reductase (MDR) from Catharanthus roseus that catalyses formation of a heteroyohimbine isomer. Here we report the discovery of additional heteroyohimbine synthases (HYSs), one of which produces a mixture of diastereomers. The crystal structures for three HYSs have been solved, providing insight into the mechanism of reactivity and stereoselectivity, with mutation of one loop transforming product specificity. Localization and gene silencing experiments provide a basis for understanding the function of these enzymes in vivo. This work sets the stage to explore how MDRs evolved to generate structural and biological diversity in specialized plant metabolism and opens the possibility for metabolic engineering of new compounds based on this scaffold.

Regioselectivity and stereoselectivity of Diels-Alder reaction: a DFT study on the functionalization of organic semiconductor crystals

Diels–Alder (DA) reaction is one of the most commonly tools in functionalizing organic semiconductor crystals. The DA reactions of two organic semiconductors, i.e. tetracene () and rubrene (), to several dienophiles ( to ) were performed experimentally recently. But the kinetics and mechanism of stereoselectivity and regioselectivity remain unknown. In the current study, all related 20 DA reactions (totally 32 possible pathways) were investigated by density functional theory. It was found that the reaction of and a–b position of is the most favorable one. The c–d position of is more reactive than its a–b position when combines with , but is less reactive when combines with to . The endo and exo pathways have similar activation barriers in each reaction. The rate coefficients were calculated using the canonical variational transition state theory and their Arrhenius expressions were fitted. The theoretical conclusion agrees with the experimental observations and is of general importance for similar reactions. Solvent has a slight effect on these reactions. Copyright © 2016 John Wiley & Sons, Ltd.

Mechanism and origin of stereoselectivity in Robinson annulations leading to bicyclo[3.3.1]nonanes: a rare Curtin–Hammet scenario

Computational studies on the mechanism and diastereoselectivity of base catalyzed synthesis of bicyclo[3.3.1]nonanes by Robinson annulation are reported. Three possible mechanisms were considered, and only the methanol assisted H‐shift process could be the favorable pathway. We have discovered a rare Curtin–Hammet scenario: rate determining steps for the two diastereomeric products formed are completely different reactions, and a correction factor should be considered when gauging the ratio of products from competing pathways. The pathway leading to the anti product is kinetically preferred, which is consistent with experimental results. Finally, the ratio of the two products was rationalized. Copyright © 2016 John Wiley & Sons, Ltd.

Crystal structure, computational studies, and stereoselectivity in the synthesis of 2-aryl-thiazolidine-4-carboxylic acids via in situ imine intermediate

ABSTRACTThis article presents the synthesis of (2R/2S,4R)-2-aryl-thiazolidine-4-carboxylic acids via nucleophilic addition of L-Cysteine on aromatic aldehydes involving a yield and time-effective room temperature reaction in an aqueous DMSO medium in the presence of NaHCO3 as a base. The synthesized diastereomers were spectroscopically characterized and quantified for diastereomeric excess by liquid chromatography-mass spectrometry analysis. The impact of the type and position of substituent in aromatic aldehydes on reaction time, % yield, 1H NMR shift at newly formed chiral center [C(2)-H], and diastereomeric excess (de%) have been investigated. A plausible mechanism for stereoselectivity via an in situ imine intermediate is proposed using real-time IR monitoring of the synthetic reaction based on the significant signals at 1597, 1593 cm−1 for imine (C=N) stretching. The imine mechanism for stereoselectivity was further supported by NMR studies of azomethine 13C NMR signals at 159, 160 δ ppm and by the single crystal structure of hitherto unknown (2S,4R)-3-(tert-butoxycarbonyl)-2-(2-hydroxyphenyl)thiazolidine-4-carboxylic acid (3a) obtained as a major diastereomer in the synthesis of the butyloxy carbonyl (BOC) derivative of (2R/2S,4R)-2-(2-hydroxyphenyl)thiazolidine-4-carboxylic acid. The significant ortho-OH effect of phenolic hydroxyl group leading to strong hydrogen bondings plays a vital role in the formation of 2S,4R BOC derivative stereoselectively. The frontier molecular orbitals, possible electronic excitations, IR band characterizations, and reactivity parameters of newly reported compound (3a) have been predicted using quantum chemical descriptors from density functional theory. The theoretical exploration of experimental spectra using time-dependent DFT indicated a (π–π*) transition between HOMO and LUMO in the ultraviolet region.

Development and Pharmacological Characterization of Selective Blockers of 2-Arachidonoyl Glycerol Degradation with Efficacy in Rodent Models of Multiple Sclerosis and Pain

We report the discovery of compound 4a, a potent β-lactam-based monoacylglycerol lipase (MGL) inhibitor characterized by an irreversible and stereoselective mechanism of action, high membrane permeability, high brain penetration evaluated using a human in vitro blood-brain barrier model, high selectivity in binding and affinity-based proteomic profiling assays, and low in vitro toxicity. Mode-of-action studies demonstrate that 4a, by blocking MGL, increases 2-arachidonoylglycerol and behaves as a cannabinoid (CB1/CB2) receptor indirect agonist. Administration of 4a in mice suffering from experimental autoimmune encephalitis ameliorates the severity of the clinical symptoms in a CB1/CB2-dependent manner. Moreover, 4a produced analgesic effects in a rodent model of acute inflammatory pain, which was antagonized by CB1 and CB2 receptor antagonists/inverse agonists. 4a also relieves the neuropathic hypersensitivity induced by oxaliplatin. Given these evidence, 4a, as MGL selective inhibitor, could represent a valuable lead for the future development of therapeutic options for multiple sclerosis and chronic pain.

Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1.

As one of the most successful anticancer drugs, crizotinib is found to be efficient in the suppression of MTH1, a new therapeutic target for RAS-dependent cancers. Deep analysis shows that stereospecificity is prevalent in the binding of crizotinib to MTH1, where the target is more preferred to bind with the (S)-enantiomer of crizotinib. Surprisingly, very similar binding modes were found for the two enantiomers (Huber et al. Nature 2014, 508, 222-227), which puzzled us to ask a question as to why such a subtle structural variation could lead to so large of a binding affinity difference. Thereafter, by using advanced all-atom molecular dynamics simulations, we characterized the free energy surfaces of the binding/unbinding processes of the (S) and (R)-crizotinib enantiomers to/from MTH1. Interestingly, we found that rather than the induced-fit process, which is prevalent in drug selectivity and specificity (Wilson et al. Science 2015, 347, 882-886), the directly binding process has dominated impact on the binding affinity difference of the enantiomers, implying a common mechanism of stereoselectivity of enantiomers.

Pentanidium-Catalyzed Asymmetric Phase-Transfer Conjugate Addition: Prediction of Stereoselectivity via DFT Calculations and Docking Sampling of Transition States, and Origin of Stereoselectivity

Density functional theory (DFT) study, at the M06–2X/6–311+G(d,p)//M06–2X/6–31G(d,p) level, was carried out to examine the catalytic mechanism and origin of stereoselectivity of pentanidium-catalyzed asymmetric phase-transfer conjugate addition. We employed a hybrid approach by combining automated conformation generation through molecular docking followed by subsequent DFT calculation to locate various possible transition states for the enantioselective conjugate addition. The calculated enantioselectivity (enantiomeric excess), based on the key diastereomeric C–C bond-forming transition states, is in good accord with experimental result. Non-covalent interaction analysis of the key transition states reveals extensive non-covalent interactions, including aromatic interactions, hydrogen bonds, and non-classical C–H⋯O interactions between the pentanidium catalyst and substrates. The origin of stereoselectivity was analysed using a strain-interaction model.

Human Liver Cytochrome P450 Enzymes and Microsomal Thiol Methyltransferase Are Involved in the Stereoselective Formation and Methylation of the Pharmacologically Active Metabolite of Clopidogrel.

Clopidogrel, a thienopyridine antiplatelet prodrug, is metabolized by oxidation to 2-oxo-clopidogrel, followed by conversion to its pharmacologically active thiol metabolite. After oral administration of clopidogrel to humans, two thiol isomers (H3 and H4) are observed in plasma, with similar concentrations, and only H4 is active in humans. In this work, the mechanism of stereoselectivity in the formation and S-methylation of H3 and H4 was investigated in vitro. The two diastereomers of 2-oxo-clopidogrel were epimerized rapidly at physiologic pH. The intrinsic clearance (CLint) for H3 formation from 2-oxo-clopidogrel in human liver microsomes (HLMs) was 3.1-fold higher than that for H4 formation, indicating stereoselective metabolism. Kinetic studies using expressed enzymes demonstrated that the contributions of CYP2B6, CYP2C19, and CYP3A4 to the formation of H4 from 2-oxo-clopidogrel were 18.5%, 26.1%, and 53.5%, respectively. The CLint ratios of H3 formation to H4 formation from 2-oxo-clopidogrel by CYP2B6, CYP2C19, and CYP3A4 were 2.2, 1.0, and 1.7, respectively. In HLMs, H3 and H4 were further S-methylated, and the S-methylation was inhibited by 2,3-dichloromethyl benzylamine, indicating the involvement of thiol S-methyltransferase. The CLint value for the S-methylation of H3 in HLMs was 98.1-fold higher than that for H4. The stereoselective formation of H3 from 2-oxo-clopidogrel and the stereoselective S-methylation of H3 may lead to the similar exposure levels of H3 and H4 previously reported in humans. The epimerization of 2-oxo-clopidogrel and the variations of thiol S-methyltransferase may affect the exposure to H4 in humans.