A research team led by HONG Sungwoo, Associate Director of the Center for Catalytic Hydrocarbon Functionalizations within the Institute for Basic Science (IBS) and Professor at the Korea Advanced Institute of Science and Technology (KAIST), has developed a new molecular editing strategy that can directly convert pyridine compounds into their positional isomers. Instead of moving individual substituents around the molecule, the method relocates the nitrogen atom within the pyridine ring itself, allowing existing molecular structures to be reorganized while preserving their substituents.

Pyridine, a six-membered aromatic ring containing five carbon atoms and one nitrogen atom, is one of the most common structural motifs in pharmaceutical compounds. Even when two pyridine molecules contain exactly the same substituents, changing where those substituents are positioned relative to the nitrogen atom can substantially alter properties such as solubility, metabolic stability, and interactions with biological targets.

For this reason, medicinal chemists routinely compare different positional isomers when investigating structure–activity relationships. Obtaining these isomers, however, has traditionally required separate starting materials and independently designed synthetic routes. Attempts to move substituents directly are also difficult to generalize because different functional groups can require different reaction conditions.

The IBS team approached the problem from a different direction - rather than moving the substituents, they moved the nitrogen atom that defines their positions. Because positions around a pyridine ring are defined relative to its nitrogen atom, relocating the nitrogen changes the positional relationship of the substituents even though the substituents themselves remain attached to the same carbon atoms.

Moving the Reference Point Instead of the Substituents

Carrying out this idea required selectively removing the original nitrogen atom from the highly stable pyridine ring while inserting a new nitrogen atom at another position, without disrupting the surrounding carbon framework or functional groups.

The researchers accomplished this through a sequence of nitrogen insertion and deletion. A new nitrogen atom is first introduced into the pyridine framework, temporarily generating an expanded nitrogen-containing intermediate. The original pyridine nitrogen is then removed, while the externally supplied nitrogen remains in the reconstructed ring.

A key feature of the reaction is that the original nitrogen ultimately leaves as nitrogen gas (N₂), an exceptionally stable molecule. This provides a strong thermodynamic driving force for the transformation.

Because the intermediates involved are too short-lived to isolate directly, the researchers used isotope-labeling experiments to determine how the atoms move during the reaction. Reagents containing the heavier nitrogen isotope ¹⁵N showed that the nitrogen occupying the new position in the final pyridine came from the external reagent.

Additional experiments confirmed that the original pyridine nitrogen was expelled as part of nitrogen gas, while ¹³C labeling showed that the carbon atoms of the ring retained their original positions. Together, these results demonstrated that the reaction proceeds through genuine nitrogen transposition rather than wholesale rearrangement of the molecular framework.

The researchers also found that changing the solvent could influence which positional isomer was formed. Toluene strongly favored one positional arrangement, while more polar solvents produced different mixtures of isomers. This provides an additional means of accessing different molecular structures from the same starting material.

From Simple Pyridines to Existing Drugs

The method worked across mono-, di-, and multisubstituted pyridines and tolerated a wide range of functional groups commonly encountered in medicinal chemistry.

Importantly, because the substituents themselves do not need to participate directly in the reaction, several groups can effectively change their positional relationship at the same time while their identities and relative arrangement remain intact.

The researchers demonstrated the method on structurally complex molecules derived from compounds including menthol, sulindac, paracetamol, flurbiprofen, indomethacin, tedizolid, picamilon, oxaprozin, and estrone.

They then applied the strategy directly to marketed pyridine-containing drugs. Vismodegib, a Hedgehog pathway inhibitor used to treat advanced basal cell carcinoma, was converted into a corresponding positional isomer while preserving the rest of its molecular structure. The team likewise generated positional isomers of abiraterone acetate, used in prostate cancer treatment, and etoricoxib, a selective COX-2 inhibitor used for inflammatory disorders.

These examples demonstrate that nitrogen transposition can be applied even after substantial molecular complexity has already been built into a compound.

Turning Pyridine Position into a Design Variable

Previous approaches generally treated the substituent itself as the part of the molecule that needed to be moved. The new strategy instead changes the atomic framework of the pyridine ring while leaving the substituents untouched.

This distinction makes it possible to approach positional isomerization in a more general way. Rather than regarding the position of nitrogen within a pyridine ring as permanently fixed when the molecule is first synthesized, chemists can potentially treat it as a variable that can be altered at a later stage.

The approach could be particularly useful for structure–activity relationship studies in drug discovery. Starting from an existing molecular scaffold, researchers could generate positional isomers and directly compare how changes in substitution pattern affect physicochemical properties and biological activity, without designing an entirely separate synthesis for every candidate.

“The most important step was to stop asking how to move a substituent and instead ask whether it had to be moved at all,” said Associate Director Hong. “Paradoxically, adding an extra nitrogen was what let us strip the original nitrogen from an exceptionally stable pyridine as N₂ gas. That reversal of perspective was the breakthrough.”

The researchers plan to extend the concept to other nitrogen-containing heteroaromatic rings, with the goal of generating positional-isomer libraries more efficiently and establishing skeletal editing as a broader strategy for medicinal chemistry and organic synthesis.

The study was published in Nature.