Putative Identification of New Phragmaline-Type Limonoids from the Leaves of Swietenia macrophylla King: A Case Study Using Mass Spectrometry-Based Molecular Networking

Abstract

Swietenia macrophylla King is a plant commonly known as Brazilian mahogany. The wood from its stem is highly prized for its exceptional quality, while its leaves are valued for their high content of phragmalin-type limonoids, a subclass of compounds known for their significant biological activities, including antimalarial, antitumor, antiviral, and anti-inflammatory properties. In this context, twelve isolated limonoids from S. macrophylla leaves were employed as standards in mass spectrometry-based molecular networking to unveil new potential mass spectrometry signatures for phragmalin-type limonoids. Consequently, ultra-performance liquid chromatography coupled with high-resolution mass spectrometry was utilized for data acquisition. Subsequently, the obtained data were analyzed using the Global Natural Products Social Molecular Networking platform based on spectral similarity. In summary, this study identified 24 new putative phragmalin-type limonoids for the first time in S. macrophylla. These compounds may prove valuable in guiding future drug development efforts, leveraging the already established biological activities associated with limonoids.

Keywords: GNPS; Meliaceae; limonoids; mahogany; mass spectrometry; molecular networking.

Figure 1

Workflow to putative identification of new phragmaline-type limonoids from the leaves of Swietenia macrophylla King.

Figure 2

Total Ion Chromatograms (TIC) from Swietenia macrophylla King leaves for DCMEt extract (A) and 12 standards (B) were obtained using UHPLC-HRMS in positive ionization mode (ESI⁺). The RT shift to compounds 1–3 is explained by the matrix effect in the extract caused by many compounds in the same range.

Figure 3

General fragmentation pathways proposed for the standards (isolated limonoids). Main functional groups and reactions are highlighted: (A) hydroxy in blue shadow; (B) acetate in green shadow; (C) carbomethoxy in pink shadow; and (D) tiglate or benzoate in orange shadow. The neutral loss of H₂O described in mechanism D1 could also occur via mechanism A, followed by loss of tiglate; (E) furan in yellow shadow; and (F) orthoester in red shadow. Loss of R-CO and R-COOH are characteristic for the 8,9,30-orthoester unit (R could be a methyl, isopropyl, tigloyl, or 2-methylbutyl).

Figure 4

Matches between reference MS/MS spectra of standards and experimental MS/MS spectra of annotated limonoids, considering the mass shift/difference in red shadow (A,B). Molecular network of the main cluster (C). The V-shaped node corresponds to isolated limonoids and their respective structure. The text below the structures indicates the parent ion and RT of the isolated compounds. The thickness limit (the line that connects two nodes) represents a spectral similarity (thicker, more similar MS Spectrum 0.65 < r > 0.95) and the dotted edge shows ion identity feature grouping.

Figure 5

Molecular network of the main cluster (A) (subfigures A1 and A2) and nodes group (B). Arrows indicate the propagated limonoids (diamond node) and their possible structure. The text below the structures indicates the parent ion and RT of the propagated compounds. The thickness limit (the line that connects two nodes) represents a spectral similarity (thicker, more similar MS Spectrum 0.65 < r > 0.95) and the dotted edge shows ion identity feature grouping.