Tetrapyrrolic Pigments from Heme- and Chlorophyll Breakdown are Actin-Targeting Compounds.

Chlorophyll and heme are among the "pigments of life", tetrapyrrolic structures, without which life on Earth would not be possible. Their catabolites, the phyllobilins and the bilins, respectively, share not only structural features, but also a similar story: Long considered waste products of detoxification processes, important bioactivities for both classes have now been demonstrated. For phyllobilins, however, research on physiological roles is sparse. Here, we introduce actin, the major component of the cytoskeleton, as the first discovered target of phyllobilins and as a novel target of bilins. We demonstrate the inhibition of actin dynamics in vitro and effects on actin and related processes in cancer cells. A direct interaction with G-actin is shown by in silico studies and confirmed by affinity chromatography. Our findings open a new chapter in bioactivities of tetrapyrroles-especially phyllobilins-for which they form the basis for broad implications in plant science, ecology, and physiology.

Concerted [4 + 2] and Stepwise (2 + 2) Cycloadditions of Tetrafluoroethylene with Butadiene: DFT and DLPNO-UCCSD(T) Explorations.

Tetrafluoroethylene and butadiene form the 2 + 2 cycloadduct under kinetic control, but the Diels-Alder cycloadduct is formed under thermodynamic control. Borden and Getty showed that the preference for 2 + 2 cycloaddition is due to the necessity for syn-pyramidalization of the two CF2 groups in the 4 + 2 transition state. We have explored the full potential energy surface for the concerted and stepwise reactions of tetrafluoroethylene and butadiene with density functional theory, DFT (B3LYP and M06-2X), DLPNO-UCCSD(T), and CASSCF-NEVPT2 methods and with the distortion/interaction-activation strain model to explain the energetics of different pathways. The 2 + 2 cycloadduct is formed by an anti-transition state followed by two rotations and a final bond formation transition state. Energetics are compared to the reaction of maleic anhydride and ethylene.

Navigating Past a Fork in the Road: Carbocation-π Interactions Can Manipulate Dynamic Behavior of Reactions Facing Post-Transition-State Bifurcations.

Dynamics calculations are described for carbocation rearrangements involving product-forming pathways with post-transition-state bifurcations. We show that noncovalent interactions with associated benzene rings (a simple model of aromatic amino acid side chains) can switch inherent dynamical tendencies for competing modes of disrotation, establishing that meaningful changes in dynamically controlled product selectivity can be achieved with few weak noncovalent interactions.

Activation Pathway of a Nucleoside Analog Inhibiting Respiratory Syncytial Virus Polymerase.

Human respiratory syncytial virus (RSV) is a negative-sense RNA virus and a significant cause of respiratory infection in infants and the elderly. No effective vaccines or antiviral therapies are available for the treatment of RSV. ALS-8176 is a first-in-class nucleoside prodrug inhibitor of RSV replication currently under clinical evaluation. ALS-8112, the parent molecule of ALS-8176, undergoes intracellular phosphorylation, yielding the active 5'-triphosphate metabolite. The host kinases responsible for this conversion are not known. Therefore, elucidation of the ALS-8112 activation pathway is key to further understanding its conversion mechanism, particularly given its potent antiviral effects. Here, we have identified the activation pathway of ALS-8112 and show it is unlike other antiviral cytidine analogs. The first step, driven by deoxycytidine kinase (dCK), is highly efficient, while the second step limits the formation of the active 5'-triphosphate species. ALS-8112 is a 2'- and 4'-modified nucleoside analog, prompting us to investigate dCK recognition of other 2'- and 4'-modified nucleosides. Our biochemical approach along with computational modeling contributes to an enhanced structure-activity profile for dCK. These results highlight an exciting potential to optimize nucleoside analogs based on the second activation step and increased attention toward nucleoside diphosphate and triphosphate prodrugs in drug discovery.

Predicting hydration propensities of biologically relevant α-ketoamides.

Quantum chemical calculations coupled to experiments were used to predict covalent hydration propensities of biologically relevant α-ketoamides. Experimentally determined hydration equilibrium constants for related ketones and aldehydes were compared to computationally determined values to develop a method for predicting hydration equilibrium constants. This method was used on six newly synthesized α-ketoamides to experimentally verify computational predictions. A correlation between calculation and experiment was observed and applied to models of several pertinent APIs. Our results indicate that the keto form is favored for practically all α-ketoamides in biological environs.

Total Synthesis of the Galbulimima Alkaloids Himandravine and GB17 Using Biomimetic Diels-Alder Reactions of Double Diene Precursors.

The enantioselective total syntheses of himandravine and GB17 were completed through a common biomimetic strategy involving Diels-Alder reactions of unusual double diene containing linear precursors. The double diene precursors, containing or lacking a C12 substituent as required to produce GB17 or himandravine, respectively, were found to undergo Diels-Alder reactions to afford mixtures of regioisomeric cycloadducts that map onto the alternative carbocyclic frameworks of both himandravine and GB17. Computational investigations revealed that these Diels-Alder reactions proceed via transition state structures of similar energy that have a high degree of bispericyclic character and that the low levels of regioselectivity observed in the reactions are a consequence of competing orbital interaction and distortion energies. The combined experimental and computational results provide valuable insights into the biosynthesis of the Galbulimima alkaloids.

Carbocations and the Complex Flavor and Bouquet of Wine: Mechanistic Aspects of Terpene Biosynthesis in Wine Grapes.

Computational chemistry approaches for studying the formation of terpenes/terpenoids in wines are presented, using five particular terpenes/terpenoids (1,8-cineole, α-ylangene, botrydial, rotundone, and the wine lactone), volatile compounds (or their precursors) found in wine and/or wine grapes, as representative examples. Through these examples, we show how modern computational quantum chemistry can be employed as an effective tool for assessing the validity of proposed mechanisms for terpene/terpenoid formation.

Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined.

Biomimetic total synthesis of santalin†Y.

A biomimetic total synthesis of santalin Y, a structurally complex but racemic natural product, is described. The key step is proposed to be a (3+2) cycloaddition of a benzylstyrene to a "vinylogous oxidopyrylium", which is followed by an intramolecular Friedel-Crafts reaction. This cascade generates the unique oxafenestrane framework of the target molecule and sets its five stereocenters in one operation. Our work provides rapid access to santalin Y and clarifies its biosynthetic relationship with other colorants isolated from red sandalwood.

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase.

The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase (epi-isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi-isozizaene appear to play important roles.

The viability of nitrone-alkene (3 + 2) cycloadditions in alkaloid biosynthesis.

Although evidence has mounted in recent years for the biosynthetic relevance of [4 + 2] cycloaddition reactions, other cycloadditions have received much less attention. Herein we used density functional theory (DFT) calculations to assess the viability of nitrone-alkene (3 + 2) cycloaddition reactions proposed to occur during the biosynthesis of several alkaloid natural products (flueggines and virosaines). The results of our calculations indicate that these reactions have low enough intrinsic barriers and diastereoselectivity that they can proceed without enzymatic intervention.

Brønsted acid catalyzed enantioselective indole aza-Claisen rearrangement mediated by an arene CH-O interaction.

Although the aromatic aza-Claisen rearrangement is a general strategy for accessing substituted aromatic amines, there are no highly enantioselective examples of this process. We report the first Brønsted acid catalyzed enantioselective indole aza-Claisen rearrangement for the synthesis of chiral 3-amino-2-substituted indoles. We present evidence for an arene CH-O interaction as a source of activation and stereoinduction, which is an unprecedented phenomenon in enantioselective Brønsted acid catalysis. The products of this reaction can be transformed into 3-aminooxindoles, which are prevalent in many biologically active small molecules.

Re-examining the mechanisms of competing pericyclic reactions of 1,3,7-octatriene.

DFT (both B3LYP and M06-2X), CASSCF, and CASPT2 calculations were used to investigate competing [3, 3] and [3, 5] sigmatropic shifts and intramolecular [4+2] cycloaddition of 1,3,7-octatriene. In accord with previous results on 1,5-hexadiene, CASSCF calculations found both stepwise and concerted pathways for the [3, 3] rearrangement. For the competing [3, 5] sigmatropic rearrangement, CASSCF and CASPT2 calculations revealed three stepwise pathways with similar barriers. UB3LYP and UM06-2X calculations predicted a different potential energy landscape: no stepwise [3, 3] pathway, only two competing [3, 5] sigmatropic shifts, and an intramolecular Diels-Alder cycloaddition/homolytic ring-opening pathway. Significant lowering of barriers for all rearrangements was predicted for some 1,3,7-octatrienes with substituents at the 4- and 7-positions.

Dynamic processes in [16]annulene: Möbius bond-shifting routes to configuration change.

Density functional and ab initio methods have been used to study the mechanisms for key dynamic processes of the experimentally known S4-symmetric [16]annulene (1a). Using BH&HLYP/6-311+G** and B3LYP/6-311+G**, we located two viable stepwise pathways with computed energy barriers (Ea = 8-10 kcal/mol) for conformational automerization of 1a, in agreement with experimental data. The transition states connecting these conformational minima have Möbius topology and serve as starting points for non-degenerate pi-bond shifting (configuration change) via Möbius aromatic transition states. The key transition state, TS1-2, that connects the two isomers of [16]annulene (CTCTCTCT, 1 --> CTCTTCTT, 2) has an energy, relative to the S4 isomer, that ranged from 6.9 kcal/mol (B3LYP/6-311+G**) to 16.7 kcal/mol (BH&HLYP/6-311+G**), bracketing the experimental barrier. At our best level of theory, CCSD(T)/cc-pVDZ(est), this barrier is 13.7 kcal/mol. Several other Möbius bond-shifting transition states, as well as Möbius topology conformational minima, were found with BH&HLYP energies within 22 kcal/mol of 1a, indicating that many possibilities exist for facile thermal configuration change in [16]annulene. This bond-shifting mechanism and the corresponding low barriers contrast sharply with those observed for cis/trans isomerization in acyclic polyenes, which occurs via singlet diradical transition states. All Möbius bond-shifting transition states located in [16]- and [12]annulene were found to have RHF --> UHF instabilities with the BH&HLYP method but not with B3LYP. This result appears to be an artifact of the BH&HLYP method. These findings support the idea that facile thermal configuration change in [4n]annulenes can be accounted for by mechanisms involving twist-coupled bond shifting.

[10]Annulene: bond shifting and conformational mechanisms for automerization.

We report density-functional and coupled-cluster calculations on conformation change and degenerate bond shifting in [10]annulene isomers 1-5. At the CCSD(T)/cc-pVDZ//CCSD/6-31G level, conversion of the twist (1) to the heart (2) has a barrier of 10.1 kcal/mol, compared to Ea = 16.2 kcal/mol for degenerate "two-twist" bond shifting in 1. Pseudorotation in the all-cis boat isomer (3) proceeds with a negligible barrier. The naphthalene-like isomer 4 has a 3.9 kcal/mol barrier to degenerate bond shifting. The azulene-like isomer 5 is the only species for which the nature of the bond-equalized form (5-eq) depends on the method. At the CCSD(T)/cc-pVDZ//CCSD/6-31G level, 5-eq is 1.2 kcal/mol more stable than the bond-alternating form 5-alt. Conversion of 5-eq to 4 has a barrier of 12.6 kcal/mol. Despite being significantly nonplanar, both 5-eq and the transition state for bond shifting in 4 are highly aromatic based on magnetic susceptibility exaltations. On the basis of a detailed consideration of these mechanisms and barriers, we can now, with greater confidence, rule out 4 and 5 as candidates to explain the NMR spectra observed by Masamune. Our results support Masamune's original assignments for both isolated isomers.

Möbius aromaticity in [12]annulene: cis-trans isomerization via twist-coupled bond shifting.

Density functional and coupled cluster calculations show that facile thermal configuration change in [12]annulene occurs via a twist-coupled bond-shifting mechanism. The transition state for this process is highly aromatic with Möbius topology. At the CCSD(T)/cc-pVDZ//BH&HLYP/6-311+G** level, the isomerization of tri-trans-[12]annulene 1a (CTCTCT) to its di-trans isomer 2 (CCCTCT) via such a mechanism has a barrier of 18.0 kcal/mol, in good agreement with earlier experiments. Two other aromatic Möbius bond-shifting transition states were located that result in configuration change for other [12]annulene conformers. This mechanism contrasts sharply with diradical configuration change for acyclic polyenes and with planar bond-shifting mechanisms generally assumed for annulenes. This constitutes evidence that neutral Möbius aromatic annulenes play a role in the dynamic processes of neutral [4n]annulenes.