Elucidating the Binding Mode of Sulfur- and Selenium-Based Cationic Chalcogen-Bond Donors.

For a comparison of the interaction modes of various chalcogen-bond donors, 2-chalcogeno-imidazolium salts have been designed, synthesized, and studied by single crystal X-ray diffraction, solution NMR and DFT as well as for their ability to act as activators in an SN1-type substitution reaction. Their interaction modes in solution were elucidated based on NMR diffusion and chemical shift perturbation experiments, which were supported by DFT-calculations. Our finding is that going from lighter to the heavier chalcogens, hydrogen bonding plays a less, while chalcogen bonding an increasingly important role for the coordination of anions. Anion-π interactions also show importance, especially for the sulfur and selenium derivatives.

Antiviral Rotenoids and Isoflavones Isolated from Millettia oblata ssp. teitensis.

Three new (1-3) and six known rotenoids (5-10), along with three known isoflavones (11-13), were isolated from the leaves of Millettia oblata ssp. teitensis. A new glycosylated isoflavone (4), four known isoflavones (14-18), and one known chalcone (19) were isolated from the root wood extract of the same plant. The structures were elucidated by NMR and mass spectrometric analyses. The absolute configuration of the chiral compounds was established by a comparison of experimental ECD and VCD data with those calculated for the possible stereoisomers. This is the first report on the use of VCD to assign the absolute configuration of rotenoids. The crude leaves and root wood extracts displayed anti-RSV (human respiratory syncytial virus) activity with IC50 values of 0.7 and 3.4 µg/mL, respectively. Compounds 6, 8, 10, 11, and 14 showed anti-RSV activity with IC50 values of 0.4-10 µM, while compound 3 exhibited anti-HRV-2 (human rhinovirus 2) activity with an IC50 of 4.2 µM. Most of the compounds showed low cytotoxicity for laryngeal carcinoma (HEp-2) cells; however compounds 3, 11, and 14 exhibited low cytotoxicity also in primary lung fibroblasts. This is the first report on rotenoids showing antiviral activity against RSV and HRV viruses.

Unexpected effect of halogenation on the water solubility of small organic compounds.

Halogenation is an indispensable method in the structural modification of lead compounds. It is known to increase lipophilicity and is hence used to improve membrane permeability and thus bioavailability. In this study, we compare the water solubility (logS) of organohalogen compounds and their non-halogenated parent compounds using the molecular matched pair (MMP) analysis method. Unexpectedly, 19.9% of the compounds increased their water solubility upon halogenation. Iodination was observed to have the greatest effect on solubility, followed by chlorination, bromination, and fluorination. Introducing amino, hydroxyl and carboxyl groups into organohalogens improves their aqueous solubilities, whereas introducing a trifluoromethyl group has the opposite effect. According to our quantum chemical calculations, the increased water solubility upon halogenation is, at least partially, attributed to an increased polarity and polarizability. These results improve our understanding of the influence of halogenation on bioactivity.

Exploring the chemical space of orally bioavailable PROTACs.

A principal challenge in the discovery of proteolysis targeting chimeras (PROTACs) as oral medications is their bioavailability. To facilitate drug design, it is therefore essential to identify the chemical space where orally bioavailable PROTACs are more likely to be situated. To this aim, we extracted structure-bioavailability insights from published data using traditional 2D descriptors, thereby shedding light on their potential and limitations as drug design tools. Subsequently, we describe cutting-edge experimental, computational and hybrid design strategies based on 3D descriptors, which show promise for enhancing the probability of discovering PROTACs with high oral bioavailability.

Is Simultaneous Binding to DNA and Gyrase Important for the Antibacterial Activity of Cystobactamids?

Cystobactamids are aromatic oligoamides that exert their natural antibacterial properties by inhibition of bacterial gyrases. Such aromatic oligoamides were proposed to inhibit α-helix-mediated protein-protein interactions and may serve for specific recognition of DNA. Based on this suggestion, we designed new derivatives that have duplicated cystobactamid triarene units as model systems to decipher the specific binding mode of cystobactamids to double stranded DNA. Solution NMR analyses revealed that natural cystobactamids as well as their elongated analogues show an overall bent shape at their central aliphatic unit, with an average CX-CY-CZ angle of ~110 degrees. Our finding is corroborated by the target-bound structure of close analogues, as established by cryo-EM very recently. Cystobactamid CN-861-2 binds directly to the bacterial gyrase with an affinity of 9 µM, and also exhibits DNA-binding properties with specificity for AT-rich DNA. Elongation/dimerization of the triarene subunit of native cystobactamids is demonstrated to lead to an increase in DNA binding affinity. This implies that cystobactamids' gyrase inhibitory activity necessitates not just interaction with the gyrase itself, but also with DNA via their triarene unit.

Fluorinated captopril analogues inhibit metallo-ß-lactamases and facilitate structure determination of NDM-1 binding pose.

Bacterial resistance to the majority of clinically used ß-lactam antibiotics is a global health threat and, consequently, the driving force for the development of metallo-ß-lactamase (MBL) inhibitors. The rapid evolution of new MBLs calls for new strategies and tools for inhibitor development. In this study, we designed and developed a series of trifluoromethylated captopril analogues as probes for structural studies of enzyme-inhibitor binding. The new compounds showed activity comparable to the non-fluorinated inhibitors against the New Delhi Metallo-ß-lactamase-1 (NDM-1). The most active compound, a derivative of D-captopril, exhibited an IC50 value of 0.3 µM. Several compounds demonstrated synergistic effects, restoring the effect of meropenem and reducing the minimum inhibitory concentration (MIC) values in NDM-1 (up to 64-fold), VIM-2 (up to 8-fold) and IMP-26 (up to 8-fold) harbouring Escherichia coli. NMR spectroscopy and molecular docking of one representative inhibitor determined the binding pose in NDM-1, demonstrating that fluorinated analogues of inhibitors are a valuable tool for structural studies of MBL-inhibitor complexes.

Halogen Bonds of Halogen(I) Ions─Where Are We and Where to Go?

Halenium ions, X+, are particularly strong halogen-bond donors that interact with two Lewis bases simultaneously to form linear [D···X···D]+-type halonium complexes. Their three-center, four-electron halogen bond is both fundamentally interesting and technologically valuable as it tames the reactivity of halogen(I) ions, opening up new horizons in a variety of fields including synthetic organic and supramolecular chemistry. Understanding this bonding situation enables the development of improved halogen(I) transfer reactions and of advanced functional materials. Following a decade of investigations of basic principles, the range of applications is now rapidly widening. In this Perspective, we assess the status of the field and identify its key advances and the main bottlenecks. Clearing common misunderstandings that may hinder future progress, we aim to inspire and direct future research efforts.

Molecular chameleons in drug discovery.

Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.

α-Aminophosphonate inhibitors of metallo-ß-lactamases NDM-1 and VIM-2.

The upswing of antibiotic resistance is an escalating threat to human health. Resistance mediated by bacterial metallo-ß-lactamases is of particular concern as these enzymes degrade ß-lactams, our most frequently prescribed class of antibiotics. Inhibition of metallo-ß-lactamases could allow the continued use of existing ß-lactam antibiotics, such as penicillins, cephalosporins and carbapenems, whose applicability is becoming ever more limited. The design, synthesis, and NDM-1, VIM-2, and GIM-1 inhibitory activities (IC50 4.1-506 µM) of a series of novel non-cytotoxic α-aminophosphonate-based inhibitor candidates are presented herein. We disclose the solution NMR spectroscopic and computational investigation of their NDM-1 and VIM-2 binding sites and binding modes. Whereas the binding modes of the inhibitors are similar, VIM-2 showed a somewhat higher conformational flexibility, and complexed a larger number of inhibitor candidates in more varying binding modes than NDM-1. Phosphonate-type inhibitors may be potential candidates for development into therapeutics to combat metallo-ß-lactamase resistant bacteria.

Do non-coordinating polymers function as host materials for solid polymer electrolytes? The case of PVdF-HFP.

In the search for novel solid polymer electrolytes (SPEs), primarily targeting battery applications, a range of different polymers is currently being explored. In this context, the non-coordinating poly(vinylidene fluoride-co-hexafluoropropylene) (PVdF-HFP) polymer is a frequently utilized system. Considering that PVdF-HFP should be a poor solvent for cation salts, it is counterintuitive that this is a functional host material for SPEs. Here, we do an in-depth study of the salt dissolution properties and ionic conductivity of PVdF-HFP-based electrolytes, using two different fabrication methods and also employing a low-molecular-weight solvent analogue. It is seen that PVdF-HFP is remarkably poor as an SPE host, despite its comparatively high dielectric constant, and that the salt dissolution properties instead are controlled by fluorophilic interactions of the anion with the polymer.

Ensemble determination by NMR data deconvolution.

Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.

Benzo[b]naphtho[2,1-d]furans and 2-Phenylnaphthalenes from Streblus usambarensis.

Three new benzo[b]naphtho[2,1-d]furans, usambarins A-C (1-3), five new 2-phenylnaphthalenes, usambarins D-H (4-8), a new flavan (9), and a new phenyl-1-benzoxepin (10) as well as two known compounds (11 and 12) were isolated from the extract of the stem and roots of Streblus usambarensis (Moraceae). The structures were deduced using NMR spectroscopic and mass spectrometric analyses, and those of compounds 1 and 4 were confirmed by X-ray crystallography. Usambarin D (4) demonstrated moderate antibacterial activity (MIC 9.0 µM) against Bacillus subtilis, while none of the tested compounds were effective against Escherichia coli.

1-Phospha-Butadienes and 1H-Phospholes via Alkynylation of Acetylenic Phosphaalkenes.

Carbon-rich motifs are important building blocks for the fabrication of functional and opto-electronic materials. Electronic tuning can be achieved by alteration of bonding topologies but also via incorporation of heteroelements, for example phosphorus. Herein we present the palladium/copper mediated formation of branched 1-phospha-butadiene derivatives through an unusual alkynylation of a phospha-enyne fragment. Structural and NMR studies provide mechanistic insights into this alkynylation. Furthermore, we disclose a complex cyclisation of the thus obtained 3-yne-1-phosphabutadiene motifs to give highly substituted phosphole derivatives identified by 2D NMR and SC-XRD analysis.

Crotofolane Diterpenoids and Other Constituents Isolated from Croton kilwae.

Six new crotofolane diterpenoids (1-6) and 13 known compounds (7-19) were isolated from the MeOH-CH2Cl2 (1:1, v/v) extracts of the leaves and stem bark of Croton kilwae. The structures of the new compounds were elucidated by extensive analysis of spectroscopic and mass spectrometric data. The structure of crotokilwaepoxide A (1) was confirmed by single-crystal X-ray diffraction, allowing for the determination of its absolute configuration. The crude extracts and the isolated compounds were investigated for antiviral activity against respiratory syncytial virus (RSV) and human rhinovirus type-2 (HRV-2) in HEp-2 and HeLa cells, respectively, for antibacterial activity against the Gram-positive Bacillus subtilis and the Gram-negative Escherichia coli, and for antimalarial activity against the Plasmodium falciparum Dd2 strain. ent-3ß,19-Dihydroxykaur-16-ene (7) and ayanin (16) displayed anti-RSV activities with IC50 values of 10.2 and 6.1 µM, respectively, while exhibiting only modest cytotoxic effects on HEp-2 cells that resulted in selectivity indices of 4.9 and 16.4. Compounds 2 and 5 exhibited modest anti-HRV-2 activity (IC50 of 44.6 µM for both compounds), while compound 16 inhibited HRV-2 with an IC50 value of 1.8 µM. Compounds 1-3 showed promising antiplasmodial activities (80-100% inhibition) at a 50 µM concentration.

Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds.

The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.

Modified ent-Abietane Diterpenoids from the Leaves of Suregada zanzibariensis.

The leaf extract of Suregada zanzibariensis gave two new modified ent-abietane diterpenoids, zanzibariolides A (1) and B (2), and two known triterpenoids, simiarenol (3) and ß-amyrin (4). The structures of the isolated compounds were elucidated based on NMR and MS data analysis. Single-crystal X-ray diffraction was used to establish the absolute configurations of compounds 1 and 2. The crude leaf extract inhibited the infectivity of herpes simplex virus 2 (HSV-2, IC50 11.5 µg/mL) and showed toxicity on African green monkey kidney (GMK AH1) cells at CC50 52 µg/mL. The isolated compounds 1-3 showed no anti-HSV-2 activity and exhibited insignificant toxicity against GMK AH1 cells at ≥100 µM.

Linker-Dependent Folding Rationalizes PROTAC Cell Permeability.

Proteolysis-targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and molecular dynamics (MD) simulations independently to gain insights into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with a low solvent-accessible 3D polar surface area in an apolar environment is correlated to high cell permeability. The chemical nature and the flexibility of the linker were essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, π-π interactions, and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs.

Do 2-coordinate iodine(I) and silver(I) complexes form nucleophilic iodonium interactions (NIIs) in solution?

The interaction of a [bis(pyridine)iodine(I)]+ cation with a [bis(pyridine)silver(I)]+ cation, in which an iodonium ion acts as a nucleophile by transferring electron density to the silver(I) cation, is reinvestigated herein. No measurable interaction is observed between the cationic species in solution by NMR; DFT reveals that if there is an attractive interaction between these complexes in solution, it is dominantly the π-π interaction of pyridines.

Polyoxygenated cyclohexene derivatives and flavonoids from the leaves of Uvaria pandensis.

Three new oxygenated cyclohexene derivatives, pandensenol D - F (1-3), two new flavanoids, pandensone A and B (4-5), and seven known compounds (6-12) were isolated from the methanol extract of the leaves of Uvaria pandensis Verdc. (Annonaceae). The structures were characterized by NMR spectroscopic and mass spectrometric analyses. The isolated metabolites were evaluated for their antibacterial activity against the Gram-positive bacteria Bacillus subtilis and Staphylococcus epidermidis, the Gram-negative bacteria Enterococcus raffinosus, Escherichia coli, Paraburkholderia caledonica, Pectobacterium carotovorum and Pseudomonas putida, and for cytotoxicity against the MCF-7 human breast cancer cell line. Out of the tested compounds, pandensenol D (1) and (6',7'-dihydro-8'α,9'ß-dihydroxy)-3-farnesylindole (12) showed weak activity, whereas (8'α,9'ß-dihydroxy)-3-farnesylindole (11) strong activity against B. subtilis. Four of the isolated compounds (1, 4, 11 and 12) showed moderate cytotoxicity against MCF-7 breast cancer cells (EC50 > 100 µM).

Metallo-ß-Lactamase Inhibitor Phosphonamidate Monoesters.

Being the second leading cause of death and the leading cause of disability-adjusted life years worldwide, infectious diseases remain-contrary to earlier predictions-a major consideration for the public health of the 21st century. Resistance development of microbes to antimicrobial drugs constitutes a large part of this devastating problem. The most widely spread mechanism of bacterial resistance operates through the degradation of existing ß-lactam antibiotics. Inhibition of metallo-ß-lactamases is expected to allow the continued use of existing antibiotics, whose applicability is becoming ever more limited. Herein, we describe the synthesis, the metallo-ß-lactamase inhibition activity, the cytotoxicity studies, and the NMR spectroscopic determination of the protein binding site of phosphonamidate monoesters. The expression of single- and double-labeled NDM-1 and its backbone NMR assignment are also disclosed, providing helpful information for future development of NDM-1 inhibitors. We show phosphonamidates to have the potential to become a new generation of antibiotic therapeutics to combat metallo-ß-lactamase-resistant bacteria.