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. 2022 Nov 8;12(11):1083.
doi: 10.3390/metabo12111083.

The Roots of Deguelia nitidula as a Natural Antibacterial Source against Staphylococcus aureus Strains

Suzana Helena Campelo Nogueira-Lima  1 , Paulo Wender P Gomes  2   3 , Kely C Navegantes-Lima  4 , José Diogo E Reis  5 , Alice Rhelly Veloso Carvalho  6 , Sônia das Graças Santa R Pamplona  5 , Abraão de Jesus B Muribeca  5 , Milton N da Silva  5 , Marta C Monteiro  1   4 , Consuelo Yumiko Yoshioka E Silva  1
Affiliations

The Roots of Deguelia nitidula as a Natural Antibacterial Source against Staphylococcus aureus Strains

Suzana Helena Campelo Nogueira-Lima et al. Metabolites. .

Abstract

Deguelia nitidula (Benth.) A.M.G.Azevedo & R.A.Camargo (Fabaceae) is an herbaceous plant distributed in the Brazilian Amazon, and it is called "raiz do sol" (sun roots). On Marajó Island, quilombola communities use its prepared roots to treat skin diseases commonly caused by fungi, viruses, and bacteria. Thus, in this study, the extract, and its fractions from D. nitidula roots were used to perform in vitro cytotoxic and antibacterial assays against Staphylococcus aureus strains. Thereafter, liquid chromatography-mass spectrometry (LC-MS) was used for the metabolite annotation process. The ethanolic extract of D. nitidula roots show significant bactericidal activity against S. aureus with IC50 82 μg.mL-1 and a selectivity index (SI) of 21.35. Furthermore, the SREFr2 and SREFr3 fractions show a potent bactericidal activity, i.e., MIC of 46.8 μg.mL-1 for both, and MBC of 375 and 93.7 μg.mL-1, respectively. As showcased, SREFr3 shows safe and effective antibacterial activity mainly in respect to the excellent selectivity index (SI = 82.06). On the other hand, SREFr2 shows low selectivity (SI = 6.8), which characterizes it as not safe for therapeutic use. Otherwise, due to a limited amount of reference MS2 spectra in public libraries, up to now, it was not possible to perform a complete metabolite annotation. Despite that, our antibacterial results for SREFr3 and correlated substructures of amino acid derivatives show that the roots of D. nitidula are a natural source of specialized metabolites, which can be isolated in the future, and then used as a support for further bio-guided research, as well as natural drug development.

Keywords: Staphylococcus aureus; amino acid derivative; antibacterial activity; liquid chromatography–mass spectrometry.

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Conflict of interest statement

We declare no current or potential conflict of interest related to this article.

Figures

Figure 1
Figure 1
Cell viability was assessed by MTT assays with the extract and its fractions from D. nitidula roots. (A) Ethanolic extract of D. nitidula roots (SREE). (B) Hexane fraction (SREFr1). (C) Dichloromethane fraction (SREFr2). (D) Ethyl acetate fraction (SREFr3). (E) Methanol fraction (SREFr4). Data presented as mean ± SD. (* p < 0.05 extract, its fractions from D. nitidula roots or Triton 1% vs. RPMI control). RPMI: Gibco Roswell Park Memorial Institute 1640 Medium; Tri 1%: Triton X-100 1% (v/v).
Figure 2
Figure 2
(A) The LC–MS fingerprints of the extract and its fractions from D. nitidula roots. (B) Matches between experimental MS/MS spectra and reference MS/MS spectra from GNPS libraries for the annotated flavonoid derivatives (1–4) in the SREE.B1-B4 in the SREE, SREFr2, and SREFr4 (link to see the mirror plots: https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=7cfcdd2029174559a7c87182189fc568&view=view_all_annotations_DB (accessed on 7 October 2022)).
Figure 3
Figure 3
Principal component of analysis (PCA) for the extract and its fractions in duplicates (a); main bioactive metabolites for the SREFr3 highlighted in green (b); and fold change chart between SREE and SREFr3. Red points refer to metabolites in high relative concentration in SREE with at least a double change; Green points refer to metabolites in high relative concentration in SREFr3 with at least a double change; Grey points no significant fold changes were observed (c).
Figure 4
Figure 4
SREFr3 MS/MS spectrum highlighting annotated product ions of m/z 281 and m/z 111, which have amino acid derivatives from asparagine (green shadow).
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