The three-year collaboration builds on the framework the companies have developed under a cancer metabolism partnership, which started in 2013.
Merck and Selvita will contribute funding and resources to support the latest collaboration.
The companies will bring their expertise in target validation, bioinformatics, medicinal chemistry, in vitro and in vivo biology, and toxicology.
Under the deal, Merck will have an exclusive license to the joint intellectual property. The company will make payments and royalties to Selvita after the development and commercialization of products.
The three-year collaboration includes a joint research phase up to lead identification, after which Merck will undertake additional research and develop the projects on its own.
Merck head of the translational innovation platform oncology Andree Blaukat said: "We are making strong progress in the area of cancer metabolism, and remain focused on bringing innovative new therapeutic options to patients that have the potential to make a substantial difference in their lives."
Selvita chief scientific officer Krzysztof Brzozka said: "Collaboration between Merck and Selvita is an excellent example of a successful joint drug discovery platform where both parties contribute their expertise to identify and validate novel therapeutic targets, in parallel developing new compounds and advancing them towards clinical development."