Cheminformatic characterization of natural products from Panama

Abstract

In this work, we discuss the characterization and diversity analysis of 354 natural products (NPs) from Panama, systematically analyzed for the first time. The in-house database was compared to NPs from Brazil, compounds from Traditional Chinese Medicine, natural and semisynthetic collections used in high-throughput screening, and compounds from ChEMBL. An analysis of the “global diversity” was conducted using molecular properties of pharmaceutical interest, three molecular fingerprints of different design, molecular scaffolds, and molecular complexity. The global diversity was visualized using consensus diversity plots that revealed that the secondary metabolites in the Panamanian flora have a large scaffold diversity as compared to other composite databases and also have several unique scaffolds. The large scaffold diversity is in agreement with the broad range of biological activities that this collection of NPs from Panama has shown. This study also provided further quantitative evidence of the large structural complexity of NPs. The results obtained in this study support that NPs from Panama are promising candidates to identify selective molecules and are suitable sources of compounds for virtual screening campaigns.

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Abbreviations

NPs:

Natural products

CIFPMA:

NPs database of CIFLORPAN, The University of Panama, Republic of Panama

UEFS:

NPs database of UEFS, The State University of Feira De Santana, Bahia, Brazil

MEGx:

NPs screening compounds

NATx:

Semisynthetic screening compounds

TCM:

Traditional Chinese Medicine, Taiwan

CDPs:

Consensus diversity plots

ECFP:

Extended connectivity fingerprints

MACCS:

Molecular Access System keys

CDF:

Cumulative distribution function

MOE:

Molecular operating environment

PCA:

Principal component analysis

MEQI:

Molecular equivalent indices

CSR:

Cyclic system recovery

Mol. Glob.:

Molecular globularity

\(\hbox {Fsp}^{3}\) :

Fraction of sp3-hybridized atoms

FCC:

Fraction of chiral centers

PMI:

Principal moment of inertia

NRP:

Ratio of normalized moment of inertia

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Acknowledgements

We thank the Faculty of Chemistry of the Univer sidad Nacional Autónoma de México for granting a postdoctoral stay. Authors thank the research group DIFACQUIM for their collaboration. DAO thanks the Office of Vice President for Academic affairs of the University of Panama for granting paid leave of absence for the accomplishment of the postdoctoral internship at UNAM. MPG and DAO acknowledge SNI awards from SENACYT of Panama. We also thank funding from the ‘Programa de Apoyo a la Investigaciónn y el Posgrado (PAIP) 50009163, Facultad de Química, UNAM.

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Correspondence to Dionisio A. Olmedo or José L. Medina-Franco.

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Olmedo, D.A., González-Medina, M., Gupta, M.P. et al. Cheminformatic characterization of natural products from Panama. Mol Divers 21, 779–789 (2017). https://doi.org/10.1007/s11030-017-9781-4

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Keywords

  • Cheminformatics
  • Chemical space
  • Chemical diversity
  • Consensus diversity plots
  • Natural products
  • Structural similarity
  • Panamanian biodiversity