Bioorthogonal Chemical Reporters for Selective In Situ Probing of Mycomembrane Components in Mycobacteria

The global pathogen Mycobacterium tuberculosis and other species in the suborder Corynebacterineae possess a distinctive outer membrane called the mycomembrane (MM). The MM is composed of mycolic acids, which are either covalently linked to an underlying arabinogalactan layer or incorporated into trehalose glycolipids that associate with the MM non‐covalently. These structures are generated through a process called mycolylation, which is central to mycobacterial physiology and pathogenesis and is an important target for tuberculosis drug development. Current approaches to investigating mycolylation rely on arduous analytical methods that occur outside the context of a whole cell. Herein, we describe mycobacteria‐specific chemical reporters that can selectively probe either covalent arabinogalactan mycolates or non‐covalent trehalose mycolates in live mycobacteria. These probes, in conjunction with bioorthogonal chemistry, enable selective in situ detection of the major MM components.     

Small Data Can Play a Big Role in Chemical Discovery

The chemistry community is currently witnessing a surge of scientific discoveries in organic chemistry supported by machine learning (ML) techniques. Whereas many of these techniques were developed for big data applications, the nature of experimental organic chemistry often confines practitioners to small datasets. Herein, we touch upon the limitations associated with small data in ML and emphasize the impact of bias and variance on constructing reliable predictive models. We aim to raise awareness to these possible pitfalls, and thus, provide an introductory guideline for good practice. Ultimately, we stress the great value associated with statistical analysis of small data, which can be further boosted by adopting a holistic data-centric approach in chemistry.     

Reliability of Click Chemistry on Drug Discovery: A Personal Account

The unprecedented efficiency, reliability and adaptability in drug discovery, with the growing number of applications and impact, have made Click Chemistry fascinating to the scientific community. The specificity, biocompatibility along with other principles of click chemistry offers a reliable platform for the synthesis of drug‐like molecules that can expedite the drug discovery process. This account summarizes such successes of versatile click reactions from our research group towards the development of functional molecules.     

Rational Design in Photopharmacology with Molecular Photoswitches

Photopharmacology is an attractive approach for achieving targeted drug action with the use of light. In photopharmacology, molecular photoswitches are introduced into the structure of biologically active small molecules to allow for the optical control of their potency. Going beyond trial and error, photopharmacology has progressively applied rational drug design methodologies to devise light-controlled bioactive ligands. In this review, we categorize photopharmacological efforts from the standpoint of medicinal chemistry strategies, focusing on diffusible photochromic ligands modified with photoswitches that operate through E-Z bond isomerization. In the vast majority of cases, photoswitchable ligands are designed as analogs of existing compounds, through a variety of approaches. By analyzing in detail a comprehensive list of instructive examples, we describe the state of the art and discuss future opportunities for rational design in photopharmacology.     

Automated and Efficient Generation of General Molecular Aggregate Structures

Modeling intermolecular interactions of complex non-covalent structures is important in many areas of chemistry. To facilitate the generation of reasonable dimer, oligomer, and general aggregate geometries, we introduce an automated computational interaction site screening (aISS) workflow. This easy-to-use tool combines a genetic algorithm employing the intermolecular force-field xTB-IFF for initial search steps with the general force-field GFN-FF and the semi-empirical GFN2-xTB method for geometry optimizations. Compared with the alternative CREST program, aISS yields similar results but with computer time savings of 1–3 orders of magnitude. This allows for the treatment of systems with thousands of atoms composed of elements up to radon, e.g., metal-organic complexes, or even polyhedra and zeolite cut-outs which were not accessible before. Moreover, aISS can identify reactive sites and provides options like site-directed (user-guided) screening.     

Controlled Chemical and Drug Delivery via the Internal and External Surfaces of Layered Compounds

Abstract

We demonstrate, and review the very small, but growing body of literature regarding a recently discovered application of layered compounds, which involves the ability of layered materials to sequester and later release molecules of chemical and biological significance. The application relies upon intercalation chemistry; a reversible process whereby atoms, molecules, macromolecules, and polymers may be inserted into the interstices of a layered matrix. We demonstrate that layered materials are able to effectively getter water‐soluble atoms and molecules from aqueous dispersions, and further demonstrate that the absorbed molecules can be later released from the interlayer region to perform a desired chemical function. Work in our laboratory involving the application of layered hybrid materials in photographic media is described in detail and we establish two general release mechanisms whereby intercalated functional chemistry can be first sequestrated and later delivered via a chemical switch to perform a desired function. The process has enormous potential as a general method for the controlled, temporal release of materials of chemical and biological significance.     

A General Organophotoredox Strategy to Difluoroalkyl Bicycloalkane (CF2-BCA) Hybrid Bioisosteres**

Here, we report a general approach to the synthesis of the difluoroalkyl bicycloalkanes (CF₂-BCAs), as structural surrogates of aryl ketones and ethers. The chemistry is driven by a dihydrobenzoacridine photocatalyst, that engages in a catalytic electron-donor acceptor (EDA) complex, or directly reduces the fluorinated substrate. These two convergent manifolds lead to the generation of the R-CF₂ radical, that reacts with the [1.1.1]- or [3.1.1.]-propellane. The method is extremely general, and extendable to complex bioactive molecules (30 examples, up to 87 % yield). The structural features of the CF₂-BCP hybrid bioisostere were investigated by single crystal X-ray. Finally, we synthesised a CF₂-BCP analogue of a Leukotriene A₄ hydrolase inhibitor, replacing the original aryl ether motif. In silico docking studies indicated that this new analogue maintains the same arrangement within the enzyme pocket, profiling the use of the CF₂-BCA hybrid bioisostere in medicinal chemistry settings.     

Cycling a Tether into Multiple Rings: Pt-Bridged Macrocycles for Differentiated Guest Recognition,Pseudorotaxane Transformations,and Guest Capture and Release

Macrocycle engineering is a key topic in supramolecular chemistry. When synthesizing a ring, one can obtain either complex mixtures of macrocycles of different sizes or a single ring if a template is utilized. Here, we unite these approaches along with post-synthetic modifications to transform a single tether into multiple rings—up to five per tether. The macrocycles contain two bridged phenylpyridine ligands that are connected through a Pt atom, which defines the rings’ shape, size, and host activity. All rings undergo redox reactions (between Pt^II and Pt^IV) that allow for large conformational changes. Their reactivity, together with their host performance, is a convenient way to control the capture and release of guests, to mediate ring transformations, and to control pseudorotaxane-to-pseudorotaxane conversions. This novel approach could serve to assemble other libraries of small ring molecules, create cyclic polymers bridged by responsive-at-metal nodes, and produce processable mechanically interlocked molecules.     

NH4+ Charge Carrier Coordinated H-Bonded Organic Small Molecule for Fast and Superstable Rechargeable Zinc Batteries

Organic small molecules as high-capacity cathodes for Zn-organic batteries have inspired numerous interests, but are trapped by their easy-dissolution in electrolytes. Here we knit ultrastable lock-and-key hydrogen-bonding networks between 2, 7-dinitropyrene-4, 5, 9, 10-tetraone (DNPT) and NH₄⁺ charge carrier. DNPT with octuple-active carbonyl/nitro centers (H-bond acceptor) are redox-exclusively accessible for flexible tetrahedral NH₄⁺ ions (H-bond donator) but exclude larger and rigid Zn²⁺, due to a lower activation energy (0.14 vs. 0.31 eV). NH₄⁺ coordinated H-bonding chemistry conquers the stability barrier of DNPT in electrolyte, and gives fast diffusion kinetics of non-metallic charge carrier. A stable two-step 4e⁻ NH₄⁺ coordination with DNPT cathode harvests a high capacity (320 mAh g⁻¹), a high-rate capability (50 A g⁻¹) and an ultralong life (60,000 cycles). This finding points to a new paradigm for H-bond stabilized organic small molecules to design advanced zinc batteries.     

The Chemistry of the Cyaphide Ion

We review the known chemistry of the cyaphide ion, (C≡P)⁻. This remarkable diatomic anion has been the subject of study since the late nineteenth century, however its isolation and characterization eluded chemists for almost a hundred years. In this mini-review, we explore the pioneering synthetic experiments that first allowed for its isolation, as well as more recent developments demonstrating that cyaphide transfer is viable in well-established salt-metathesis protocols. The physical properties of the cyaphide ion are also explored in depth, allowing us to compare and contrast the chemistry of this ion with that of its lighter congener cyanide (an archetypal strong field ligand and important organic functional group). Recent studies show that the cyaphide ion has the potential to be used as a versatile chemical regent for the synthesis of novel molecules and materials, hinting at many interesting future avenues of investigation.     

Acute Modulation of Mycobacterial Cell Envelope Biogenesis by Front‐Line Tuberculosis Drugs

Front‐line tuberculosis (TB) drugs have been characterized extensively in vitro and in vivo with respect to gene expression and cell viability. However, little work has been devoted to understanding their effects on the physiology of the cell envelope, one of the main targets of this clinical regimen. Herein, we use metabolic labeling methods to visualize the effects of TB drugs on cell envelope dynamics in mycobacterial species. We developed a new fluorophore–trehalose conjugate to visualize trehalose monomycolates of the mycomembrane using super‐resolution microscopy. We also probed the relationship between mycomembrane and peptidoglycan dynamics using a dual metabolic labeling strategy. Finally, we found that metabolic labeling of both cell envelope structures reports on drug effects on cell physiology in two hours, far faster than a genetic sensor of cell envelope stress. Our work provides insight into acute drug effects on cell envelope biogenesis in live mycobacteria.     

Editorial

This review details the combination of supramolecular chemistry and dendrimer chemistry. The use of supramolecular chemistry in the synthesis and modification of dendrimers, along with the application of dendrimers in supramolecular chemistry, is described. Many excellent examples exist within these areas; this review includes key examples intended to illustrate the main principles involved, and demonstrate the large number of possibilities presented through combining supramolecular and dendrimer chemistry.     

Ethene-1,1-disulfonyl Difluoride (EDSF) for SuFEx Click Chemistry: Synthesis of SuFExable 1,1-Bissulfonylfluoride Substituted Cyclobutene Hubs

We present the synthesis of 1,1-bis(fluorosulfonyl)-2-(pyridin-1-ium-1-yl)ethan-1-ide, a bench-stable precursor to ethene-1,1-disulfonyl difluoride (EDSF). The novel SuFEx reagent, EDSF, is demonstrated in the preparation of 26 unique 1,1-bissulfonylfluoride substituted cyclobutenes via a cycloaddition reaction. The regioselective click cycloaddition reaction is rapid, straightforward, and highly efficient, enabling the generation of highly functionalized 4-membered ring (4MR) carbocycles. These carbocycles are valuable structural motifs found in numerous bioactive natural products and pharmaceutically relevant small molecules. Additionally, we showcase diversification of the novel cyclobutene cores through selective Cs₂CO₃-activated SuFEx click chemistry between a single S−F group and an aryl alcohol, yielding the corresponding sulfonate ester products with high efficiency. Finally, density functional theory calculations offer mechanistic insights about the reaction pathway.     

Stabilization of Guest Molecules inside Cation-Lidded Cucurbiturils Reveals that Hydration of Receptor Sites Can Impede Binding

Docking of alkali metal ions to water-soluble macrocyclic receptors generally reduces the affinity of guest molecules due to competitive binding. The idea that solvation water molecules could display a larger steric hindrance towards guest binding than cations has not been considered to date. We show that the docking of large cations to cucurbit[5]uril (CB5) unexpectedly increases (by a factor of 5–8) the binding of hydrophobic guests, methane and ethane. This is due to the removal of water molecules from the carbonyl portals of CB5 during cation binding, which frees up space for hydrophobe encapsulation. In contrast, smaller cations like sodium protrude deeply into the cavity of CB5 and cause the expected decrease in binding, such that the rational selection of alkali cations allows for a variation of up to a factor of 20 in binding of methane and ethane. The statistical analysis of crystallographic data shows that the cavity volume of CB5 can be enlarged by placing large alkali ions (Rb⁺ and Cs⁺) centro-symmetrically at the portals. The results reveal a hitherto elusive steric hindrance of solvation water molecules near receptor binding sites, which is pertinent for the design of supramolecular catalysts and the understanding of biological receptors.     

Ex situ Generation of Thiazyl Trifluoride (NSF3) as a Gaseous SuFEx Hub**

Sulfur(VI)-fluoride exchange (SuFEx) chemistry, an all-encompassing term for substitution events that replace fluoride at an electrophilic sulfur(VI), enables the rapid and flexible assembly of linkages around a S^VI core. Although a myriad of nucleophiles and applications works very well with the SuFEx concept, the electrophile design has remained largely SO₂-based. Here, we introduce S≡N-based fluorosulfur(VI) reagents to the realm of SuFEx chemistry. Thiazyl trifluoride (NSF₃) gas is shown to serve as an excellent parent compound and SuFEx hub to efficiently synthesize mono- and disubstituted fluorothiazynes in an ex situ generation workflow. Gaseous NSF₃ was evolved from commercial reagents in a nearly quantitative fashion at ambient conditions. Moreover, the mono-substituted thiazynes could be extended further as SuFEx handles and be engaged in the synthesis of unsymmetrically disubstituted thiazynes. These results provide valuable insights into the versatility of these understudied sulfur functionalities paving the way for future applications.     

Biocompatible α-Methylenation of Metabolic Butyraldehyde in Living Bacteria

Small molecule organocatalysts are abundant in all living organisms. However, their use as organocatalysts in cells has been underexplored. Herein, we report that organocatalytic aldol chemistry can be interfaced with living Escherichia coli to enable the α-methylenation of cellular aldehydes using biogenic amines such as L-Pro or phosphate. The biocompatible reaction is mild and can be interfaced with butyraldehyde generated from D-glucose via engineered metabolism to enable the production of 2-methylenebutanal (2-MB) and 2-methylbutanal (2-MBA) by anaerobic fermentation, and 2-methylbutanol (2-MBO) by whole-cell catalysis. Overall, this study demonstrates the combination of non-enzymatic organocatalytic and metabolic reactions in vivo for the sustainable synthesis of valuable non-natural chemicals that cannot be accessed using enzymatic chemistry alone.     

Looking at orbitals in the laboratory: The experimental investigation of molecular wavefunctions and binding energies by electron momentum spectroscopy

The experimental technique of electron momentum spectroscopy (EMS ) (i.e., binary (e, 2e) spectroscopy) is discussed together with typical examples of its applications over the past decade in the area of experimental quantum chemistry. Results interpreted within the framework of the plane wave impulse and the target Hartree—Fock approximations provide direct measurements of, spherically averaged, orbital electron momentum distributions. Results for a variety of atoms and small molecules are compared with calculations using a range of Fourier transformed SCF position space wavefunctions of varying sophistication. Measured momentum distributions (MD ) provide a “direct” view of orbitals. In addition to offering a sensitive experimental diagnostic for semiempirical molecular wavefunctions, the MD's provide a chemically significant, additional experimental constraint to the usual variational optimization of wavefunctions. The measured MD's clearly reflect well known characteristics of various chemical and physical properties. It appears that EMS and momentum space chemistry offer the promise of supplementary perspectives and new vistas in quantum chemistry, as suggested by Coulson more than 40 years ago. Binding energy spectra in the inner valence region reveal, in many cases, a major breakdown of the simple MO model for ionization in accord with the predictions of many-body calculations. Results are considered for atomic targets, including H and the noble gases. The measured momentum distribution for H₂ is also compared with results from Compton scattering. Results for H₂ and H are combined to provide a direct experimental assessment of the bond density in H₂, which is compared with calculations. The behavior of the outer valence MD ''s for small row two and row three hydride molecules such as H₂O and H₂S, NH₃, HF, and HCl are consistent with well known differences in chemical and physical behavior such as ligand-donor activity and hydrogen bonding. MD measurements for the outermost valence orbitals of HF, H₂O and NH₃ show significant differences from those calculated using even very high-quality wavefunctions. Measurements of MD's for outer σ_g orbitals of small polyatomic molecules such as CO₂, COS, CS₂, and CF₄ show clear evidence of mixed s and p character. It is apparent that EMS is a sensitive probe of details of electronic structure and electron motion in atoms and molecules.     

Water-soluble Self-assembled {Pd84}Ac Polyoxopalladate Nano-wheel as a Supramolecular Host

Polyoxopalladates (POPs) are a class of self-assembling palladium-oxide clusters that span a variety of sizes, shapes and compositions. The largest of this family, {Pd₈₄}^Ac, is constructed from 14 building units of {Pd₆} and lined on the inner and outer torus by 28 acetate ligands. Due to its high water solubility, large hydrophobic cavity and distinct ¹H NMR fingerprint {Pd₈₄}^Ac is an ideal molecule for exploring supramolecular behaviour with small organic molecules in aqueous media. Molecular visualisation studies highlighted potential binding sites between {Pd₈₄}^Ac and these species. Nuclear Magnetic Resonance (NMR) techniques, including ¹H NMR, ¹H Diffusion Ordered Spectroscopy (DOSY) and Nuclear Overhauser Spectroscopy (NOESY), were employed to study the supramolecular chemistry of this system. Here, we provide conclusive evidence that {Pd₈₄}^Ac forms a 1 : 7 host-guest complex with benzyl viologen (BV²⁺) in aqueous solution.     

An Antibacterial β‐Lactone Kills Mycobacterium tuberculosis by Disrupting Mycolic Acid Biosynthesis

The spread of antibiotic resistance is a major challenge for the treatment of Mycobacterium tuberculosis infections. In addition, the efficacy of drugs is often limited by the restricted permeability of the mycomembrane. Frontline antibiotics inhibit mycomembrane biosynthesis, leading to rapid cell death. Inspired by this mechanism, we exploited β‐lactones as putative mycolic acid mimics to block serine hydrolases involved in their biosynthesis. Among a collection of β‐lactones, we found one hit with potent anti‐mycobacterial and bactericidal activity. Chemical proteomics using an alkynylated probe identified Pks13 and Ag85 serine hydrolases as major targets. Validation through enzyme assays and customized ¹³C metabolite profiling showed that both targets are functionally impaired by the β‐lactone. Co‐administration with front‐line antibiotics enhanced the potency against M. tuberculosis by more than 100‐fold, thus demonstrating the therapeutic potential of targeting mycomembrane biosynthesis serine hydrolases.     

A Dicyanomethyl Radical Conjugated with a Pyridylamino Group: Combining Radical-based Dynamic Covalent Chemistry and Coordination Chemistry

In this work, we aimed to develop a dicyanomethyl radical that undergoes both reversible C−C bond formation/dissociation and metal-ligand coordination reactions to combine dynamic covalent chemistry (DCC) based on organic radicals with coordination chemistry. We have previously reported a dicyanomethyl radical conjugated with a triphenylamine ( 1 ⋅) that exhibits a monomer/dimer equilibrium between the σ-bonded dimer ( 1₂ ). We designed and synthesized a novel dicyanomethyl radical with a pyridyl group as a coordination point ( 2 ⋅) by replacing the phenyl group of 1 ⋅ with a 3-pyridyl group. We showed that 2 ⋅ is also in an equilibrium with the σ-bonded dimer ( 2₂ ) in solution and has suitable thermodynamic parameters for application in DCC. 2₂ coordinates to PdCl₂ in a 2 : 2 ratio to selectively form a metallamacrocycle ( 2₂ )₂(PdCl₂)₂, and its structure was clarified by single crystal X-ray analysis. Variable-temperature NMR, ESR, and electronic absorption measurements revealed that ( 2₂ )₂(PdCl₂)₂ also undergoes the reversible C−C bond formation/dissociation reaction. Ligand-exchange experiment showed that 2₂ was liberated from ( 2₂ )₂(PdCl₂)₂ by the addition of another ligand with a higher affinity for Pd^II. This work demonstrated that DCC based on dicyanomethyl radicals works orthogonally to metal-ligand coordination reactions.