NP Navigator: a New Look at the Natural Products Chemical Space

Natural products (NPs), being evolutionary selected over millions of years to bind to biological macromolecules, remain an important source of inspiration for medicinal chemists even after the advent of efficient drug discovery technologies such as combinatorial chemistry and high-throughput screening. Thus, there is a strong demand for efficient and user-friendly computational tools that allow to analyze large libraries of NPs. In this context, we present NP Navigator – a free, intuitive online tool for visualization and navigation through the chemical space of NPs and NP-like molecules^[1] (https://infochm.chimie.unistra.fr/npnav/chematlas_userspace ). It is based on the hierarchical ensemble of more than 200 Generative Topographic Maps(GTM)^[2], featuring NPs from the COlleCtion of Open NatUral producTs (COCONUT), bioactive compounds from ChEMBL and commercially available molecules from ZINC. NP Navigator allows to efficiently analyze different aspects of NPs - chemotype distribution, physicochemical properties, reported and/or predicted biological activity and commercial availability of NPs. Users are welcome not only to browse through hundreds of thousands of compounds from ZINC, ChEMBL and COCONUT but also project a several external molecules that play the role of “chemical trackers” allowing to trace particular chemotypes in the NP chemical space and detect analogs of the compound of interest.

[1] Y. Zabolotna, P. Ertl, D. Horvath, F. Bonachera, G. Marcou, A. Varnek, NP Navigator: a New Look at the Natural Product Chemical Space, 2021.
[2] C. M. Bishop, M. Svensén, C. K. I. Williams, Neural Comput. 1998, 10, 215-234.