The story of pantoprazole's discovery is a good example of the stepwise development of PPIs. The main focus of modification of timoprazole was the benzimidazole part of its structure. Addition of a trifluoromethyl group to the benzimidazole moiety led to a series of very active compounds with varying solution-stability. In general fluoro substituents were found to block metabolism at the point where they were attached. Later the more balanced fluoroalkoxy substituent, instead of the highly lipophilic and strongly electron-withdrawing trifluoromethyl substituent, led to highly active compounds with supposed longer half-lives and higher solution stability.
It was realized that activity was somehow linked to instability in solution and then came to the conclusion that the cyclic sulfenamides, formed in acidic conditions, were the active principle of the PPIs. Finally, it was understood that seemingly small alterations in the backbone of timoprazole led nowhere, and focus had to be centered on the substituents on the backbone. However, necessary intramolecular rearrangement of the benzimidazole into sulfenamide posed severe geometric constraints. Optimal compounds would be those that were stable at neutral pH but were quickly activated at low pH.
A clear-cut design of active inhibitors was still not possible because in the complex multi-step chemistry the influence of a substituent on each step in the cascade could be different, and therefore not predictable for the overall rate of the prerequisite acid activation. Smith Kline and French, that entered into collaboration with Byk Gulden mid-1984, greatly assisted in determining criteria for further development. From 1985, the aim was to identify a compound with good stability at neutral pH, sustaining this higher level of stability down to pH 5 but being rapidly activateable at lower pHs, combined with a high level of H/K ATPase inhibition. From the numerous already synthesized and tested compounds that fulfilled these criteria the most promising candidates were pantoprazole and its salt, pantoprazole sodium.
In 1986 pantoprazole sodium sesquihydrate was synthesized and from 1987 onwards the development of pantoprazole was switched to the sodium salt which is more stable and has better compatibility with other excipients used in the drug formulation.
Pantoprazole was identified after nearly seven years of research and registered for clinical use after a further seven years of development, and finally reached its first market in 1994 in Germany. During the course of the studies on pantoprazole, more than 650 PPIs had been synthesized and evaluated. Pantoprazole obtained high selection criteria in its development process — especially concerning the favorable low potential for interaction with other drugs. Good solubility of pantoprazole and a very high solution stability allowed it to become the first marketed PPI for intravenous use in critical care patients.