Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, E_int, using relationships between E_int and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between E_int and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]⁻ and [Z–Hal···I]⁻ types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol.     

Query-guided protein–protein interaction inhibitor discovery

Protein–protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein–protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and ¹H–¹⁵N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure–activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.

Small-molecule protein–protein interaction inhibitors were prioritised on the basis of shape similarity to secondary structure-based queries incorporating hot-spot residues.     

Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

Dynamic ligation screening is used to identify acylhydrazone-linked peptide-fragment hybrids which bind to the SHANK1 PDZ domain with comparable affinity to the native GKAP peptide as shown by biophysical and structural analyses.     

Comparative Structural Study of Three Tetrahalophthalic Anhydrides: Recognition of X···O(anhydride) Halogen Bond and πh···O(anhydride) Interaction

Structures of three tetrahalophthalic anhydrides (TXPA: halogen = Cl (TCPA), Br (TBPA), I (TIPA)) were studied by X-ray diffraction, and several types of halogen bonds (HaB) and lone pair···π-hole (lp···πh) contacts were revealed in their structures. HaBs involving the central oxygen atom of anhydride group (further X···O(anhydride) were recognized in the structures of TCPA and TBPA. In contrast, for the O(anhydride) atom of TIPA, only interactions with the π system (π-hole) of the anhydride ring (further lp(O)···πh) were observed. Computational studies by a number of theoretical methods (molecular electrostatic potentials, the quantum theory of atoms in molecules, the independent gradient model, natural bond orbital analyses, the electron density difference, and symmetry-adapted perturbation theory) demonstrated that the X···O(anhydride) contacts in TCPA and TBPA and lp(O)···πh in TIPA are caused by the packing effect. The supramolecular architecture of isostructural TCPA and TBPA was mainly affected by X···O(acyl) and X···X HaBs, and, for TIPA, the main contribution provided I···I HaBs.     

The Bifurcated σ-Hole···σ-Hole Stacking Interactions

The bifurcated σ-hole···σ-hole stacking interactions between organosulfur molecules, which are key components of organic optical and electronic materials, were investigated by using a combined method of the Cambridge Structural Database search and quantum chemical calculation. Due to the geometric constraints, the binding energy of one bifurcated σ-hole···σ-hole stacking interaction is in general smaller than the sum of the binding energies of two free monofurcated σ-hole···σ-hole stacking interactions. The bifurcated σ-hole···σ-hole stacking interactions are still of the dispersion-dominated noncovalent interactions. However, in contrast to the linear monofurcated σ-hole···σ-hole stacking interaction, the contribution of the electrostatic energy to the total attractive interaction energy increases significantly and the dispersion component of the total attractive interaction energy decreases significantly for the bifurcated σ-hole···σ-hole stacking interaction. Another important finding of this study is that the low-cost spin-component scaled zeroth-order symmetry-adapted perturbation theory performs perfectly in the study of the bifurcated σ-hole···σ-hole stacking interactions. This work will provide valuable information for the design and synthesis of novel organic optical and electronic materials.     

Discovering protein–protein interaction stabilisers by native mass spectrometry

Protein–protein interactions (PPIs) are key therapeutic targets. Most PPI-targeting drugs in the clinic inhibit these important interactions; however, stabilising PPIs is an attractive alternative in cases where a PPI is disrupted in a disease state. The discovery of novel PPI stabilisers has been hindered due to the lack of tools available to monitor PPI stabilisation. Moreover, for PPI stabilisation to be detected, both the stoichiometry of binding and the shift this has on the binding equilibria need to be monitored simultaneously. Here, we show the power of native mass spectrometry (MS) in the rapid search for PPI stabilisers. To demonstrate its capability, we focussed on three PPIs between the eukaryotic regulatory protein 14-3-3σ and its binding partners estrogen receptor ERα, the tumour suppressor p53, and the kinase LRRK2, whose interactions upon the addition of a small molecule, fusicoccin A, are differentially stabilised. Within a single measurement the stoichiometry and binding equilibria between 14-3-3 and each of its binding partners was evident. Upon addition of the fusicoccin A stabiliser, a dramatic shift in binding equilibria was observed with the 14-3-3:ERα complex compared with the 14-3-3:p53 and 14-3-3:LRRK2 complexes. Our results highlight how native MS can not only distinguish the ability of stabilisers to modulate PPIs, but also give important insights into the dynamics of ternary complex formation. Finally, we show how native MS can be used as a screening tool to search for PPI stabilisers, highlighting its potential role as a primary screening technology in the hunt for novel therapeutic PPI stabilisers.

Stabilising protein–protein interactions is challenging, yet therapeutically important. Native mass spectrometry can be used to monitor binding equilibria, allowing identification and measurement of novel protein–protein interaction stabilisers.     

Stimuli Responsive Materials Supported by Orthogonal Hydrogen and Halogen Bonding or I···Alkene Interaction

Smart materials represent an elegant class of (macro)-molecules endowed with the ability to react to chemical/physical changes in the environment. Herein, we prepared new photo responsive azobenzenes possessing halogen bond donor groups. The X-ray structures of two molecules highlight supramolecular organizations governed by unusual noncovalent bonds. In azo dye I-azo-NO₂, the nitro group is engaged in orthogonal H···O···I halogen and hydrogen bonding, linking the units in parallel undulating chains. As far as compound I–azo–NH–MMA is concerned, a non-centrosymmetric pattern is formed due to a very rare I···π interaction involving the alkene group supplemented by hydrogen bonds. The Cambridge Structural Database contains only four structures showing the same I···CH₂=C contact. For all compounds, an ¹⁹F-NMR spectroscopic analysis confirms the formation of halogen bonds in solution through a recognition process with chloride anion, and the reversible photo-responsiveness is demonstrated upon exposing a solution to UV light irradiation. Finally, the intermediate I–azo–NH₂ also shows a pronounced color change due to pH variation. These azobenzenes are thereby attractive building blocks to design future multi-stimuli responsive materials for highly functional devices.     

A Nanoporous Supramolecular Metal–Organic Framework Based on a Nucleotide: Interplay of the π···π Interactions Directing Assembly and Geometric Matching of Aromatic Tails

Self-assembly is the most powerful force for creating ordered supramolecular architectures from simple components under mild conditions. π···π stacking interactions have been widely explored in modern supramolecular chemistry as an attractive reversible noncovalent tool for the nondestructive fabrication of materials for different applications. Here, we report on the self-assembly of cytidine 5’-monophosphate (CMP) nucleotide and copper metal ions for the preparation of a rare nanoporous supramolecular metal-organic framework in water. π···π stacking interactions involving the aromatic groups of the ancillary 2,2’-bipyridine (bipy) ligands drive the self-assemblies of hexameric pseudo-amphiphilic [Cu6(bipy)6(CMP)2(µ-O)Br4]²⁺ units. Owing to the supramolecular geometric matching between the aromatic tails, a nanoporous crystalline phase with hydrophobic and hydrophilic chiral pores of 1.2 and 0.8 nanometers, respectively, was successfully synthesized. The encoded chiral information, contained on the enantiopure building blocks, is transferred to the final supramolecular structure, assembled in the very unusual topology 8T6. These kinds of materials, owing to chiral channels with chiral active sites from ribose moieties, where the enantioselective recognition can occur, are, in principle, good candidates to carry out efficient separation of enantiomers, better than traditional inorganic and organic porous materials.     

Schiff Base in Ketoamine Form and Rh(η4-cod)-Schiff Base Complex with Z′ = 2 Structure from Pairwise C-H···Metallochelate-π Contacts

Condensation of 2-hydroxybenzaldehyde (salicylaldehyde) or 2-hydroxy-1-naphthaldehyde with 2-ethylaniline yields the Schiff base compound of (E)-2-(((2-ethylphenyl)imino)methyl)phenol (HL¹) or (E)-1-(((2-ethylphenyl)imino)methyl)naphthalen-2-ol (HL²), which in turn react with the dinuclear complex of [Rh(η⁴-cod)(µ-O₂CCH₃)]₂ (cod = cycloocta-1,5-diene) to afford the mononuclear (η⁴-cod){(E)-2-(((2-ethylphenyl)imino)methyl)phenolato-κ²N,O}rhodium(I), [Rh(η⁴-cod)(L¹)] (1) or (η⁴-cod){(E)-1-(((2-ethylphenyl)imino)methyl)naphthalen-2-olato-κ²N,O}rhodium(I), [Rh(η⁴-cod)(L²)] (2) (L¹ or L² = deprotonated Schiff base ligand). The X-ray structure determination revealed that the HL² exists in the solid state not as the usual (imine)N···H-O(phenol) form (enolamine form) but as the zwitterionic (imine)N-H⁺···^–O(phenol) form (ketoamine form). ¹H NMR spectra for HL² in different solvents demonstrated the existence of keto-enol tautomerism (i.e., keto ⇆ enol equilibrium) in solution. The structure for 1 and 2 showed that the deprotonated Schiff base ligand coordinates to the Rh(η⁴-cod)-fragment as a six-membered N^O-chelate around the rhodium atom with a close-to-square-planar geometry. Two symmetry-independent molecules (with Rh1 and Rh2) were found in the asymmetric unit in 1 in a structure with Z’ = 2. The supramolecular packing in HL² was organized by π-π and C-H···π contacts, while only two recognized C-H···π contacts were revealed in 1 and 2. Remarkably, there were reciprocal or pairwise C-H···π contacts between a pair of each of the symmetry-independent molecules in 1. This pairwise C-H contact to the Rh-N^O chelate (metalloaromatic) ring may be a reason for the two symmetry-independent molecules in 1. Differential scanning calorimetry (DSC) analyses revealed an irreversible phase transformation from the crystalline-solid to the isotropic-liquid phase and subsequently confirmed the thermal stability of the compounds. Absorption spectra in solution were explained by excited state properties from DFT/TD-DFT calculations.     

Cooperative stabilisation of 14-3-3σ protein–protein interactions via covalent protein modification

14-3-3 proteins are an important family of hub proteins that play important roles in many cellular processes via a large network of interactions with partner proteins. Many of these protein–protein interactions (PPI) are implicated in human diseases such as cancer and neurodegeneration. The stabilisation of selected 14-3-3 PPIs using drug-like ‘molecular glues’ is a novel therapeutic strategy with high potential. However, the examples reported to date have a number of drawbacks in terms of selectivity and potency. Here, we report that WR-1065, the active species of the approved drug amifostine, covalently modifies 14-3-3σ at an isoform-unique cysteine residue, Cys38. This modification leads to isoform-specific stabilisation of two 14-3-3σ PPIs in a manner that is cooperative with a well characterised molecular glue, fusicoccin A. Our findings reveal a novel stabilisation mechanism for 14-3-3σ, an isoform with particular involvement in cancer pathways. This mechanism can be exploited to harness the enhanced potency conveyed by covalent drug molecules and dual ligand cooperativity. This is demonstrated in two cancer cell lines whereby the cooperative behaviour of fusicoccin A and WR-1065 leads to enhanced efficacy for inducing cell death and attenuating cell growth.

The aminothiol WR-1065 covalently modifies 14-3-3σ to stabilse its interactions with p53 and ERα. It enhances the effect of fusicoccin A via a cooperative mechanism that leads to 14-3-3 partner-protein specific activty against cancer cells.      

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein–protein interactions

The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors.

A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.     

Molecular basis for acyl carrier protein–ketoreductase interaction in trans-acyltransferase polyketide synthases

The biosynthesis of polyketides by type I modular polyketide synthases (PKS) relies on co-ordinated interactions between acyl carrier protein (ACP) domains and catalytic domains within the megasynthase. Despite the importance of these interactions, and their implications for biosynthetic engineering efforts, they remain poorly understood. Here, we report the molecular details of the interaction interface between an ACP domain and a ketoreductase (KR) domain from a trans-acyltransferase (trans-AT) PKS. Using a high-throughput mass spectrometry (MS)-based assay in combination with scanning alanine mutagenesis, residues contributing to the KR-binding epitope of the ACP domain were identified. Application of carbene footprinting revealed the ACP-binding site on the KR domain surface, and molecular docking simulations driven by experimental data allowed production of an accurate model of the complex. Interactions between ACP and KR domains from trans-AT PKSs were found to be specific for their cognate partner, indicating highly optimised interaction interfaces driven by evolutionary processes. Using detailed knowledge of the ACP:KR interaction epitope, an ACP domain was engineered to interact with a non-cognate KR domain partner. The results provide novel, high resolution insights into the ACP:KR interface and offer valuable rules for future engineering efforts of biosynthetic assembly lines.

The interaction epitope between a cognate KR–ACP domain pairing from a trans-AT polyketide synthase is elucidated in molecular detail, providing unique insights into recognition and specificity of the interface.     

A proximity labeling method for protein–protein interactions on cell membrane

Antibodies targeting specific antigens are widely utilized in biological research to investigate protein interactions or to quantify target antigens. Here, we introduce antigen–antibody proximity labeling (AAPL), a novel method to map the antigen interaction sites as well as interactors of antibody-targeted proteins. As a proof of concept, AAPL was demonstrated using sodium/potassium transporting ATPase (ATP1A1) and epidermal growth factor receptor 2 (ERBB2)-specific antibodies that were modified with an Fe(iii) catalytic probe. Once bound to their target proteins, Fe(iii)-induced catalytic oxidation occurred in proximity of the antigen''s epitope. Oxidative proteomic analysis was then used to determine the degree of oxidation, the site of oxidation within the targeted antigen, and the interacting proteins that were in close proximity to the targeted antigen. An AAPL score was generated for each protein yielding the specificity of the oxidation and proximity of the interacting protein to the target antigen. As a final demonstration of its utility, the AAPL approach was applied to map the interactors of liver–intestine-cadherin (CDH17) in colon cancer cells.

Modified catalytic antibodies targeting specific antigens are employed to investigate protein interactions and antigen interaction sites.     

Dating Sediments by EPR Using Al-h Centre: A Comparison between the Properties of Fine (4–11 µm) and Coarse (>63 µm) Quartz Grains

The possibility of EPR dating for sediments using Al-h signals of fine (4–11 μm) grains of quartz has not been previously discussed. Here, the Al-h and peroxy EPR spectra of fine (4–11 μm) and coarse (63–90, 125–180 μm) sedimentary quartz from thoroughly investigated loess sites in Eastern Europe were examined. By comparing experimental spectra with a simulated signal, we evaluated the overestimation observed when using the standard approach established by Toyoda and Falguères to measure Al-h intensity for different doses of radiation, up to 40,000 Gy. This overestimation, caused by the presence of peroxy signals, was much more pronounced for fine grains. Fine grains exhibited some additional dose-dependent signals, which, for some samples, caused a complete distortion of the Al-h spectra at high doses, making it impossible to measure the standard amplitude. We propose a new approach to measuring Al-h signal intensity, focusing on the peak-to-baseline amplitude of the part of the signal at g ≈ 2.0603, which is not affected by the peroxy signals and therefore has the potential of providing more accurate results. The shapes of dose response curves constructed for coarse and fine grains using the new approach show considerable similarity, suggesting that Al-h centre formation in fine and coarse grains upon artificial radiation at room temperature follows the same pattern.     

七水合三氯化铈-碘化钠催化氨基苯硫酚与高位阻α, β-不饱和酮的迈克尔加成反应

对七水合三氯化铈-碘化钠(CeCl₃·7H₂O-NaI)化邻氨基苯硫酚、 对氯邻氨基苯硫酚、 间氨基苯硫酚、 对氨基苯硫酚和对甲基苯硫酚与α,β-不饱和酮(1a~1o)的迈克尔加成反应进行了系统研究. 结果表明, CeCl₃·7H₂O-NaI-SiO₂复合催化剂能有效催化邻氨基苯硫酚及对氯邻氨基苯硫酚与α,β-不饱和酮(1a~1o)的迈克尔加成反应. 在优化的反应条件下, 即n(CeCl₃·7H₂O):n(NaI):n(α,β-不饱和酮)=1:2:2, m(CeCl₃·7H₂O):m(SiO₂)=1:1.6, 三氯甲烷作溶剂, 反应温度为回流温度, 反应时间为2 h, 反应可达到中等产率(43.1%~58.8%). 催化剂重复使用4次基本稳定. 此外, 提出了可能的催化机理.