NAOMInext

NAOMInext is a software tool supporting medicinal chemists during hit-to-lead optimization. Starting from a co-crystallized small fragment, synthetic feasible lead compounds are generated directly within the proteins binding site. Thus, the software implicitly perfoms target-focused library design.
The NAOMInext software package [1] comes with an easy-to-use graphical user interface providing access to robust organic synthesis reaction. [2] The 3D viewer allows for inspection of available extension vectors. Beyond that, user-defined constraints may be easily defined to guide the growing process into a specific sub pocket. Published vendor catalogues can be downloaded from ZINC [3,4].

[1] K. Sommer, F. Flachsenberg, M. Rarey, NAOMInext – Synthetically feasible fragment growing in a structure-based design context, Eur. J. Med. Chem. (2018). doi:10.1016/J.EJMECH.2018.11.075.

[2] M. Hartenfeller, M. Eberle, P. Meier, C. Nieto-Oberhuber, K.H. Altmann, G. Schneider, E. Jacoby, S. Renner, A collection of robust organic synthesis reactions for in silico molecule design, J. Chem. Inf. Model. 51 (2011) 3093–3098. doi:10.1021/ci200379p.

[3] J.J. Irwin, B.K. Shoichet, ZINC - A free database of commercially available compounds for virtual screening, J. Chem. Inf. Model. 45 (2005) 177–182. doi:10.1021/ci049714+

[4] ZINC - Building Blocks Catalogs

Software Availability

The tool NAOMInext is freely available for academic users for Linux (64 and 32bit) as well as Mac and Windows as part of our NAOMI ChemiBio Suite. Non-academic users can get an evaluation license free of charge. No setup steps are required to run NAOMInext. All feedback is hightly appreciated.