The cation-π interaction

Dynamic Control of Self-Assembly of Amphiphilic Conjugated Alkenes in Water by Reactions

Nature sets a great example of how to precisely control self-assembly to obtain distinct structures upon external stimuli and perform specific functions to sustain important biological tasks. In the present study, we report the design and control of self-assembly of an amphiphilic conjugated alkene in water. The morphologies of the self-assembled structures are highly dependent on the anions. The hydrophilic tosylate group can trigger the formation of nanotubes, while the less-hydrophilic inorganic bromide generates vesicles. The interchange of the two different structures can be controlled by employing different anions combined with a couple of reactions that act as signals. The result shown here provides an important tool for manipulating self-assembled behaviors in water and paves the way toward more complex systems.

π-π Stacking Interaction of Metal Phenoxyl Radical Complexes

π-π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π-π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.

Binding of raloxifene to human complement fragment 5a (hC5a): a perspective on cytokine storm and COVID19

Human C5a (hC5a), one of the pro-inflammatory glycoproteins of the complement system is known to undergo production hyperdrive in response to stress and infection. hC5a has been associated with the pathogenesis of many chronic and acute diseases, due to its proven ability in triggering the 'cytokine storm', by binding to its cognate receptor C5aR, expressed in myriad of tissues. Given the pleiotropic downstream function of hC5a, it is logical to consider the hC5a or its precursors as potential drug targets, and thus, we have been rationally pursuing the idea of neutralizing the harmful effect of excessive hC5a, by implementing the repurposing strategies for FDA-approved drugs. Indeed, the proof of principle biophysical studies published recently is encouraging, which strongly supports the potential of this strategy. Considering BSA-carprofen as a reference model system, the current study further explores the inherent conformational plasticity of hC5a and its effect in accommodating more than one drug molecule cooperatively at multiple sites. The data generated by recruiting a battery of experimental and computational biology techniques strongly suggest that hC5a can sequentially accommodate more than one raloxifene molecule with an estimated Ki ∼ 0.5 µM and Ki ∼ 3.58 µM on its surface at non-analogous sites. The study hints at exploration of polypharmacology approach, as a new avenue for discovering synergistic drug molecule pairs, or drug molecules with 'broad-range' binding affinity for targeting the different 'hot spots' on hC5a, as an alternative combination therapy for possible management of the 'cytokine storm'-related inflammatory diseases, like COVID19.Communicated by Ramaswamy H. Sarma.

Structural Selectivity of PAH Removal Processes in Soil, and the Effect of Metal Co-Contaminants

Polycyclic aromatic hydrocarbons (PAHs) form a convenient structural series of molecules with which to examine the selectivity exerted on their removal by soil microbiota. It is known that there is an inverse relationship between PAH molecular size and degradation rates in soil. In this paper, we look at how the magnitude of the slope for this relationship, m, can be used as an indicator of the effect of metal co-contaminants on degradation rates across a range of PAH molecular weights. The analysis utilises data collected from our previous microcosm study (Deary, M.E.; Ekumankama, C.C.; Cummings, S.P. Development of a novel kinetic model for the analysis of PAH biodegradation in the presence of lead and cadmium co-contaminants. Journal of Hazard Materials 2016, 307, 240–252) in which we followed the degradation of the 16 US EPA PAHs over 40 weeks in soil microcosms taken from a high organic matter content woodland soil. The soil was amended with a PAH mixture (total concentration of 2166 mg kg−1) and with a range of metal co-contaminant concentrations (lead, up to 782 mg kg−1; cadmium up to 620 mg kg−1; and mercury up to 1150 mg kg−1). It was found that the magnitude of m increases in relation to the applied concentration of metal co-contaminant, indicating a more adverse effect on microbial communities that participate in the removal of higher molecular weight PAHs. We conclude that m is a useful parameter by which we might measure the differential effects of environmental contaminants on the PAH removal. Such information will be useful in planning and implementing remediation strategies.

Computational simulations of identified marine-derived natural bioactive compounds as potential inhibitors of oral cancer

Oral squamous cell carcinoma is characterized by the upregulation of RAC-alpha serine/threonine-protein kinase (Akt1) and RAC-beta serine/threonine-protein kinase (Akt2). In this work, Akt1 and Akt2 were inhibited using a cocktail of 20 marine algae chemicals. From the PyRx Virtual Screening Tool, dieckol, 6,6′-bieckol, siphonaxanthin and sargachromanol E were chosen as the best four compounds for Akt1 based on the scoring. Similarly, dieckol, 6,6′-bieckol, dioxinodehydroeckol and caulerpenyne were chosen as Akt2 inhibitors. Additionally, the results of the Lipinski rule of five indicated that some of the selected compounds, such as dieckol, 6,6′-bieckol and siphonaxanthin, violated some Lipinski rules, but they demonstrated excellent binding in terms of scoring. Thus, this study demonstrates that the identified lead compounds may act against Akt1 and Akt2 in oral cancer.

Highly Similar Sequence and Structure Yet Different Biophysical Behavior: A Computational Study of Two Triosephosphate Isomerases

Homodimeric triosephosphate isomerases (TIMs) from Trypanosoma cruzi (TcTIM) and Trypanosoma brucei (TbTIM) have markedly similar amino-acid sequences and three-dimensional structures. However, several of their biophysical parameters, such as their susceptibility to sulfhydryl agents and their reactivation speed after being denatured, have significant differences. The causes of these differences were explored with microsecond-scale molecular dynamics (MD) simulations of three different TIM proteins: TcTIM, TbTIM, and a chimeric protein, Mut1. We examined their electrostatic interactions and explored the impact of simulation length on them. The same salt bridge between catalytic residues Lys 14 and Glu 98 was observed in all three proteins, but key differences were found in other interactions that the catalytic amino acids form. In particular, a cation-π interaction between catalytic amino acids Lys 14 and His 96 and both a salt bridge and a hydrogen bond between catalytic Glu 168 and residue Arg 100 were only observed in TcTIM. Furthermore, although TcTIM forms less hydrogen bonds than TbTIM and Mut1, its hydrogen bond network spans almost the entire protein, connecting the residues in both monomers. This work provides new insight into the mechanisms that give rise to the different behavior of these proteins. The results also show the importance of long simulations.

Detection of weak non-covalent cation-π interactions in NGAL by single-molecule force spectroscopy

Cation-π interaction is an electrostatic interaction between a cation and an electron-rich arene. It plays an essential role in many biological systems as a vital driving force for protein folding, stability, and receptor-ligand interaction/recognition. To date, the discovery of most cation-π interactions in proteins relies on the statistical analyses of available three-dimensional (3D) protein structures and corresponding computational calculations. However, their experimental verification and quantification remain sparse at the molecular level, mainly due to the limited methods to dynamically measure such a weak non-covalent interaction in proteins. Here, we use atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of protein neutrophil gelatinase-associated lipocalin (also known as NGAL, siderocalin, lipocalin 2) that can bind iron through the cation-π interactions between its three cationic residues and the iron-binding tri-catechols. Based on a site-specific cysteine engineering and anchoring method, we first characterized the stability and unfolding pathways of apo-NGAL. Then, the same NGAL but bound with the iron-catechol complexes through the cation-π interactions as a holo-form was characterized. AFM measurements demonstrated stronger stabilities and kinetics of the holo-NGAL from two pulling sites, F122 and F133. Here, NGAL is stretched from the designed cysteine close to the cationic residues for a maximum unfolding effect. Thus, our work demonstrates high-precision detection of the weak cation-π interaction in NGAL.

Electronic Supplementary Material

Supplementary material (additional SDS-PAGE, UV-vis, protein sequences, and more experimental methods) is available in the online version of this article at 10.1007/s12274-021-4065-9.

Stacked but not Stuck: Unveiling the Role of π→π* Interactions with the Help of the Benzofuran-Formaldehyde Complex

The 1:1 benzofuran-formaldehyde complex has been chosen as model system for analyzing π→π* interactions in supramolecular organizations involving heteroaromatic rings and carbonyl groups. A joint "rotational spectroscopy-quantum chemistry" strategy unveiled the dominant role of π→π* interactions in tuning the intermolecular interactions of such adduct. The exploration of the intermolecular potential energy surface led to the identification of 14 low-energy minima, with 4 stacked isomers being more stable than those linked by hydrogen bond or lone-pair→π interactions. All energy minima are separated by loose transition states, thus suggesting an effective relaxation to the global minimum under the experimental conditions. This expectation has been confirmed by the experimental detection of only one species, which was unambiguously assigned owing to the computation of accurate spectroscopic parameters and the characterization of 11 isotopologues. The large number of isotopic species opened the way to the determination of the first semi-experimental equilibrium structure for a molecular complex of such a dimension.

Copper(ii) salen-based complexes as potential anticancer agents

The systematic design and synthesis of four Cu(ii) salen compounds and their potential as excellent anticancer agents is discussed using biological studies.

Constructing a shape memory network with controllable stability and dynamic features through cation–π interactions

A dynamic shape memory network, PCL-Pyr, with excellent shape memory effects, mechanical performance and reprocessability was constructed based on cation–π interactions.

A new supramolecular bonding motif involving NH bonds of ammonium salts and macrocycles derived from platinum corners and butadiynediyl linkers

The title Pt4C16 species can give roughly planar geometries in crystals, but afford folded forms with ammonium cations, which are captured like unsuspecting prey and potentially fossilized as with the ancient creatures who once roamed the galaxy.

Clustering of Aromatic Amino Acid Residues around Methionine in Proteins

Short-range, non-covalent interactions between amino acid residues determine protein structures and contribute to protein functions in diverse ways. The interactions of the thioether of methionine with the aromatic rings of tyrosine, tryptophan, and/or phenylalanine has long been discussed and such interactions are favorable on the order of 1–3 kcal mol⁻¹. Here, we carry out a new bioinformatics survey of known protein structures where we assay the propensity of three aromatic residues to localize around the [-CH₂-S-CH₃] of methionine. We term these groups “3-bridge clusters”. A dataset consisting of 33,819 proteins with less than 90% sequence identity was analyzed and such clusters were found in 4093 structures (or 12% of the non-redundant dataset). All sub-classes of enzymes were represented. A 3D coordinate analysis shows that most aromatic groups localize near the CH₂ and CH₃ of methionine. Quantum chemical calculations support that the 3-bridge clusters involve a network of interactions that involve the Met-S, Met-CH₂, Met-CH₃, and the π systems of nearby aromatic amino acid residues. Selected examples of proposed functions of 3-bridge clusters are discussed.

Improvement of the Solubilization and Extraction of Curcumin in an Edible Ternary Solvent Mixture

A water-free, ternary solvent mixture consisting of a natural deep eutectic solvent (NADES), ethanol, and triacetin was investigated concerning its ability to dissolve and extract curcumin from Curcuma longa L. To this purpose, 11 NADES based on choline chloride, acetylcholine, and proline were screened using UV–vis measurements. A ternary phase diagram with a particularly promising NADES, based on choline chloride and levulinic acid was recorded and the solubility domains of the monophasic region were examined and correlated with the system’s structuring via light scattering experiments. At the optimum composition, close to the critical point, the solubility of curcumin could be enhanced by a factor of >1.5 with respect to acetone. In extraction experiments, conducted at the points of highest solubility and evaluated via HPLC, a total yield of ~84% curcuminoids per rhizome could be reached. Through multiple extraction cycles, reusing the extraction solvent, an enrichment of curcuminoids could be achieved while altering the solution. When counteracting the solvent change, even higher concentrated extracts can be obtained.

Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower K_m values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

Cyclotrimerization of Acetylene on Clusters Con+/Fen+/Nin+(n = 1-16)

Cyclotrimerization of acetylene to benzene has attracted significant interest, but the role of geometric and electronic effects on catalytic chemistry remains unclear. To fully elucidate the mechanism of catalytic acetylene-to-benzene conversion, we have performed a gas-phase reaction study of the Fe_n⁺, Co_n⁺, and Ni_n⁺ (n = 1-16) clusters with acetylene utilizing a customized mass spectrometer. It is found that their reactions with acetylene are initiated by C₂H₂ molecular adsorption and allow for dominant dehydrogenation with the relatively low partial pressure of the acetylene gas. However, at high acetylene concentrations, the cyclotrimerization in M_n⁺ + 3C₂H₂ (M = Fe, Co, Ni) becomes the dominant reaction channel. We demonstrate theoretically the favorable thermodynamics and reaction dynamics leading to the formation of the M⁺(C₆H₆) products. The results are discussed in terms of a cluster-catalyzed multimolecule synergistic effect and the cation-π interactions.

Nonequilibrium, weak-field-induced cyclotron motion: A mechanism for magnetobiology

There is a long-time quest for understanding physical mechanisms of weak magnetic field interaction with biological matter. Two factors impeded the development of such mechanisms: first, a high (room) temperature of a cellular environment, where a weak, static magnetic field induces a (classically) zero equilibrium response. Second, the friction in the cellular environment is large, preventing a weak field to alter nonequilibrium processes such as a free diffusion of charges. Here we study a class of nonequilibrium steady states of a cellular ion in a confining potential, where the response to a (weak, homogeneous, static) magnetic field survives strong friction and thermal fluctuations. The magnetic field induces a rotational motion of the ion that proceeds with the cyclotron frequency. Such nonequilibrium states are generated by a white noise acting on the ion additionally to the nonlocal (memory-containing) friction and noise generated by an equilibrium thermal bath. The intensity of this white noise can be weak, i.e., much smaller than the thermal noise intensity.

Alkaline Stability Evaluation of Polymerizable Hexyl-Tethered Ammonium Cations

One of the important challenges in designing robust alkaline anion exchange membranes is the difficulty associated with the chemical stability of covalently bound cationic units. Here, a systematic study exploring alkaline stabilities of polymerizable hexyltrimethylammonium cations is presented, where the hexyl chain is linked to a phenyl ring through a direct carbon-carbon, phenyl ether, or benzyl ether functionality. For this work, small molecule model compounds, styrenic monomer analogs, and their homopolymers are synthesized. Alkaline stabilities of the small molecule cations and their homopolymers are compared to alkaline stability of benzyltrimethylammonium (BTMA) cation and its homopolymer poly(BTMA), respectively. All the hexyl-tethered cations and their homopolymers are significantly more stable under strongly alkaline conditions (2 m KOD at 80 °C). Moreover, ether-linked cations show comparable stability to the direct carbon-carbon linked cation. Via ¹ H NMR analyses, possible degradation mechanisms are investigated for each small molecule cation. Findings of this study strongly suggest that the alkaline stability is dictated by the steric hindrance around the β-hydrogen. This study expands beyond the limits of general knowledge on alkaline stability of alkyl-tethered ammonium cations via the Hofmann elimination route, highlights important design parameters for stable ammonium cations, and demonstrates accessible directly polymerizable alkaline stable ammonium cations.

Disulfide metathesis via sulfur⋯iodine interaction and photoswitchability

The idea of constitutional dynamic chemistry (CDC) and dynamic combinatorial chemistry (DCC) is widespread in the literature using the chemistry of disulfides. The synthesis of unsymmetrical diaryl disulfides is challenging due to the presence of a weak S-S bond. We report herein the synthesis of unsymmetrical diaryl disulfides from two symmetrical disulfides via a cross-metathesis reaction which was controlled by a weak sulfur⋯iodine (S⋯I) interaction. The unsymmetrical disulfides were stable in acetonitrile solution in the presence of N-iodosuccinimide (NIS), and found to be reversibly photoswitchable to the symmetrical disulfides under visible light irradiation.

The Bis(η6 -benzene)lithium Cation: A Fundamental Main-Group Organometallic Species

The synthesis and characterization of the bis(η⁶ -benzene)lithium cation, the benzene metallocene of the lightest metal, is reported. The boron compound FmesBCl₂ [Fmes: 2,4,6-tris(trifluoromethyl)phenyl] reacted with three molar equivalents of the lithio-acetylene reagent Li-C≡C-Fmxyl [Fmxyl: 3,5-bis(trifluoromethyl)phenyl]. Subsequent crystallization from benzene gave the [bis(η⁶ -benzene)Li]⁺ cation with the [{FmesB(-C≡C-Fmxyl)₃ }₂ Li]^- anion. This parent [(arene)₂ Li]⁺ cation shows an eclipsed arrangement of the pair of benzene ligands at the central lithium cation with uniform carbon-lithium bond lengths. The corresponding [(η⁶ -toluene)₂ Li]⁺ and [(η⁶ -durene)₂ Li]⁺ containing salts were similarly prepared. The bis(arene)lithium cations were characterized by X-ray diffraction, by solid-state ⁷ Li MAS NMR spectroscopy and their bonding features were analyzed by DFT calculations.

A tris-oxovanadium pyrogallate complex: synthesis, structure, and magnetic and electronic properties

With the aim of identifying new cation-phenolate complexes, we herein investigated the reactivity of pyrogallol (H₃pgal) with vanadium salts. A trimetallic anionic complex was identified, and found to be formed under a broad set of reaction conditions. This complex, with the formula V₃O₃(pgal)₃^3-, consists of three oxovanadium(IV) units connected together by three pyrogallate ligands to afford a bowl-shaped species presenting a pseudo 3-fold symmetry axis. Its crystal structure is reported, as well as its characterisation by a broad set of techniques, including powder X-ray diffraction, thermogravimetric analysis, infrared and Raman spectroscopy, and solid state UV-visible diffuse reflectance. Its redox activity both in solution and in the solid state is described, together with its magnetic behavior. Finally, the relevance of this trimetallic unit in the field of phenolic-based biocoatings and Metal Organic Framework (MOF) synthesis is briefly discussed.

Membrane electrostatics sensed by tryptophan anchors in hydrophobic model peptides depends on non-aromatic interfacial amino acids: implications in hydrophobic mismatch

WALPs are synthetic α-helical membrane-spanning peptides that constitute a well-studied system for exploring hydrophobic mismatch. These peptides represent a simplified consensus motif for transmembrane domains of intrinsic membrane proteins due to their hydrophobic core of alternating leucine and alanine flanked by membrane-anchoring aromatic tryptophan residues. Although the modulation of mismatch responses in WALPs by tryptophan anchors has been reported earlier, there have been limited attempts to utilize the intrinsic tryptophan fluorescence of this class of peptides in mismatch sensors. We have previously shown, utilizing the red edge excitation shift (REES) approach, that interfacial WALP tryptophan residues in fluid phase bilayers experience a dynamically constrained membrane microenvironment. Interestingly, emerging reports suggest the involvement of non-aromatic interfacially localized residues in modulating local structure and dynamics in WALP analogs. In this backdrop, we have explored the effect of interfacial amino acids, such as lysine (in KWALPs) and glycine (in GWALPs), on the tryptophan microenvironment of WALP analogs in zwitterionic and negatively charged membranes. We show that interfacial tryptophans in KWALP and GWALP experience a more restricted microenvironment, as reflected in the substantial increase in magnitude of REES and apparent rotational correlation time, relative to those in WALP in zwitterionic membranes. Interestingly, in contrast to WALP, the tryptophan anchors in KWALP and GWALP appear insensitive to the presence of negatively charged lipids in the membrane. These results reveal a subtle interplay between non-aromatic flanking residues in transmembrane helices and negatively charged lipids at the membrane interface, which could modulate the membrane microenvironment experienced by interfacially localized tryptophan residues. Since interfacial tryptophans are known to influence mismatch responses in WALPs, our results highlight the possibility of utilizing the fluorescence signatures of tryptophans in membrane proteins or model peptides such as WALP as markers for assessing protein responses to hydrophobic mismatch. More importantly, these results constitute one of the first reports on the influence of lipid headgroup charge in fine-tuning hydrophobic mismatch in membrane bilayers, thereby enriching the existing framework of hydrophobic mismatch.

Mechanisms of melatonin binding and destabilizing the protofilament and filament of tau R3-R4 domains revealed by molecular dynamics simulation

The accumulation of β-amyloid (Aβ) and tau protein is considered to be an important pathological characteristic of Alzheimer's disease (AD). Failure of medicine targeting Aβ has drawn more attention to the influence of tau protein and its fibrillization on neurodegeneration. Increasing evidence shows that melatonin (Mel) can effectively inhibit the formation of tau fibrils and disassemble preformed tau fibrils. However, the underlying mechanism is poorly understood. In this work, we investigated the kinetics of melatonin binding and destabilizing the tetrameric protofilament and octameric filament of tau R3-R4 domains by performing microsecond all-atom molecular dynamics simulations. Our results show that Mel is able to disrupt the C-shaped structure of the tau protofilament and filament, and destabilizes the association between N- and C-termini. Mel predominantly binds to β1 and β6-β8 regions and favors contact with the elongation surface, which is dominantly driven by hydrogen bonding interactions and facilitated by other interactions. The strong π-π stacking interaction of Mel with Y310 impedes the intramolecular CH-π interaction between I308 and Y310, and the cation-π interaction of Mel with R379 interferes with the formation of the D348-R379 salt bridge. Moreover, Mel occupies the protofilament surface in the tetrameric protofilament and prevents the formation of intermolecular hydrogen bonds between residues K331 and Q336 in the octameric filament. Our work provides molecular insights into Mel hindering tau fibrillization or destabilizing the protofilament and filament, and the revealed inhibitory mechanisms provide useful clues for the design of efficient anti-amyloid agents.

Calcium-Modified Fe3O4 Nanoparticles Encapsulated in Humic Acid for the Efficient Removal of Heavy Metals from Wastewater

Ca-modified Fe₃O₄ nanoparticles encapsulated in humic acid (HA-Ca/Fe₃O₄) were produced using a co-precipitation method. Furthermore, the adsorption performance of HA-Ca/Fe₃O₄ as well as the effect of coexisting ions and mechanisms were evaluated. A good description of the adsorption process was given using pseudo-second-order kinetic and Langmuir models. The adsorption capacities of HA-Ca/Fe₃O₄ for Pb²⁺, Cu²⁺, and Cd²⁺ were 208.33, 98.33, and 99.01 mg g^-1, respectively. The 0.02-0.1 times concentrations in alkali and alkaline-earth metals promoted Pb²⁺ and Cd²⁺ adsorption; however, any concentration of alkali and alkaline-earth metals inhibited Cu²⁺-ion adsorption, probably owing to the differences in ionic radii between the interfering and heavy-metal ions. Pb²⁺, Cu²⁺, and Cd²⁺ removal using HA-Ca/Fe₃O₄ occurred via ion exchange, complexation of O-containing functional groups, mineral precipitation, and π-electron coordination. A method was proposed to calculate the contribution of these mechanisms to the adsorption process. In practice, HA-Ca/Fe₃O₄ can remove 99% Pb²⁺ and 91% Cu²⁺ and Cd²⁺ from real wastewater samples. Following five adsorption-desorption cycles, HA-Ca/Fe₃O₄ adsorption capacity did not change significantly. The aforementioned results indicated that HA-Ca/Fe₃O₄ presented a good potential in removing heavy metals in wastewater.

Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure

Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 ​Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 ​Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 ​Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 ​Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.

Molecular mechanisms of resveratrol and EGCG in the inhibition of Aβ42 aggregation and disruption of Aβ42 protofibril: similarities and differences

The aggregation of amyloid-β protein (Aβ) into fibrillary deposits is implicated in Alzheimer's disease (AD), and inhibiting Aβ aggregation and clearing Aβ fibrils are considered as promising strategies to treat AD. It has been reported that resveratrol (RSV) and epigallocatechin-3-gallate (EGCG), two of the most extensively studied natural polyphenols, are able to inhibit Aβ fibrillization and remodel the preformed fibrillary aggregates into amorphous, non-toxic species. However, the mechanisms by which RSV inhibits Aβ₄₂ aggregation and disrupts Aβ₄₂ protofibril, as well as the inhibitory/disruptive mechanistic similarities and differences between RSV and EGCG, remain mostly elusive. Herein, we performed extensive all-atom molecular dynamics (MD) simulations on Aβ₄₂ dimers (the early aggregation state of Aβ₄₂) and protofibrils (the intermediate of Aβ₄₂ fibril formation and elongation) in the absence/presence of RSV or EGCG molecules. Our simulations show that both RSV and EGCG can bind with Aβ₄₂ monomers and inhibit the dimerization of Aβ₄₂. The binding of RSV with Aβ₄₂ peptide is mostly viaπ-π stacking interactions, while the binding of EGCG with Aβ₄₂ is mainly through hydrophobic, π-π stacking, and hydrogen-bonding interactions. Moreover, both RSV and EGCG disrupt the β-sheet structure and K28-A42 salt bridges, leading to a disruption of Aβ₄₂ protofibril structure. RSV mainly binds with residues whose side-chains point inwards from the surface of the protofibril, while EGCG mostly binds with residues whose side-chains point outwards from the surface of the protofibril. Furthermore, RSV interacts with Aβ₄₂ protofibrils mostly viaπ-π stacking interactions, while EGCG interacts with Aβ₄₂ protofibrils mainly via hydrogen-bonding and hydrophobic interactions. For comparison, we also explore the effects of RSV/EGCG molecules on the aggregation inhibition and protofibril disruption of the Iowa mutant (D23N) Aβ. Our findings may pave the way for the design of more effective drug candidates as well as the utilization of cocktail therapy using RSV and EGCG for the treatment of AD.

The First Cytoplasmic Loop in the Core Structure of the ABCC1 (Multidrug Resistance Protein 1; MRP1) Transporter Contains Multiple Amino Acids Essential for Its Expression

ABCC1 (human multidrug resistance protein 1 (hMRP1)) is an ATP-binding cassette transporter which effluxes xeno- and endobiotic organic anions and confers multidrug resistance through active drug efflux. The 17 transmembrane α-helices of hMRP1 are distributed among three membrane spanning domains (MSD0, 1, 2) with MSD1,2 each followed by a nucleotide binding domain to form the 4-domain core structure. Eight conserved residues in the first cytoplasmic loop (CL4) of MSD1 in the descending α-helix (Gly³⁹², Tyr⁴⁰⁴, Arg⁴⁰⁵), the perpendicular coupling helix (Asn⁴¹², Arg⁴¹⁵, Lys⁴¹⁶), and the ascending α-helix (Glu⁴²², Phe⁴³⁴) were targeted for mutagenesis. Mutants with both alanine and same charge substitutions of the coupling helix residues were expressed in HEK cells at wild-type hMRP1 levels and their transport activity was only moderately compromised. In contrast, mutants of the flanking amino acids (G392I, Y404A, R405A/K, E422A/D, and F434Y) were very poorly expressed although Y404F, E422D, and F434A were readily expressed and transport competent. Modeling analyses indicated that Glu⁴²² and Arg⁶¹⁵ could form an ion pair that might stabilize transporter expression. However, this was not supported by exchange mutations E422R/R615E which failed to improve hMRP1 levels. Additional structures accompanied by rigorous biochemical validations are needed to better understand the bonding interactions crucial for stable hMRP1 expression.

Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof

Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.

Tryptophan, an Amino-Acid Endowed with Unique Properties and Its Many Roles in Membrane Proteins

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.

Dithiolated peptides incorporating bis(tryptophan)s for cooperative mercury(II) binding

The indole side chain of tryptophan is a versatile π-donor that can participate in various types of cation-π interactions. An understanding of how it may contribute as an auxiliary binding group in mercury(II) complexes can provide valuable insights toward the design of effective chelators for optimal mercury immobilization. In this study, we investigate how the incorporation of two tryptophan residues in model dicysteinyl peptides might participate in peptide-mercury(II) complex stabilization. Two pentapeptides consisting of a Cys-Trp-Cys sequence motif containing a second tryptophan residue at the N-terminal (BT1) or C-terminal (BT2) were designed. An analogous cyclohexapeptide (BT3) was included to evaluate how tryptophan residues, restricted in constrained peptidic turn motifs, might take part in mercury(II) complexation. Their interactions with mercury(II) were investigated by spectroscopic methods and computational modeling. UV-vis studies indicate the formation of 1:1 dithiolated mercury(II) complex, which is corroborated by ESI-MS analysis. Spectroscopic studies reveal that the tryptophan indole group(s) in BT1 and BT3 can participate in mercury(II) cation-π interactions. Optimized 1:1 mercury(II)-BT3 structures indicate that both indole rings are very close to the mercury(II) coordination site and could stabilize it by shielding it from ligand exchange. These findings provide some useful insights toward use of aromatic donor groups as hydrophobic shields in designing more effective metal chelating agents.

Assessment of the Accuracy of DFT-Predicted Li+-Nucleic Acid Binding Energies

Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li⁺ binding to nucleic acids is required. Herein, a new database of Li⁺-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li⁺-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li⁺-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.

Data Science Meets Physical Organic Chemistry

ConspectusAt the heart of synthetic chemistry is the holy grail of predictable catalyst design. In particular, researchers involved in reaction development in asymmetric catalysis have pursued a variety of strategies toward this goal. This is driven by both the pragmatic need to achieve high selectivities and the inability to readily identify why a certain catalyst is effective for a given reaction. While empiricism and intuition have dominated the field of asymmetric catalysis since its inception, enantioselectivity offers a mechanistically rich platform to interrogate catalyst-structure response patterns that explain the performance of a particular catalyst or substrate.In the early stages of an asymmetric reaction development campaign, the overarching mechanism of the reaction, catalyst speciation, the turnover limiting step, and many other details are unknown or posited based on related reactions. Considering the unclear details leading to a successful reaction, initial enantioselectivity data are often used to intuitively guide the ultimate direction of optimization. However, if the conditions of the Curtin-Hammett principle are satisfied, then measured enantioselectivity can be directly connected to the ensemble of diastereomeric transition states (TSs) that lead to the enantiomeric products, and the associated free energy difference between competing TSs (ΔΔG⧧ = -RT ln[(S)/(R)], where (S) and (R) represent the concentrations of the enantiomeric products). We, and others, speculated that this important piece of information can be leveraged to guide reaction optimization in a quantitative way.Although traditional linear free energy relationships (LFERs), such as Hammett plots, have been used to illuminate important mechanistic features, we sought to develop data science derived tools to expand the power of LFERs in order to describe complex reactions frequently encountered in modern asymmetric catalysis. Specifically, we investigated whether enantioselectivity data from a reaction can be quantitatively connected to the attributes of reaction components, such as catalyst and substrate structural features, to harness data for asymmetric catalyst design.In this context, we developed a workflow to relate computationally derived features of reaction components to enantioselectivity using data science tools. The mathematical representation of molecules can incorporate many aspects of a transformation, such as molecular features from substrate, product, catalyst, and proposed transition states. Statistical models relating these features to reaction outputs can be used for various tasks, such as performance prediction of untested molecules. Perhaps most importantly, statistical models can guide the generation of mechanistic hypotheses that are embedded within complex patterns of reaction responses. Overall, merging traditional physical organic experiments with statistical modeling techniques creates a feedback loop that enables both evaluation of multiple mechanistic hypotheses and future catalyst design. In this Account, we highlight the evolution and application of this approach in the context of a collaborative program based on chiral phosphoric acid catalysts (CPAs) in asymmetric catalysis.

Llamanade : an open-source computational pipeline for robust nanobody humanization

Nanobodies (Nbs) have recently emerged as a promising class of antibody fragments for biomedical and therapeutic applications. Despite having marked physicochemical properties, Nbs are derived from camelids and may require "humanization" to improve translational potentials for clinical trials. Here we have systematically analyzed the sequence and structural properties of Nbs based on NGS (next-generation sequencing) databases and high-resolution structures. Our analysis reveals substantial framework diversities and underscores the key differences between Nbs and human Immunoglobulin G (IgG) antibodies. We identified conserved residues that may contribute to enhanced solubility, structural stability, and antigen-binding, providing insights into Nb humanization. Based on big data analysis, we developed " Llamanade '', a user-friendly, open-source to facilitate rational humanization of Nbs. Using Nb sequence as input, Llamanade provides information on the sequence features, model structures, and optimizes solutions to humanize Nbs. The full analysis for a given Nb takes less than a minute on a local computer. To demonstrate the robustness of this tool, we applied it to successfully humanize a cohort of structurally diverse and highly potent SARS-CoV-2 neutralizing Nbs. Llamanade is freely available and will be easily accessible on a web server to support the development of a rapidly expanding repertoire of therapeutic Nbs into safe and effective trials.

AUTHOR SUMMARY

Camelid Nbs are characterized by small size, excellent pharmacological properties and high flexibility in bioengineering for therapeutic development. However, Nbs are "xeno" antibodies, which require "humanization" to improve their translational potential. Currently, there is a lack of systematic investigation of Nbs to rationally guide humanization. No dedicated software has been developed for this purpose. Here, we report the development of Llamanade , an open-source computational pipeline and the first dedicated software to facilitate rational humanization of Nbs. To subjectively evaluate Llamanade , we used it to humanize a cohort of structurally diverse and ultrapotent antiviral Nbs against SARS-CoV-2. Robust humanization by Llamanade significantly improved the humanness level of Nbs to closely resemble fully human IgGs. Importantly, these highly humanized antiviral Nbs remained excellent solubility and comparably high bioactivities to the non-humanized Nb precursors. We envision that Llamanade will help advance Nb research into therapeutic development.

Water and the Cation-π Interaction

The cation-π interaction and the hydrophobic effect are important intermolecular forces in chemistry and play major roles in controlling recognition in biological systems. We compared their relative contributions to the binding of molecular "dumbbell" guests in synthetic container hosts in water. The guests offered direct, intramolecular competition between trimethylammonium groups, -N⁺(CH₃)₃, and tert-butyl groups, -C(CH₃)₃, for the internal surfaces (aromatic panels) of the containers. In contrast with previous studies, the container molecules consistently preferred binding to the uncharged tert-butyl groups, regardless of the presence of anionic, cationic, or zwitterionic groups on the container peripheries. This preference is determined by solvation of the polar trimethylammonium group in water, which outcompetes the attraction between the positive charge and the π-surfaces in the container. The synthetic container complexes provide a direct measure of the relative strengths of cation-π interactions and desolvation in water. Interactions with the uncharged tert-butyl group are more than 12 kJ mol^-1 more favorable than the cation-π interactions with the trimethylammonium group in these cavitand complexes.

Anthrax toxin channel: What we know based on over 30 years of research

Protective antigen channel is the central component of the deadly anthrax exotoxin responsible for binding and delivery of the toxin's enzymatic lethal and edema factor components into the cytosol. The channel, which is more than three times longer than the lipid bilayer membrane thickness and has a 6-Å limiting diameter, is believed to provide a sophisticated unfoldase and translocase machinery for the foreign protein transport into the host cell cytosol. The tripartite toxin can be reengineered, one component at a time or collectively, to adapt it for the targeted cancer therapeutic treatments. In this review, we focus on the biophysical studies of the protective antigen channel-forming activity, small ion transport properties, enzymatic factor translocation, and blockage comparing it with the related clostridial binary toxin channels. We address issues linked to the anthrax toxin channel structural dynamics and lipid dependence, which are yet to become generally recognized as parts of the toxin translocation machinery.

One-Component Multifunctional Sequence-Defined Ionizable Amphiphilic Janus Dendrimer Delivery Systems for mRNA

Efficient viral or nonviral delivery of nucleic acids is the key step of genetic nanomedicine. Both viral and synthetic vectors have been successfully employed for genetic delivery with recent examples being DNA, adenoviral, and mRNA-based Covid-19 vaccines. Viral vectors can be target specific and very efficient but can also mediate severe immune response, cell toxicity, and mutations. Four-component lipid nanoparticles (LNPs) containing ionizable lipids, phospholipids, cholesterol for mechanical properties, and PEG-conjugated lipid for stability represent the current leading nonviral vectors for mRNA. However, the segregation of the neutral ionizable lipid as droplets in the core of the LNP, the "PEG dilemma", and the stability at only very low temperatures limit their efficiency. Here, we report the development of a one-component multifunctional ionizable amphiphilic Janus dendrimer (IAJD) delivery system for mRNA that exhibits high activity at a low concentration of ionizable amines organized in a sequence-defined arrangement. Six libraries containing 54 sequence-defined IAJDs were synthesized by an accelerated modular-orthogonal methodology and coassembled with mRNA into dendrimersome nanoparticles (DNPs) by a simple injection method rather than by the complex microfluidic technology often used for LNPs. Forty four (81%) showed activity in vitro and 31 (57%) in vivo. Some, exhibiting organ specificity, are stable at 5 °C and demonstrated higher transfection efficiency than positive control experiments in vitro and in vivo. Aside from practical applications, this proof of concept will help elucidate the mechanisms of packaging and release of mRNA from DNPs as a function of ionizable amine concentration, their sequence, and constitutional isomerism of IAJDs.

Bicolour fluorescent molecular sensors for cations: design and experimental validation

Molecular entities whose fluorescence spectra are different when they bind metal cations are termed bicolour fluorescent molecular sensors. The basic design criteria of this kind of compound are presented and the different fluorescent responses are discussed in terms of their chemical behaviour and electronic features. These latter elements include intramolecular charge transfer (ICT), formation of intramolecular and intermolecular excimer/exciplex complexes and Förster resonance energy transfer (FRET). Changes in the electronic properties of the fluorophore based on the decoupling between its constitutive units upon metal binding are also discussed. The possibility of generating fluorescent bicolour indicators that can capture metal cations in the gas phase and at solid-gas interfaces is also discussed.

Cytosolic Protein Delivery for Intracellular Antigen Targeting Using Supercharged Polypeptide Delivery Platform

Despite the well-recognized clinical success of therapeutic proteins, especially antibodies, their inability to penetrate the cell membrane restricts them to secretory extracellular or membrane-associated targets. Developing a direct cytosolic protein delivery system would offer unique opportunities for intracellular target-related therapeutic proteins. Here, we generated a supercharged polypeptide (SCP) with high cellular uptake efficiency, endosomal escape ability, and good biosafety and developed an SCP with an unnatural amino acid containing the phenylboronic acid (PBA) group, called PBA-SCP. PBA-SCP is capable of potently delivering proteins with various isoelectric points and molecular sizes into the cytosol of living cells without affecting their bioactivities. Importantly, cytosolically delivered antibodies remain functional and are capable of targeting, labeling, and manipulating diverse intracellular antigens. This study demonstrates an efficient and versatile intracellular protein delivery platform, especially for antibodies, and provides new possibilities for expanding protein-based therapeutics to intracellular "undruggable" targets.

Spectroscopic and Theoretical Studies of Hg(II) Complexation with Some Dicysteinyl Tetrapeptides

Tetrapeptides containing a Cys-Gly-Cys motif and a propensity to adopt a reverse-turn structure were synthesized to evaluate how O-, N-, H-, and aromatic π donor groups might contribute to mercury(II) complex formation. Tetrapeptides Xaa-Cys-Gly-Cys, where Xaa is glycine, glutamate, histidine, or tryptophan, were prepared and reacted with mercury(II) chloride. Their complexation with mercury(II) was studied by spectroscopic methods and computational modeling. UV-vis studies confirmed that mercury(II) binds to the cysteinyl thiolates as indicated by characteristic ligand-to-metal-charge-transfer transitions for bisthiolated S-Hg-S complexes, which correspond to 1 : 1 mercury-peptide complex formation. ESI-MS data also showed dominant 1 : 1 mercury-peptide adducts that are consistent with double deprotonations from the cysteinyl thiols to form thiolates. These complexes exhibited a strong positive circular dichroism band at 210 nm and a negative band at 193 nm, indicating that these peptides adopted a β-turn structure after binding mercury(II). Theoretical studies confirmed that optimized 1 : 1 mercury-peptide complexes adopt β-turns stabilized by intramolecular hydrogen bonds. These optimized structures also illustrate how specific N-terminal side-chain donor groups can assume intramolecular interactions and contribute to complex stability. Fluorescence quenching results provided supporting data that the indole donor group could interact with the coordinated mercury. The results from this study indicate that N-terminal side-chain residues containing carboxylate, imidazole, or indole groups can participate in stabilizing dithiolated mercury(II) complexes. These structural insights on peripheral mercury-peptide interactions provide additional understanding of the chemistry of mercury(II) with side-chain donor groups in peptides.

Introducing Intermolecular Cation-π Interactions for Water-Stable Low Dimensional Hybrid Lead Halide Perovskites

Optoelectronically active hybrid lead halide perovskites dissociate in water. To prevent this dissociation, here, we introduce long-range intermolecular cation-π interactions between A-site cations of hybrid perovskites. An aromatic diamine like 4,4'-trimethylenedipyridine, if protonated, can show a long-range cation-π stacking, and therefore, serves as our A-site cation. Consequently, 4,4'-trimethylenedipyridinium lead bromide [(4,4'-TMDP)Pb₂ Br₆ ], a one-dimensional hybrid perovskite, remains completely stable after continuous water treatment for six months. Mechanistic insights about the cation-π interactions are obtained by single-crystal X-ray diffraction and nuclear magnetic resonance spectroscopy. The concept of long-range cation-π interaction is further extended to another A-site cation 4,4'-ethylenedipyridinium ion (4,4'-EDP), forming water-stable (4,4'-EDP)Pb₂ Br₆ perovskite. These water-stable perovskites are then used to fabricate white light-emitting diode and for light up-conversion through tunable third-harmonic generation. Note that the achieved water stability is the intrinsic stability of perovskite composition, unlike the prior approach of encapsulating the unstable perovskite material (or device) by water-resistant materials. The introduced cation-π interactions can be a breakthrough strategy in designing many more compositions of water-stable low-dimensional hybrid perovskites.