Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.

Synthesis of Bis(amino acids) Containing the Styryl-cyclobutane Core by Photosensitized [2+2]-Cross-cycloaddition of Allylidene-5(4H)-oxazolones

The irradiation of 2-aryl-4-(E-3'-aryl-allylidene)-5(4H)-oxazolones 1 with blue light (456 nm) in the presence of [Ru(bpy)₃](BF₄)₂ (bpy = 2,2'-bipyridine, 5% mol) gives the unstable cyclobutane-bis(oxazolones) 2 by [2+2]-photocycloaddition of two oxazolones 1. Each oxazolone contributes to the formation of 2 with a different C=C bond, one of them reacting through the exocyclic C=C bond, while the other does so through the styryl group. Treatment of unstable cyclobutanes 2 with NaOMe/MeOH produces the oxazolone ring opening reaction, affording stable styryl-cyclobutane bis(amino acids) 3. The reaction starts with formation of the T₁ excited state of the photosensitizer ³[Ru*(bpy)₃]²⁺, which reacts with S₀ of oxazolones 1 through energy transfer to give the oxazolone T₁ state ³(oxa*)-1, which is the reactive species and was characterized by transient absorption spectroscopy. Measurement of the half-life of ³(oxa*)-1 for 1a, 1b and 1d shows large values for 1a and 1b (10-12 μs), while that of 1d is shorter (726 ns). Density functional theory (DFT) modeling displays strong structural differences in the T₁ states of the three oxazolones. Moreover, study of the spin density of T₁ state ³(oxa*)-1 provides clues to understanding the different reactivity of 4-allylidene-oxazolones described here with respect to the previously reported 4-arylidene-oxazolones.

Mechanistic Aspects on [3+2] Cycloaddition (32CA) Reactions of Azides to Nitroolefins: A Computational and Kinetic Study

[3+2] cycloadditions of nitroolefins have emerged as a selective and catalyst-free alternative for the synthesis of 1,2,3-triazoles from azides. We describe mechanistic studies into the cycloaddition/rearomatization reaction sequence. DFT calculations revealed a rate-limiting cycloaddition step proceeding via an asynchronous TS with high kinetic selectivity for the 1,5-triazole. Kinetic studies reveal a second-order rate law, and ¹³ C kinetic isotopic effects at natural abundance were measured with a significant normal effect at the conjugated olefinic centers of 1.0158 and 1.0216 at the α and β-carbons of β-nitrostyrene. Distortion/interaction-activation strain and energy decomposition analyses revealed that the major regioisomeric pathway benefits from an earlier and less-distorted TS, while intermolecular interaction terms dominate the preference for 1,5- over 1,4-cycloadducts. In addition, the major regioisomer also has more favorable electrostatic and dispersion terms. Additionally, while static DFT calculations suggest a concerted but highly asynchronous Ei-type HNO₂ elimination mechanism, quasiclassical direct-dynamics calculations reveal the existence of a dynamic intermediate.

Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine

The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21^st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.

Mechanistic Studies Yield Improved Protocols for Base-Catalyzed Anti-Markovnikov Alcohol Addition Reactions

The catalytic anti-Markovnikov addition of alcohols to simple alkenes is a longstanding synthetic challenge. We recently disclosed the use of organic superbase catalysis for the nucleophilic addition of alcohols to activated styrene derivatives. This article describes mechanistic studies on this reversible reaction, including thermodynamic and kinetic profiling as well as computational modeling. Our findings show the negative entropy of addition is counterbalanced by an enthalpy that is most favored in nonpolar solvents. However, a large negative alcohol rate order under these conditions indicates excess alcohol sequesters the active alkoxide ion pairs, slowing the reaction rate. These observations led to an unexpected solution to a thermodynamically challenging reaction: use of less alcohol enables faster addition, which in turn allows for lower reaction temperatures to counteract Le Chatelier's principle. Thus, our original method has been improved with new protocols that do not require excess alcohol stoichiometry, enable an expanded alkene substrate scope, and allow for the use of more practical catalyst systems. The generality of this insight for other challenging hydroetherification reactions is also demonstrated through new alkenol cyclization and oxa-Michael addition reactions.

Homologation of Electron-Rich Benzyl Bromide Derivatives via Diazo C-C Bond Insertion

The ability to manipulate C-C bonds for selective chemical transformations is challenging and represents a growing area of research. Here, we report a formal insertion of diazo compounds into the "unactivated" C-C bond of benzyl bromide derivatives catalyzed by a simple Lewis acid. The homologation reaction proceeds via the intermediacy of a phenonium ion, and the products contain benzylic quaternary centers and an alkyl bromide amenable to further derivatization. Computational analysis provides critical insight into the reaction mechanism, in particular the key selectivity-determining step.

Phosphorus-mediated sp2-sp3 couplings for C-H fluoroalkylation of azines

Fluoroalkyl groups profoundly affect the physical properties of pharmaceuticals and influence almost all metrics associated with their pharmacokinetic and pharmacodynamic profile^1-4. Drug candidates increasingly contain trifluoromethyl (CF₃) and difluoromethyl (CF₂H) groups, and the same trend in agrochemical development shows that the effect of fluoroalkylation translates across human, insect and plant life^5,6. New fluoroalkylation reactions have undoubtedly stimulated this shift; however, methods that directly convert C-H bonds into C-CF₂X groups (where X is F or H) in complex drug-like molecules are rare^7-13. Pyridines are the most common aromatic heterocycles in pharmaceuticals¹⁴, but only one approach-via fluoroalkyl radicals-is viable for achieving pyridyl C-H fluoroalkylation in the elaborate structures encountered during drug development^15-17. Here we develop a set of bench-stable fluoroalkylphosphines that directly convert the C-H bonds in pyridine building blocks, drug-like fragments and pharmaceuticals into fluoroalkyl derivatives. No preinstalled functional groups or directing groups are required. The reaction tolerates a variety of sterically and electronically distinct pyridines, and is exclusively selective for the 4-position in most cases. The reaction proceeds through initial formation of phosphonium salts followed by sp²-sp³ coupling of phosphorus ligands-an underdeveloped manifold for forming C-C bonds.

Asymmetric Total Synthesis and Determination of the Absolute Configuration of (+)-Srilankenyne via Sequence-Sensitive Halogenations Guided by Conformational Analysis

This first asymmetric total synthesis of (+)-srilankenyne (1), a halogenated C15 tetrahydropyran acetogenin isolated from Aplysia oculifera, features a sequence-sensitive process guided by conformational analysis to solve the challenging problem of introducing halogens. A competing semipinacol rearrangement during the installation of C(12)-bromide was suppressed by our A^1,3 strain-controlled bromination protocol with support from X-ray crystallographic and computational studies. The C(10)-chloride was then placed by the Nakata chloromesylate-mediated chlorination.

Visible-Light-Mediated Heterocycle Functionalization via Geometrically Interrupted [2+2] Cycloaddition

The [2+2] photocycloaddition is the most valuable and intensively investigated photochemical process. Here we demonstrate that irradiation of N‐acryloyl heterocycles with blue LED light (440 nm) in the presence of an Ir^III complex leads to efficient and high yielding fused γ‐lactam formation across a range of substituted heterocycles. Quantum calculations show that the reaction proceeds via cyclization in the triplet excited state to yield a 1,4‐diradical; intersystem crossing leads preferentially to the closed shell singlet zwitterion. This is geometrically restricted from undergoing recombination to yield a cyclobutane by the planarity of the amide substituent. A prototropic shift leads to the observed bicyclic products in what can be viewed as an interrupted [2+2] cycloaddition.

Selective Halogenation of Pyridines Using Designed Phosphine Reagents

Halopyridines are key building blocks for synthesizing pharmaceuticals, agrochemicals, and ligands for metal complexes, but strategies to selectively halogenate pyridine C-H precursors are lacking. We designed a set of heterocyclic phosphines that are installed at the 4-position of pyridines as phosphonium salts and then displaced with halide nucleophiles. A broad range of unactivated pyridines can be halogenated, and the method is viable for late-stage halogenation of complex pharmaceuticals. Computational studies indicate that C-halogen bond formation occurs via an S_NAr pathway, and phosphine elimination is the rate-determining step. Steric interactions during C-P bond cleavage account for differences in reactivity between 2- and 3-substituted pyridines.

Asymmetric Organocatalyzed Aza-Henry Reaction of Hydrazones: Experimental and Computational Studies

The first asymmetric catalyzed aza-Henry reaction of hydrazones is presented. In this process, quinine was used as the catalyst to synthesize different alkyl substituted β-nitrohydrazides with ee up to 77 %. This ee was improved up to 94 % by a further recrystallization and the opposite enantiomer can be obtained by using quinidine as the catalyst, opening exciting possibilities in fields in which the control of chirality is vital, such as the pharmaceutical industry. Additionally, experimental and ab initio studies were performed to understand the reaction mechanism. The experimental results revealed an unexpected secondary kinetic isotope effect (KIE) that is explained by the calculated reaction pathway, which shows that the protonation of the initial hydrazone and the C-C bond forming reaction occur during a concerted process. This concerted mechanism makes the catalysis conceptually different to traditional base-promoted Henry and aza-Henry reactions.

Sulfonamide as amide isostere for fine-tuning the gelation properties of physical gels

(S)-2-Stearamidopentanedioic acid (C18-Glu) is a known LMW gelator that forms supramolecular gels in a variety of solvents. In this work, we have carried out the isosteric substitution of the amide group by a sulfonamide moiety yielding the new isosteric gelator (S)-2-(octadecylsulfonamido)pentanedioic acid (Sulfo-Glu). The gelation ability and the key properties of the corresponding gels were compared in terms of gelation concentration, gel-to-sol transition temperature, mechanical properties, morphology, and gelation kinetics in several organic solvents and water. This comparison was also extended to (S)-2-(4-hexadecyl-1H-1,2,3-triazol-4-yl)pentanedioic acid (Click-Glu), which also constitutes an isostere of C18-Glu. The stabilizing interactions were explored through computational calculations. In general, Sulfo-Glu enabled the formation of non-toxic gels at lower concentrations, faster, and with higher thermal-mechanical stabilities than those obtained with the other isosteres in most solvents. Furthermore, the amide-sulfonamide isosteric substitution also influenced the morphology of the gel networks as well as the release rate of an embedded antibiotic (vancomycin) leading to antibacterial activity in vitro against Staphylococcus aureus.

Simple iodoalkyne-based organocatalysts for the activation of carbonyl compounds

A novel approach for the formation of bisindolylmethane derivatives (BIMs) is described as a proof of concept to evaluate the catalytic capacity of iodoalkynes. The use of these derivatives is reported as an example of simple halogen bond-based organocatalyst. This kind of activation has not been used before for the synthesis of bisindolylmethane derivatives 3. Interestingly, the preparation of 3-(1H-indol-3-yl)-1-phenylbutan-1-one (8) has been also achieved for the first time with an iodoalkyne derivative. We prove the efficiency of this family of new catalysts by developing a simple and easy operational methodology, opening the door to the development of alternative catalysts in the area of halogen bond-based organocatalysts.

Unconventional Reactivity of Ethynylbenziodoxolone Reagents and Thiols: Scope and Mechanism

1,2-Dithio-1-alkenes are biologically active compounds widely implemented throughout organic synthesis, functional materials, coordination chemistry, and pharmaceuticals. Traditional methods for accessing 1,2-dithio-1-alkenes often demand transition metal catalysts, specialized or air-sensitive ligands, high temperatures, and disulfides (R2 S2 ). Herein, a general and efficient strategy utilizing ethynylbenziodoxolone (EBX) reagents and thiols is presented that results in the formation of 1,2-dithio-1-alkenes with excellent regioselectivity and stereoselectivity through unprecedented reactivity between the EBX and the thiol. This operationally simple procedure utilizes mild conditions, which result in a broad substrate scope and high functional-group tolerance. The observed unexpected reactivity has been rationalized through both experimental results and DFT calculations.

Heterobiaryl synthesis by contractive C-C coupling via P(V) intermediates

Heterobiaryls composed of pyridine and diazine rings are key components of pharmaceuticals and are often central to pharmacological function. We present an alternative approach to metal-catalyzed cross-coupling to make heterobiaryls using contractive phosphorus C-C couplings, also termed phosphorus ligand coupling reactions. The process starts by regioselective phosphorus substitution of the C-H bonds para to nitrogen in two successive heterocycles; ligand coupling is then triggered via acidic alcohol solutions to form the heterobiaryl bond. Mechanistic studies imply that ligand coupling is an asynchronous process involving migration of one heterocycle to the ipso position of the other around a central pentacoordinate P(V) atom. The strategy can be applied to complex drug-like molecules containing multiple reactive sites and polar functional groups, and also enables convergent coupling of drug fragments and late-stage heteroarylation of pharmaceuticals.

Proline bulky substituents consecutively act as steric hindrances and directing groups in a Michael/Conia-ene cascade reaction under synergistic catalysis

In this study, we report a highly stereoselective and versatile synthesis of spiro pyrazolones, promising motifs that are being employed as pharmacophores.

In this study, we report a highly stereoselective and versatile synthesis of spiro pyrazolones, promising motifs that are being employed as pharmacophores. The new synthetic strategy merges organocatalysis and metal catalysis to create a synergistic catalysis using proline derivatives and Pd catalysts. This protocol is suitable for late-stage functionalization, which is very important in drug discovery. Additionally, a thorough computational study proved to be very useful to elucidate the function of the different catalysts along the reaction, showing a peculiar feature: the –CPh₂OSiMe₃ group of the proline catalyst switches its role during the reaction. In the initial Michael reaction, this group plays its commonly-assumed role of bulky blocking group, but the same group generates π–Pd interactions and acts as a directing group in the subsequent Pd-catalyzed Conia-ene reaction. This finding might be very relevant especially for processes with many steps, such as cascade reactions, in which functional groups are assumed to play the same role during all reaction steps.

Understanding hydrogelation processes through molecular dynamics

Molecular dynamics (MD) is currently one of the preferred techniques employed to understand hydrogelation processes for its ability to include large amounts of atoms in computational calculations, since substantial amounts of solvent molecules are involved in gel formation.

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

We describe the preparation and characterization of two new unsymmetrical squaramide-based organogelators. The synthesis of the compounds was carried out by subsequent amine condensations starting from dimethyl squarate. The design of the gelators involved a squaramide core connected on one side to a long aliphatic chain and on the other side to a glutamic acid residue. The gelator bearing the free carboxylic groups showed a lower gelation capacity than its precursor diester derivative. Some selected gels were further studied by infrared spectroscopy, rheology and electron microscopy. Critical gelation concentrations and gel-to-sol transition temperatures were also determined for each case. In addition, the superior squaramide diester gelator was compared with an analogue triazole-based gelator in terms of critical gelation concentration, gelation kinetics and thermal phase transition.

Self-assembled fibrillar networks of a multifaceted chiral squaramide: supramolecular multistimuli-responsive alcogels

Chiral N,N'-disubstituted squaramide has been found to undergo self-assembly in a variety of alcoholic solvents at low concentrations leading to the formation of novel nanostructured supramolecular alcogels. The gels responded to thermal, mechanical, optical and chemical stimuli. Solubility studies, gelation ability tests and computer modeling of a series of structurally related squaramides proved the existence of a unique combination of non-covalent molecular interactions and favorable hydrophobic/hydrophilic balance in that drive the anisotropic growth of alcogel networks. The results have also revealed a remarkable effect of ultrasound on both the gelation kinetics and the properties of the alcogels.

Synthesis of luminescent squaramide monoesters: cytotoxicity and cell imaging studies in HeLa cells

Luminescent squaramide monoesters functionalised with fluorophore groups have been explored as cytotoxic and imaging agents. The biodistribution behaviour differs depending on the fluorescent moiety; lysosomal and nuclear localisation have been observed.

Regulatory parameters of self-healing alginate hydrogel networks prepared via mussel-inspired dynamic chemistry

Key parameters that influence the self-healing and water retention properties of hydrogels made of alginate–dopamine conjugates have been revealed.

Squaramides with cytotoxic activity against human gastric carcinoma cells HGC-27: synthesis and mechanism of action

A series of squaramates and squaramides have been synthesized and their cytotoxic activity has been investigated in different cancer cell lines.

One-pot synthesis of unsymmetrical squaramides

The results concerning the first one-pot synthesis of unsymmetrical squaramides are reported.

Organocatalytic enantioselective hydrophosphonylation of aldehydes

We report our results concerning the first squaramide-catalysed hydrophosphonylation of aldehydes. In all cases, the reactions proceeded smoothly and cleanly under mild reaction conditions rendering final α-hydroxy phosphonates in very good yields and high enantioselectivities. It is one of the few organocatalytic examples of this reaction using aldehydes. It is the first time that diphenylphosphite (1e) has been successfully employed in a chiral Pudovik reaction with aldehydes, in contrast to the dialkylphosphites used in previously published procedures, extending the generality of this asymmetric methodology.

Guanidine Motif in Biologically Active Peptides

In the past decade, guanidines have attracted attention as valuable hydrogen bond-based catalysts while they have long been considered as organic superbases with a broad scope of synthetic applicability. Their easy modification has also expanded their capacity to form complexes with a wide range of metal salts as effective metal scavengers. All these attractive aspects have promoted a huge growth in the field of organic synthesis involving guanidines and examples of such reactions have been collected in numerous reviews and some books. Moreover, this structural motif is also present in a large number of natural products and biologically active compounds that exhibit appealing properties and play important roles in medicinal chemistry. In this highlight, we will only cover the synthesis and properties of biologically active guanidine-containing peptides reported in the past 3 years.