Van Cuong Pham

Integration of Molecular Networking and In-Silico MS/MS Fragmentation for Natural Products Dereplication

Dereplication represents a key step for rapidly identifying known secondary metabolites in complex biological matrices. In this context, liquid-chromatography coupled to high resolution mass spectrometry (LC-HRMS) is increasingly used and, via untargeted data-dependent MS/MS experiments, massive amounts of detailed information on the chemical composition of crude extracts can be generated. An efficient exploitation of such data sets requires automated data treatment and access to dedicated fragmentation databases. Various novel bioinformatics approaches such as molecular networking (MN) and in-silico fragmentation tools have emerged recently and provide new perspective for early metabolite identification in natural products (NPs) research. Here we propose an innovative dereplication strategy based on the combination of MN with an extensive in-silico MS/MS fragmentation database of NPs. Using two case studies, we demonstrate that this combined approach offers a powerful tool to navigate through the chemistry of complex NPs extracts, dereplicate metabolites, and annotate analogues of database entries.

Tools for Characterizing Bacterial Protein Synthesis Inhibitors

ABSTRACT Many antibiotics inhibit the growth of sensitive bacteria by interfering with ribosome function. However, discovery of new protein synthesis inhibitors is curbed by the lack of facile techniques capable of readily identifying antibiotic target sites and modes of action. Furthermore, the frequent rediscovery of known antibiotic scaffolds, especially in natural product extracts, is time-consuming and expensive and diverts resources that could be used toward the isolation of novel lead molecules. In order to avoid these pitfalls and improve the process of dereplication of chemically complex extracts, we designed a two-pronged approach for the characterization of inhibitors of protein synthesis (ChIPS) that is suitable for the rapid identification of the site and mode of action on the bacterial ribosome. First, we engineered antibiotic-hypersensitive Escherichia coli strains that contain only one rRNA operon. These strains are used for the rapid isolation of resistance mutants in which rRNA mutations identify the site of the antibiotic action. Second, we show that patterns of drug-induced ribosome stalling on mRNA, monitored by primer extension, can be used to elucidate the mode of antibiotic action. These analyses can be performed within a few days and provide a rapid and efficient approach for identifying the site and mode of action of translation inhibitors targeting the bacterial ribosome. Both techniques were validated using a bacterial strain whose culture extract, composed of unknown metabolites, exhibited protein synthesis inhibitory activity; we were able to rapidly detect the presence of the antibiotic chloramphenicol.

Structure and total synthesis of (-)-myrionidine and (-)-schoberine, antimalarial alkaloids from Myrioneuron nutans.

Two new alkaloids, (5S,9S,10R)-myrionidine (1) and (5S,9S,10R,13S)-myrionamide (2), along with the known schoberine (3), were isolated from the leaves of Myrioneuron nutans (Rubiaceae), and their structures were determined from spectral analysis, including mass spectrometry and 2D NMR. The total asymmetric syntheses of (-)-myrionidine (1), (-)-schoberine (3), their enantiomers as well as their 9-epimers derivatives were performed, allowing the determination of their absolute configuration together with that of myrionamide (2). (-)-Myrionidine (1) and its synthetic enantiomer (18) showed a significant antimalarial activity on Plasmodium falciparum.

Antifouling 26,27-cyclosterols from the Vietnamese marine sponge Xestospongia testudinaria.

Three new C29 sterols with a cyclopropane ring cyclized between C-26 and C-27 of the side chain, aragusterol I (1), 21-O-octadecanoyl-xestokerol A (4), and 7β-hydroxypetrosterol (5b), were isolated from the Vietnamese marine sponge Xestospongia testudinaria, along with the known compounds, aragusterol B (2), xestokerol A (3), 7α-hydroxypetrosterol (5a), 7-oxopetrosterol (6), and petrosterol (7). The structures of the new compounds were established by analysis of spectroscopic data including 1D and 2D NMR, and high-resolution electrospray ionization mass spectrometry (HRESIMS). Their capacity to inhibit the adhesion of isolated bacteria from marine biofilms was evaluated against the bacterial strains Pseudoalteromonas sp. D41, Pseudoalteromonas sp. TC8, and Polaribacter sp. TC5. Aragusterol B (2) and 21-O-octadecanoyl-xestokerol A (4) exhibited the most potent antifouling activity with EC50 values close to these reported in the literature for tributyltin oxide, a marine anti-biofouling agent now considered to be a severe marine pollutant. Due to its comparable activity to tributyltin oxide and its absence of toxicity, the new 26,27-cyclosterol, 21-O-octadecanoyl-xestokerol A (4) constitutes a promising scaffold for further investigations.

Antiplasmodial alkaloids from Desmos rostrata.

Two new alkaloids, desmorostratine (1) and discretine N-oxide (2), were isolated from the stem bark of Desmos rostrata, together with five known alkaloids, discretine (3), dehydrodiscretine (4), pseudocolumbamine (5), predicentrine (6), and aristolactam AII (7). The structures were established on the basis of spectroscopic data, including mass spectrometry and 2D-NMR. Compound 1 was cytotoxic against KB cells (IC(50) 2.4 microM), while 2, 3, and 4 inhibited Plasmodium falciparum (IC(50) of 4.2, 1.6, and 0.9 microM, respectively).

Artemisinin Analogues as Potent Inhibitors of In Vitro Hepatitis C Virus Replication

We reported previously that Artemisinin (ART), a widely used anti-malarial drug, is an inhibitor of in vitro HCV subgenomic replicon replication. We here demonstrate that ART exerts its antiviral activity also in hepatoma cells infected with full length infectious HCV JFH-1. We identified a number of ART analogues that are up to 10-fold more potent and selective as in vitro inhibitors of HCV replication than ART. The iron donor Hemin only marginally potentiates the anti-HCV activity of ART in HCV-infected cultures. Carbon-centered radicals have been shown to be critical for the anti-malarial activity of ART. We demonstrate that carbon-centered radicals-trapping (the so-called TEMPO) compounds only marginally affect the anti-HCV activity of ART. This provides evidence that carbon-centered radicals are not the main effectors of the anti-HCV activity of the Artemisinin. ART and analogues may possibly exert their anti-HCV activity by the induction of reactive oxygen species (ROS). The combined anti-HCV activity of ART or its analogues with L-N-Acetylcysteine (L-NAC) [a molecule that inhibits ROS generation] was studied. L-NAC significantly reduced the in vitro anti-HCV activity of ART and derivatives. Taken together, the in vitro anti-HCV activity of ART and analogues can, at least in part, be explained by the induction of ROS; carbon-centered radicals may not be important in the anti-HCV effect of these molecules.

Acetylcholinesterase inhibitors from the leaves of Macaranga kurzii.

Bioassay-guided fractionation of an extract of leaves of Macaranga kurzii yielded four new compounds, a stilbene (furanokurzin, 1) and three flavonoids (macakurzin A-C, 2-4). Nine known compounds were also isolated (5-13). Their structures were determined by spectroscopic analyses including MS and 2D NMR. The isolates were all evaluated for acetylcholinesterase inhibitory activity. Compound 6 (trans-3,5-dimethoxystilbene) exhibited the greatest activity (IC50 9 μM). Cytotoxic evaluation against KB cells showed that compound 7 had an IC50 of 4 μM, followed by 11 (IC50 10 μM) and 3 (IC50 13 μM).

Endiandric acid analogues from Beilschmiedia ferruginea as dual inhibitors of Bcl-xL/Bak and Mcl-1/Bid interactions.

A rapid screening by (1)H and (1)H-(13)C HSQC NMR spectroscopy of EtOAc extracts of Endiandra and Beilschmiedia species allowed the selection of Beilschmiedia ferruginea leaves and flowers extract for a chemical investigation, leading to the isolation of 11 new tetracyclic endiandric acid analogues, named ferrugineic acids A-K (1-11). Their structures were determined by 1D and 2D NMR spectroscopic analysis in combination with HRMS data. These compounds were assayed for Bcl-xL and Mcl-1 binding affinities. Ferrugineic acids B, C, and J (2, 3, and 10) exhibited significant binding affinity for both antiapoptotic proteins Bcl-xL (Ki = 19.2, 12.6, and 19.4 μM, respectively) and Mcl-1 (Ki = 14.0, 13.0, and 5.2 μM, respectively), and ferrugineic acid D (4) showed only significant inhibiting activity for Mcl-1 (Ki = 5.9 μM).

Cytotoxic Steroidal Alkaloids from Kibatalia laurifolia

Four new steroids, 3-epi-gitingensine (1), N-acetylgitingensine (6), kibalaurifoline (7) and kibalaurifenone (8), along with the known paravallarine (2), 7α-hydroxyparavallarine (3), gitingensine (4), and N-methylgitingensine (5) were isolated from the leaves of Kibatalia laurifolia. Their structures were determined primarily from mass spectrometry and 2D NMR analyses. On the basis of the known absolute configurations of 2 and 4, the absolute configurations of the new compounds were proposed. Due to the structural relationships of compounds 1-8, a biosynthetic pathway was suggested. Compound 2 was cytotoxic to KB cells (IC50 12.8 μM), followed by 1 with IC50 21.2 μM.

Cytotoxic prenylated isoflavone and bipterocarpan from Millettia pachyloba.

Two new compounds, an isoflavone (1, 6-methoxybarbigerone) and a bipterocarpan (2, pachylobin) were isolated from the grains of Millettia pachyloba (Leguminosae), together with seven known compounds, 5-methoxybarbigerone (3), calopogoniumisoflavone B (4), durmillone (5), jamaicin (6), ichthynone (7), (-)-pisatin (8) and (-)-rotenone (9). The structures were established from spectroscopic analyses, including mass spectrometry and 2D-NMR. Absolute configuration of 2 was proposed based on that of the known compound (-)-pisatine (8). Compounds 1 and 2 exhibited cytotoxicity against KB cells with IC(50) values of 2.0 and 17.6 µM, respectively.