Minimally modified human blood coagulation factor X to bypass direct factor Xa inhibitors.

BACKGROUND: Direct oral factor (F)Xa inhibitors are widely used as alternatives to conventional vitamin K antagonists in managing venous thromboembolism and nonvalvular atrial fibrillation. Unfortunately, bleeding-related adverse events remain a major concern in clinical practice. In case of bleeding or emergency surgery, rapid-onset reversal agents may be required to counteract the anticoagulant activity. OBJECTIVES: The ability of FXa variants to bypass the direct oral FXa inhibitors was assessed. METHODS: Human FXa variants were generated through substitution of phenylalanine 174 (F174) for either alanine, isoleucine, or serine. FXa variants were stably expressed in HEK293 cells and purified to homogeneity using ion-exchange chromatography. RESULTS: F174-substituted human FX variants demonstrated efficacy in restoring thrombin generation in plasma containing direct FXa inhibitors (apixaban, rivaroxaban, edoxaban). Their ability to bypass the anticoagulant effects stems from a significantly reduced sensitivity for the direct FXa inhibitors due to a decrease in binding affinity determined using molecular dynamics simulations and free energy computation. Furthermore, F174 modification resulted in a partial loss of inhibition by tissue factor pathway inhibitor, enhancing the procoagulant effect of F174-substituted FX. Consequently, the F174A- and F174S-substituted FX variants effectively counteracted the effects of 2 widely used anticoagulants, apixaban and rivaroxaban, in plasma of atrial fibrillation and venous thromboembolism patients. CONCLUSION: These human FX variants have the potential to serve as a rescue reversal strategy to overcome the effect of direct FXa inhibitors in case of life-threatening bleeding events or emergency surgical interventions.

Broadening the catalytic region from the cavity to windows by M6L12 nanospheres in cyclizations.

Supramolecular cages have received tremendous attention as they can contain catalysts that exhibit confinement effects in the cavity, leading to excellent performances. Herein, we report an example wherein the catalytic region is extended from the cage cavity to the windows, and investigate its confinement effect by utilizing the Pd6LAu12 cage that contains rigidly fixed and isolated gold complexes at the windows. Pd6LAu12 exhibit three features of particular interest while assessing their properties in gold-catalyzed cyclization reactions. First, the catalysts experience a cage effect as they display higher reactivity and selectivity compared to the monomeric analogue, as a result of substrate pre-organization at the windows. Second, the metal complexes are physically separated by the cage structure, preventing the formation of less active dinuclear gold complexes making it more stable under hydrous conditions. Third, the cage windows present the characteristics of enzymatic catalysis via Michaelis-Menten-type mechanism analysis. This contribution presents an alternative way to engineer supramolecular catalysts through extending the catalytic region.

Pd12MnL24 (for n = 6, 8, 12) nanospheres by post-assembly modification of Pd12L24 spheres.

In this contribution, we describe a post-assembly modification approach to selectively coordinate transition metals in Pd12L24 cuboctahedra. The herein reported approach involves the preparation of Pd12L24 nanospheres with protonated nitrogen donor ligands that are covalently linked at the interior. The so obtained Pd12(LH+)24 nanospheres are shown to be suitable for coordinative post-modification after deprotection by deprotonation. Selective formation of tetra-coordinated MB in Pd12MB6L24, tri-coordinated MB in Pd12MB8L24 nanospheres and two-coordinated MB in Pd12MB12L24 nanospheres is achieved as a result of different nitrogen donor ligands. A combination of pulsed EPR spectroscopy (DEER) to measure Cu-Cu distances in the different spheres, NMR studies and computational investigations, support the presence of the complexes at precise locations of the Pd12MB6L24 nanosphere. The general post-assembly modification methodology can be extended using other transition metal precursors or supramolecular systems and can guide precise formation and investigation of novel transition metal-complex containing nanospheres with well-defined composition.

Selective thiazoline peptide cyclisation compatible with mRNA display and efficient synthesis.

Peptide display technologies are a powerful method for discovery of new bioactive sequences, but linear sequences are often very unstable in a biological setting. Macrocyclisation of such peptides is beneficial for target affinity, selectivity, stability, and cell permeability. However, macrocyclisation of a linear hit is unreliable and requires extensive structural knowledge. Genetically encoding macrocyclisation during the discovery process is a better approach, and so there is a need for diverse cyclisation options that can be deployed in the context of peptide display techniques such as mRNA display. In this work we show that meta-cyanopyridylalanine (mCNP) can be ribosomally incorporated into peptides, forming a macrocycle in a spontaneous and selective reaction with an N-terminal cysteine generated from bypassing the initiation codon in translation. This reactive amino acid can also be easily incorporated into peptides during standard Fmoc solid phase peptide synthesis, which can otherwise be a bottleneck in transferring from peptide discovery to peptide testing and application. We demonstrate the potential of this new method by discovery of macrocyclic peptides targeting influenza haemagglutinin, and molecular dynamics simulation indicates the mCNP cross-link stabilises a beta sheet structure in a representative of the most abundant cluster of active hits. Cyclisation by mCNP is also shown to be compatible with thioether macrocyclisation at a second cysteine to form bicycles of different architectures, provided that cysteine placement reinforces selectivity, with this bicyclisation happening spontaneously and in a controlled manner during peptide translation. Our new approach generates macrocycles with a more rigid cross-link and with better control of regiochemistry when additional cysteines are present, opening these up for further exploitation in chemical modification of in vitro translated peptides, and so is a valuable addition to the peptide discovery toolbox.

In vivo biodistribution of kinetically stable Pt2L4 nanospheres that show anti-cancer activity.

There is an increasing interest in the application of metal-organic cages (MOCs) in a biomedicinal context, as they can offer non-classical distribution in organisms compared to molecular substrates, while revealing novel cytotoxicity mechanisms. Unfortunately, many MOCs are not sufficiently stable under in vivo conditions, making it difficult to study their structure-activity relationships in living cells. As such, it is currently unclear whether MOC cytotoxicity stems from supramolecular features or their decomposition products. Herein, we describe the toxicity and photophysical properties of highly-stable rhodamine functionalized platinum-based Pt2L4 nanospheres as well as their building blocks under in vitro and in vivo conditions. We show that in both zebrafish and human cancer cell lines, the Pt2L4 nanospheres demonstrate reduced cytotoxicity and altered biodistribution within the body of zebrafish embryos compared to the building blocks. We anticipate that the composition-dependent biodistribution of Pt2L4 spheres together with their cytotoxic and photophysical properties provides the fundament for MOC application in cancer therapy.

A substrate descriptor based approach for the prediction and understanding of the regioselectivity in caged catalyzed hydroformylation.

The use of data driven tools to predict the selectivity of homogeneous catalysts has received considerable attention in the past years. In these studies often the catalyst structure is varied, but the use of substrate descriptors to rationalize the catalytic outcome is relatively unexplored. To study whether this may be an effective tool, we investigated both an encapsulated and a non-encapsulated rhodium based catalyst in the hydroformylation reaction of 41 terminal alkenes. For the non-encapsulated catalyst, CAT2, the regioselectivity of the acquired substrate scope could be predicted with high accuracy using the Δ13C NMR shift of the alkene carbon atoms as a descriptor (R2 = 0.74) and when combined with a computed intensity of the CC stretch vibration (ICC stretch) the accuracy increased further (R2 = 0.86). In contrast, a substrate descriptor approach with an encapsulated catalyst, CAT1, appeared more challenging indicating a confined space effect. We investigated Sterimol parameters of the substrates as well as computer-aided drug design descriptors of the substrates, but these parameters did not result in a predictive formula. The most accurate substrate descriptor based prediction was made with the Δ13C NMR shift and ICC stretch (R2 = 0.52), suggestive of the involvement of CH-π interactions. To further understand the confined space effect of CAT1, we focused on the subset of 21 allylbenzene derivatives to investigate predictive parameters unique for this subset. These results showed the inclusion of a charge parameter of the aryl ring improved the regioselectivity predictions, which is in agreement with our assessment that noncovalent interactions between the phenyl ring of the cage and the aryl ring of the substrate are relevant for the regioselectivity outcome. However, the correlation is still weak (R2 = 0.36) and as such we are investigating novel parameters that should improve the overall regioselectivity outcome.

Exposing Mechanisms for Defect Clearance in Supramolecular Self-Assembly: Palladium-Pyridine Coordination Revisited.

Spherical three-dimensional (3D) cages composed of palladium(II) and pyridyl ligands are a mainstay of supramolecular chemistry with demonstrated catalytic and optoelectronic applications. The widely reported self-assembly of these palladium-based cages exhibits sensitivity to the solvents, reagents, and/or reactants employed. This sensitivity, and the resulting inconsistency between synthetic protocols, hinders the development of desirable palladium-based cages. We have found that pyridyl ligand substitution─the rate-limiting step of self-assembly─is facilitated by endogenous supporting ligands derived from the solvents, reagents, and reactants employed in synthetic protocols of palladium- and platinum-based assemblies. Here, we present a systematic investigation combining 1H-NMR, electrospray ionization mass spectrometry (ESI─MS), and absorption spectroscopy to characterize the intermediates to support the mechanism of pyridyl ligand substitution on a model complex, M(py)2 (M = (N,N,N',N'-tetramethylethylenediamine)palladium(II), py = pyridine), under simulated synthetic conditions for self-assembly. Our investigation exposes mechanisms for pyridyl ligand substitution, featuring intermediates stabilized by solvent, anion, or (in situ formed) alkoxide moieties. Interrogation of destabilizing agents (2,2,2-trifluoroethanol and tetra(n-butyl)ammonium chloride) reveal similar mechanisms that ultimately facilitate the self-assembly of coordination cages. These findings rationalize widely reported solvent and anion effects in the self-assembly of coordination cages (and similar constructs) while highlighting methodologies to understand the role of supporting ligands in coordination chemistry.

Effector Regulated Catalytic Cyclization of Alkynoic Acids Using Pt2 L4 Cages.

Metabolic pathways are highly regulated by effector molecules that influences the rate of enzymatic reactions. Inspired by the catalytic regulation found in living cells, we report a Pt2 L4 cage of which the activity can be controlled by effectors that bind inside the cage. The cage shows catalytic activity in the lactonization of alkynoic acids, with the reaction rates dependent on the effector guest bound in the cage. Some effector guests enhance the rate of the lactonization by up to 19-fold, whereas one decreases it by 5-fold. When mixtures of specific substrates are used, both starting materials and products act as guests for the Pt2 L4 cage, enhancing its catalytic activity for one substrate while reducing its activity for the other. The reported regulatory behavior obtained by the addition of effector molecules paves the way to the development of more complex, metabolic-like catalyst systems.

An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in†vitro Translation.

Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work, a new approach to peptide macrocyclisation is reported, using a cyanobenzothiazole-containing amino acid that can be incorporated into peptides by both in vitro translation and solid phase peptide synthesis, meaning it should be applicable to peptide discovery by mRNA display. This cyclisation proceeds rapidly, with minimal by-products, is selective over other amino acids including non N-terminal cysteines, and is compatible with further peptide elaboration exploiting such an additional cysteine in bicyclisation and derivatisation reactions. Molecular dynamics simulations show that the new cyclisation group is likely to influence the peptide conformation as compared to previous thioether-based approaches, through rigidity and intramolecular aromatic interactions, illustrating their complementarity.

M6L12 Nanospheres with Multiple C70 Binding Sites for 1O2 Formation in Organic and Aqueous Media.

Singlet oxygen is a potent oxidant with major applications in organic synthesis and medicinal treatment. An efficient way to produce singlet oxygen is the photochemical generation by fullerenes which exhibit ideal thermal and photochemical stability. In this contribution we describe readily accessible M6L12 nanospheres with unique binding sites for fullerenes located at the windows of the nanospheres. Up to four C70 can be associated with a single nanosphere, presenting an efficient method for fullerene extraction and application. Depending on the functionality located on the outside of the sphere, they act as vehicles for 1O2 generation in organic or in aqueous media using white LED light. Excellent productivity in 1O2 generation and consecutive oxidation of 1O2 acceptors using C70⊂[Pd6L12], C60⊂[Pd6L12] or fullerene soot extract was observed. The methodological design principles allow preparation and application of highly effective multifullerene binding spheres.

Just Add Water: Modulating the Structure-Derived Acidity of Catalytic Hexameric Resorcinarene Capsules.

The hexameric undecyl-resorcin[4]arene capsule (C11R6) features eight discrete structural water molecules located at the vertices of its cubic suprastructure. Combining NMR spectroscopy with classical molecular dynamics (MD), we identified and characterized two distinct species of this capsule, C11R6-A and C11R6-B, respectively featuring 8 and 15 water molecules incorporated into their respective hydrogen-bonded networks. Furthermore, we found that the ratio of the C11R6-A and C11R6-B found in solution can be modulated by controlling the water content of the sample. The importance of this supramolecular modulation in C11R6 capsules is highlighted by its ability to perform acid-catalyzed transformations, which is an emergent property arising from the hydrogen bonding within the suprastructure. We show that the conversion of C11R6-A to C11R6-B enhances the catalytic rate of a model Diels-Alder cyclization by 10-fold, demonstrating the cofactor-derived control of a supramolecular catalytic process that emulates natural enzymatic systems.

How to Prepare Kinetically Stable Self-assembled Pt12 L24 Nanocages while Circumventing Kinetic Traps.

Supramolecular coordination-based self-assembled nanostructures have been widely studied, and currently various applications are being explored. For several applications, the stability of the nanostructure is of key importance, and this strongly depends on the metal used in the self-assembly process. Herein, design strategies and synthetic protocols to access desirable kinetically stable Pt12 L24 nanospheres are reported, and it is demonstrated that these are stable under conditions under which the palladium counterparts decompose. Descriptors previously used for palladium nanospheres are insufficient for platinum analogues, as the stronger metal-ligand bond results in a mixture of kinetically trapped structures. We report that next to the dihedral angle, the rigidity of the ditopic ligand is also a key parameter for the controlled formation of Pt12 L24 nanospheres. Catalytic amounts of coordinating additives to labilise the platinum-pyridyl bond to some extent are needed to selectively form Pt12 L24 assemblies. The formed Pt12 L24 nanospheres were demonstrated to be stable in the presence of chloride, amines and acids, unlike the palladium analogues.

Balancing Ligand Flexibility versus Rigidity for the Stepwise Self-Assembly of M12 L24 via M6 L12 Metal-Organic Cages.

Non-covalent interactions are important for directing protein folding across multiple intermediates and can even provide access to multiple stable structures with different properties and functions. Herein, we describe an approach for mimicking this behavior in the self-assembly of metal-organic cages. Two ligands, the bend angles of which are controlled by non-covalent interactions and one ligand lacking the above-mentioned interactions, were synthesized and used for self-assembly with Pd2+ . As these weak interactions are easily broken, the bend angles have a controlled flexibility giving access to M2 (L1)4 , M6 (L2)12 , and M12 (L2)24 cages. By controlling the self-assembly conditions this process can be directed in a stepwise fashion. Additionally, the multiple endohedral hydrogen-bonding sites on the ligand were found to play a role in the binding and discrimination of neutral guests.

Topological prediction of palladium coordination cages.

The preparation of functionalized, heteroleptic Pd x L2x coordination cages is desirable for catalytic and optoelectronic applications. Current rational design of these cages uses the angle between metal-binding (∠B) sites of the di(pyridyl)arene linker to predict the topology of homoleptic cages obtained via non-covalent chemistry. However, this model neglects the contributions of steric bulk between the pyridyl residues-a prerequisite for endohedrally functionalized cages, and fails to rationalize heteroleptic cages. We describe a classical mechanics (CM) approach to predict the topological outcomes of Pd x L2x coordination cage formation with arbitrary linker combinations, accounting for the electronic effects of coordination and steric effects of linker structure. Initial validation of our CM method with reported homoleptic Pd12 LFu 24 (LFu = 2,5-bis(pyridyl)furan) assembly suggested the formation of a minor topology Pd15 LFu 30, identified experimentally by mass spectrometry. Application to heteroleptic cage systems employing mixtures of LFu (∠B = 127°) and its thiophene congener LTh (∠B = 149° ∠B exp = 152.4°) enabled prediction of Pd12L24 and Pd24L48 coordination cages formation, reliably emulating experimental data. Finally, the topological outcome for exohedrally (LEx) and endohedrally (LEn) functionalized heteroleptic Pd x L2x coordination cages were predicted to assess the effect of steric bulk on both topological outcomes and coordination cage yields, with comparisons drawn to experimental data.