Halogen bonding is the electron density donation based weak interaction of halogens with Lewis bases. Its applicability for molecular recognition processes long remained unappreciated and has so far mostly been studied in silico and in solid state. As most physiological processes and chemical reactions take place in solution, investigations in solutions are of highest relevance for its use in the pharmaceutical and material scientific toolboxes. Following a short discussion of the phenomenon of halogen bonding, this tutorial review presents an overview of the methods hitherto applied for gaining an improved understanding of its behaviour in solutions and summarizes the gained knowledge in order to indicate the scope of the techniques and to facilitate exciting future developments.

Proteolysis targeting chimeras (PROTACs) induce intracellular degradation of target proteins. Their bifunctional structure puts degraders in a chemical space where ADME properties often complicate drug discovery. Herein we provide the first structural insight into PROTAC cell permeability obtained by NMR studies of a VHL-based PROTAC (1), which is cell permeable despite having a high molecular weight and polarity and a large number of rotatable bonds. We found that 1 populates elongated and polar conformations in solutions that mimic extra- and intracellular compartments. Conformations were folded and had a smaller polar surface area in chloroform, mimicking a cell membrane interior. Formation of intramolecular and nonclassical hydrogen bonds, π–π interactions, and shielding of amide groups from solvent all facilitate cell permeability by minimization of size and polarity. We conclude that molecular chameleonicity appears to be of major importance for 1 to enter into target cells.

Due to their electron deficiency, halonium ions act as particularly strong halogen bond donors. By accepting electrons in both lobes of their empty p-orbital, they are capable of simultaneously interacting with two Lewis bases. The interaction presumes the formation of three molecular orbitals and is accordingly typically entitled as a three-center halogen bond. In analogy to the [D–H–D]⁺ hydrogen bonds, which are at times entitled as short and strong bonds, the [D–X–D]⁺ halogen bonds of halonium ions show Bondi normalized interatomic distances of 0.6–0.7 and possess both charge transfer and electrostatic characteristics. The three-center halogen bond of halonium ions shows distinct differences in its properties from coordinative bonds of transition metals and is therefore applicable as a complementary synthon in supramolecular chemistry. The three-center halogen bond modulates the reactivity of halonium ions and is hence a useful tool for synthetic organic chemistry. Following the discussion of the nature and properties of halonium ions’ halogen bonds, this tutorial review provides an overview of their current applications to stimulate future developments.

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.