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Volume 7
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10.3390/ECMS2021-10829
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Abstract

NP Navigator: A New Online Tool for the Exploration of the Natural Products Chemical Space †

by
Yuliana Zabolotna
1,
Peter Ertl
2,
Dragos Horvath
1,
Fanny Bonachera
1,
Gilles Marcou
1 and
Alexandre Varnek
1,*
1
Laboratoire de Chémoinformatique, UMR 7140, CNRS, 67000 Strasbourg, France
2
Novartis Institutes for BioMedical Research, CH-4056 Basel, Switzerland
*
Author to whom correspondence should be addressed.
†
Presented at the 1st International Electronic Conference on Molecular Sciences: Druggable Targets of Emerging Infectious Diseases (ECMS 2021), 1–14 September 2021; Available online: https://ecms2021.sciforum.net/.
Med. Sci. Forum 2021, 7(1), 1; https://doi.org/10.3390/ECMS2021-10829
Published: 31 August 2021
(This article belongs to the Proceedings of The 1st International Electronic Conference on Molecular Sciences: Druggable Targets of Emerging Infectious Diseases)
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Versions Notes

Abstract

:
Over the last few billion years, countless organisms populating our planet have produced an extensive reserve of very diverse chemicals called natural products (NPs). Over time, these compounds have evolved to exhibit a wide range of bioactivity and high selectivity in different organisms. That makes them an extremely important source of potential drugs. However, considering the number of reported NPs and their high diversity, it becomes hard to explore the respective chemical space in drug design. In order to simplify this task, we have developed NP Navigator, a free, user friendly online tool allowing the navigation and analysis of the chemical space of NPs and NP-like compounds [1,2]. The basis of this tool is a hierarchical ensemble of 241 Generative Topographic Maps (GTM) [3,4], visualizing chemical space of NPs from the COlleCtion of Open Natural ProductTs (COCONUT) [5], molecules with some biological activity from ChEMBL [6], and purchasable compounds from ZINC [7]. NP Navigator can be used for an efficient analysis of various aspects of NPs, including calculated properties, chemotype distribution, biological activity, and commercial availability of NPs. Users can browse through hundreds of thousands of molecules from COCONUT, ZINC, and ChEMBL, selecting a zone of interest based on the color code of the maps, which in turn corresponds to specific values of visualized properties. In addition, it is possible to project several external molecules—“chemical trackers”—to trace regions of the NP chemical space containing compounds with desired structural features. In such a manner, the NP Navigator allows searching for NP and NP-like analogues of user-provided compounds. This study was previously published in Molecular Informatics (10.1002/minf.202100068) [1].

Figure 1. Search of the NPs and commercially available NP-like analogs of provided compound (curcumin) with the help of NP Navigator.

Supplementary Materials

The video demonstration of NP Navigator usage is available at https://sciforum.net/paper/view/10829 (accessed on 20 December 2021).

Author Contributions

All authors have participated in each stage of the research project and read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Publicly available datasets were analyzed in this study. The web implementation of the resulting interactive tool is available here: https://infochm.chimie.unistra.fr/npnav/chematlas_userspace (accessed on 20 December 2021).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Zabolotna, Y.; Ertl, P.; Horvath, D.; Bonachera, F.; Marcou, G.; Varnek, A. NP Navigator: A New Look at the Natural Product Chemical Space. Mol. Inform. 2021, 40, 2100068. [Google Scholar] [CrossRef] [PubMed]
  2. Laboratory of Chemoinformatics at the University of Strasbourg, NP Navigator. 2020. Available online: https://infochm.chimie.unistra.fr/npnav/chematlas_userspace/ (accessed on 20 December 2021).
  3. Bishop, C.M.; Svensén, M.; Williams, C.K.I. GTM: The Generative Topographic Mapping. Neural Comput. 1998, 10, 215–234. [Google Scholar] [CrossRef]
  4. Horvath, D.; Marcou, G.; Varnek, A. Generative topographic mapping in drug design. Drug. Discov. Today Technol. 2019, 32, 99–107. [Google Scholar] [CrossRef] [PubMed]
  5. Sorokina, M.; Merseburger, P.; Rajan, K.; Yirik, M.A.; Steinbeck, C. COCONUT online: Collection of Open Natural Products database. J. Cheminform. 2021, 13, 2. [Google Scholar] [CrossRef] [PubMed]
  6. Mendez, D.; Gaulton, A.; Bento, A.P.; Chambers, J.; De Veij, M.; Félix, E.; Magariños, M.P.; Mosquera, J.F.; Mutowo, P.; Nowotka, M.; et al. ChEMBL: Towards direct deposition of bioassay data. Nucleic Acids Res. 2019, 47, D930–D940. [Google Scholar] [CrossRef] [PubMed]
  7. Irwin, J.J.; Tang, K.G.; Young, J.; Dandarchuluun, C.; Wong, B.R.; Khurelbaatar, M.; Moroz, Y.S.; Mayfield, J.; Sayle, R.A. ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J. Chem. Inf. Model 2020, 60, 6065–6073. [Google Scholar] [CrossRef] [PubMed]
Msf 07 00001 g001 550
Figure 1. Search of the NPs and commercially available NP-like analogs of provided compound (curcumin) with the help of NP Navigator.
Figure 1. Search of the NPs and commercially available NP-like analogs of provided compound (curcumin) with the help of NP Navigator.
Msf 07 00001 g001
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MDPI and ACS Style

Zabolotna, Y.; Ertl, P.; Horvath, D.; Bonachera, F.; Marcou, G.; Varnek, A. NP Navigator: A New Online Tool for the Exploration of the Natural Products Chemical Space. Med. Sci. Forum 2021, 7, 1. https://doi.org/10.3390/ECMS2021-10829

AMA Style

Zabolotna Y, Ertl P, Horvath D, Bonachera F, Marcou G, Varnek A. NP Navigator: A New Online Tool for the Exploration of the Natural Products Chemical Space. Medical Sciences Forum. 2021; 7(1):1. https://doi.org/10.3390/ECMS2021-10829

Chicago/Turabian Style

Zabolotna, Yuliana, Peter Ertl, Dragos Horvath, Fanny Bonachera, Gilles Marcou, and Alexandre Varnek. 2021. "NP Navigator: A New Online Tool for the Exploration of the Natural Products Chemical Space" Medical Sciences Forum 7, no. 1: 1. https://doi.org/10.3390/ECMS2021-10829

APA Style

Zabolotna, Y., Ertl, P., Horvath, D., Bonachera, F., Marcou, G., & Varnek, A. (2021). NP Navigator: A New Online Tool for the Exploration of the Natural Products Chemical Space. Medical Sciences Forum, 7(1), 1. https://doi.org/10.3390/ECMS2021-10829

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