Designing an Orally Available Nontoxic p38 Inhibitor with a Fragment-Based Strategy

Abstract

The MAPK p38 became a focal point of inflammatory research when it was recognized that it played a key role in the production of the pro-inflammatory molecules TNF-alpha, IL-beta, and cyclooxygenase-2 (COX-2). The pharmaceutical industry devoted enormous efforts to creating p38 inhibitors, because blocking p38 had the potential of downregulating a group of pro-inflammatory mediators, and thus, one drug could have a cocktail effect. The market potential seemed to be clearly established (Bonafede et al., Clinicoecon Outcomes Res 6:381–388, 2014) with a multiplicity of TNF-alpha antibodies and a soluble receptor (Mewar and Wilson, Br J Pharmacol 162:785–791, 2011) already on the market, although the relationship between TNF-alpha production and p38 activation is a complicated two-way (Sabio and Davis, Semin Immunol 26:237–245, 2014) signal transduction process. With the discovery that activated p38 stabilizes (Mancini and Di Battista, Inflamm Res 60:1083–1092, 2011) COX-2 mRNA and upregulates expression of IL-beta (Bachstetter and Van Eldik, Aging Dis 1:199–211, 2010) probably in a similar manner, inhibiting p38 appeared to be a way of blocking TNF-alpha, COX-2, and IL-beta simultaneously. At Locus Pharmaceuticals we jumped on this opportunity, because we believed that our fragment-based drug discovery approach was ideally suited for making a potent small molecule p38 inhibitor that did not bind in the ATP site, but also had the solubility, lack of planarity, and low molecular weight required of a clinical candidate. Just to be clear, in our experience highly planar compounds often result in poor pharmacokinetics, because they tend to bind strongly to plasma proteins. At Locus we typically repeated assays by adding increasing amounts of plasma to check for potency degradation in the presence of blood. We found this to be a useful early indicator of pharmacokinetics and in vivo behavior. It became clear from our work and the work of others that binding to the ATP site resulted in nonspecific isoform toxicities, but binding in the adjacent allosteric DFG-site resulted in molecules that were too planar and too hydrophobic. Applying the computational method of Simulated Annealing of Chemical Potential (SACP) to this problem, we at Locus were able to come up with surprising fragment substitution patterns that led to potent non-ATP p38 inhibitors with the solubility and lack of planarity that resulted in potent in vivo efficacy in rodents with 33 % oral bioavailability. By using the simulations, we made only a small number of molecules and created a high quality clinical candidate. We also did extensive co-crystallography work, which demonstrated that the compounds bound in the mode predicted by the simulations. Unfortunately, all p38 programs ultimately shut down, because compelling evidence emerged that inhibiting p38 had no long-term clinical (Genovese, Arthritis Rheum 60:317–320, 2009) benefit. Devoting a large amount of limited resources to a target that ultimately turns out to be a mistake because it was not properly validated is a fatal error for a small company, and this is one of the reasons that Locus ultimately failed.