MMV Project of the Year award - 2009

Spiroindolones

Emerging from a cutting-edge screening technique and overcoming all the obstacles to become a preclinical candidate, the spiroindolone compound class provides novel chemistry with excellent antimalarial potential.

The Genomics Institute of the Novartis Research Foundation specifically developed and optimized a high throughput P. falciparum screen with the objective of identifying new compounds active against malaria. With this technology the team was able to screen the entire Novartis natural product library of more than 12,000 compounds in just one and a half days – a job that previously would have taken months to complete. The library contains compounds from a wide range of natural sources, including plants, mycobacteria and fungi, in addition to a number of synthetically derived naturalproduct- like compounds. The key strength of the library is that the compounds it contains represent much of the chemical diversity found in nature.

At a very early stage, the spiroindolones (spirotetrahydro-ß-carbolines chemical class) stood out from other compounds due to their favorable physical and chemical properties for drug development. But crucially, the class demonstrated a rapid ability to kill the blood-stages of both P. falciparum and P. vivax. Research is ongoing at the Swiss Tropical and Public Health Institute and the Genomics Institute of the Novartis Research Foundation to determine their exact mechanism of action on Plasmodium. Preliminary evidence, however, suggests that the mechanism is distinct from that of other antimalarial drugs. In the context of emerging drug resistance to artemisinin, this is excellent news.

Natural products provide an exciting starting point for drug discovery due to their structural diversity, but this diversity often comes at a cost – complexity. Such increased molecular complexity makes the task for the medicinal chemist all the more difficult. The spiroindolones, however, take advantage of being both natural productlike and fully synthetic – they maintain the chemical diversity of a natural product without the added complexity. The chemical scaffold contains only the elements believed to be active against the parasite and thus the spiroindolones are ideal for medicinal chemistry optimization.

A lead-optimization programme was initiated at the Novartis Institute for Tropical Diseases (NITD) in December 2007 with the goal to further improve the antimalarial activity and pharmacological properties of the spiroindolone class. One of the first challenges to be overcome was to determine the exact chemical structure and molecular configuration of the original sample. This was required since the spiroindolone identified from the Novartis library consisted of a mixture of enantiomers (two mirror images of a molecule which cannot be superimposed onto each other). The team employed a specific procedure to separate the pair of enantiomers followed by x-ray crystallography to clearly elucidate their structures.

Remarkably, when the individual enantiomers were tested separately for their antimalarial activity, the team found that only one enantiomer was responsible for killing the parasite; the other was completely inactive. Despite identifying the active enantiomer, further optimization was required. To assure the compound could become a long-lasting, low-dose antimalarial, the team needed to slow its metabolism down – thereby assuring its presence in the body for longer. These chemical optimizations translated to excellent in vivo efficacy in experiments carried out at the Swiss Tropical and Public Health Institute; complete cure was achieved at low doses in the P. berghei-infected mouse model. This lead optimization effort culminated in the selection of NITD 609 as a new antimalarial drug candidate.

In 2010, the selected drug candidate is expected to complete preclinical evaluation that will enable the initiation of the first trials in man (Phase I) in 2011.

The project team

The key to the success of this project has been its diversity; not only with regard to chemistry but also, importantly, in terms of the skills of the team. Lead by Thierry Diagana of the Novartis Institute for Tropical Diseases, the project team was able to draw on Novartis’ structured network of research centres from the Swiss Tropical and Public Health Institute, and the Singapore Immunology Network.

Novartis Natural Products Unit maintains the natural product library and under the leadership of Esther Schmit was able to identify and confirm the structure of the original spiroindolone hit.

Genomic Institute of the Novartis Research Foundation tailored the screening technology to the needs of the project and supported the in vitro efficacy tests. Case McNamara and Elizabeth Winzeler’s laboratory continue to work on elucidating the mode of action and the mechanism of resistance for the spiroindolones.

Novartis Institute for Tropical Diseases performed the medicinal chemistry work and lead-optimization of the synthetic spiroindolone under the leadership of Bryan Yeung.

Novartis Institute for Biomedical Research developed the method used to separate the enantiomers of the spiroindolones and identified their x-ray crystal structures.

Swiss Tropical and Public Health Institute conducted the in vitro and in vivo efficacy experiments under the leadership of Matthias Rottmann.

Singapore Immunology Network took responsibility for in vitro testing of the spiroindolones against P. vivax and P. falciparum clinical isolates under the direction of Laurent Renia.

This project is co-funded by the Wellcome Trust, Singapore Economic Development Board, Novartis and MMV.