Metabolomic Profiling, In Vitro Antimalarial Investigation and In Silico Modeling of the Marine Actinobacterium Strain Rhodococcus sp. UR111 Associated with the Soft Coral Nephthea sp.

Abstract

Malaria is a persistent illness with a great public health concern. To combat this fatal disease, developing effective antimalarial medications has become a necessity. In the present study, we described the actinomycetes associated with the Red Sea soft coral Nephthea sp. and isolated a strain that was sub-cultured in three different media (M1, ISP2, and OLIGO). Actinomycete isolate’s phylogenetic analysis of the 16S rRNA gene revealed that it belongs to the genus Rhodococcus. In vitro screening of the antimalarial activity for three extracts against Plasmodium falciparum was carried out. Non-targeted metabolomics for the chemical characterization of the isolated actinomycete species UA111 derived extracts were employed using high-resolution liquid chromatography–mass spectrometry (LC-HR-MS) for dereplication purposes. Additionally, statistical analysis of the vast LC-MS data was performed using MetaboAnalyst 5.0. Finally, an in silico analysis was conducted to investigate the potential chemical compounds that could be the source of the antimalarial potential. The results revealed that ISP2 media extract is the most effective against Plasmodium falciparum, according to antimalarial screening (IC50 8.5 µg/mL), in contrast, OLIGO media extract was inactive. LC-HRMS-based metabolomics identified a range of metabolites, mainly alkaloids, from the genus Rhodococcus. On the other hand, multivariate analysis showed chemical diversity between the analyzed samples, with ISP2 extract being optimal. The docking analysis was able to anticipate the various patterns of interaction of the annotated compounds with three malarial protein targets (P. falciparum kinase, P. falciparum cytochrome bc1 complex, and P. falciparum lysyl-tRNA synthetase). Among all of the test compounds, perlolyrine (11) and 3097-B2 (12) displayed the best docking profiles. In conclusion, this work demonstrated the value of the established method for the metabolic profiling of marine actinomycetes using the data from liquid chromatography–mass spectrometry (LC-MS), which helps to streamline the difficult isolation stages required for their chemical characterization. In addition, the antimalarial efficacy of this strain has intriguing implications for future pharmaceutical development.

Targeting antimalarial metabolites from the actinomycetes associated with the Red Sea sponge Callyspongia siphonella using a metabolomic method

“…On the other hand, the focus on target-based drug discovery and finding targeted antimalarial drugs that treat all stages of the disease became a need. Previously published data revealed the presence of various malarial targets that affects different stages of parasite infection [8], among them, lysyl-tRNA synthetase, [38] which is an enzyme central to protein translation and responsible for protein formation [39]. Earlier studies revealed that lysyl-tRNA synthetase could be considered as an attractive, druggable, antimalarial target that can be selectively inhibits protein synthesis and prevents liver and blood-stage proliferation [34][35][36][37][38].…”

“…All media were supplemented with 0.2 µm pore size filtered cycloheximide (100 µg/mL), nystatin (25 µg/mL) and nalidixic acid (25 µg/mL) to facilitate the isolation of slow-growing actinobacteria. Cycloheximide and nystatin inhibit fungal growth, while nalidixic acid inhibits many fast-growing Gram-negative bacteria [ 8 ]. All media contained Difco Bacto agar (18 g/L) and were prepared in 1 L artificial sea water (NaCl 234.7 g, MgCl 2 .6 H 2 O 106.4 g, Na 2 SO 4 39.2 g, CaCl 2 11.0 g, NaHCO 3 1.92 g, KCl 6.64 g, KBr 0.96 g, H 3 BO 3 0.26 g, SrCl 2 0,24 g, NaF 0.03 g and ddH 2 O to 10.0 L).…”

“…So far, at least 32 bacterial phyla and candidate groups have been identified in marine sponges, including Acidobacteria, Actinobacteria, Chloroflexi, Nitrospira, Cyanobacteria, Bacteriodetes, Gemmatimonadetes, Planctomycetes, Spirochaetes and Proteobacteria. Actinomycetes, particularly those associated with marine sponges are well-known for their capacity to generate novel lead molecules including phenazines, peptides and alkaloids of clinical and pharmacological significance, such as: antibacterial, antifungal, antiparasitic, immunomodulatory, anti-inflammatory, antioxidant, and anticancer activities [6][7][8]. However, many secondary metabolites encoded in actinomycete genomes are yet to be found, owing to the fact that these genes are not transcribed under standard laboratory conditions.…”

Antiplasmodial potential of phytochemicals from Citrus aurantifolia peels: a comprehensive in vitro and in silico study

“…To determine the antiplasmodial effect of isolated compounds in vitro, the Malstat assay was used as described [ 60 ]. To synchronize the culture of the Plasmodium NF54 strain, parasites with many ring stages were centrifuged, and the pellet was resuspended in the five-fold pellet volume of 5% w/v sorbitol /distilled H 2 O and incubated for 10 min at room temperature.…”

Emerging trends and applications of metabolomics in food science and nutrition

“…The steps are chosen based on the study type (untargeted vs. targeted), the sample type (solids, liquids), the separation apparatus (GC, LC), and the detection method (MS, IR, NMR). [30][31][32][33]…”