NAOMInext

Overview

NAOMInext is a software tool supporting medicinal chemists during hit-to-lead optimization. Starting with a co-crystallized small fragment, synthetically feasible lead compounds are generated directly within the protein’s binding site. Thus, the software implicitly performs target-focused library design.

The NAOMInext software package has an easy-to-use graphical user interface providing access to robust organic synthesis steps.[1] The 3D viewer allows for inspecting available extension vectors. Beyond that, users can easily define constraints to guide the growing process into a specific sub-pocket. Published vendor catalogs can be downloaded from ZINC[2] at https://zinc20.docking.org/.

[1] Hartenfeller, M.; Eberle, M.; Meier, P.; Nieto-Oberhuber, C.; Altmann, K. H.; Schneider, G.; Jacoby, E.; Renner, S. A Collection of Robust Organic Synthesis Reactions for In Silico Molecule Design. J Chem Inf Model 2011, 51 (12), 3093-3098. DOI: https://doi.org/10.1021/ci200379p
[2] Irwin, J. J.; Shoichet, B. K. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Model 2005, 45 (1), 177-182. DOI: https://doi.org/10.1021/ci049714+

Software Availability

NAOMInext is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download NAOMInext, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run NAOMInext. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Sommer, K.; Flachsenberg, F.; Rarey, M. NAOMInext - Synthetically Feasible Fragment Growing in a Structure-Based Design Context. Eur J Med Chem 2019, 163, 747-762. DOI: https://doi.org/10.1016/j.ejmech.2018.11.075