Natural Product Chemistry

Yoganathan KANAGASUNDARAM
Principal Investigator

NGE Choy Eng, CHING Kuan Chieh
Post-Doctoral Research Fellows

YANG Lay Kien
Senior Research Officer

CHEW Yi Hong, SNG Xin Yi Amanda
Research Officers

Yoganathan KANAGASUNDARAM
Principal Investigator

GROUP MEMBERS:

NGE Choy Eng, CHING Kuan Chieh
Post-Doctoral Research Fellow

YANG Lay Kien
Senior Research Officer

CHEW Yi Hong, SNG Xin Yi Amanda
Research Officers

The primary focus of my group is to explore the chemical diversity of A*STAR Natural Product Library (A*STAR NPL) plants and microbes as a source of new natural products derived compounds, enzymes and drug candidates to advance our knowledge of the nature and the development of new pharmaceuticals, agrochemicals, functional foods, flavourings, cosmetics and personal care sectors. The strategy in my group involves two possible approaches.

  1. Bio-assay Guided Purification. Rapid dereplication workflow for prioritisation of active crude extracts to reduce discovery timeline, followed by efficient purification and structure elucidation to identify active constituents.
  2. Chemometrics (Differential Metabolomics Analysis). Targeted and untargeted metabolomics workflow incorporating multivariate statistical methods as discovery tools for new metabolites discovery and functional genomics.

Platforms for Natural Product Metabolites Discovery

  1. Bio-assay Guided Purification
  2. Since 1993, the Natural Product Collection has been used for the discovery of small organic bioactive molecules. This is accomplished through the high throughput screening of the extracts through biochemical or cellular assays to identify biological activities of interest. Once active extracts have been identified, they will be subjected to a two-phase chemical characterization process. Phase I entailing dereplication and Phase II comprising of fractionation, compounds isolation and structure elucidation.

    Phase 1, Dereplication

    The purpose of bio-assay guided dereplication characterisation is to rapidly identify known compounds which account for the activity observed in a particular extract. This is achieved by simultaneously analyzing the extract mixtures by analytical HPLC coupled to a high-resolution mass spectrometry and collecting 38 fractions directly into a deep well microtiter format block for biological testing. A schematic of the process and the equipment used at Natural Product Chemistry Laboratory is shown in Figure 1.

    Figure 1
    Figure 1: Schemaic of Phase 1 analytical chemistry: dereplication

    Compounds observed within the active fractions are matched against HRMS/MS database. We have also computed an accurate mass libraries (HR-MS) where the high-resolution MS data are “coupled” with the Dictionary of Natural Products or Chemspider search, to enable dereplication of compounds not represented in the NPL database and detection of target compounds (new compounds) for isolation.

    Phase 2, Fractionation & Structure Elucidation

    Phase II analysis involves fractionation and structure elucidation of the purified active compounds is shown in Figure 2. Fractions of sufficient purity and amount will then be further analysed using HR-MS/MS and 2D-NMR techniques, as appropriate, to confirm compound identity or to solve novel structures. Tandem mass spectral data of novel compounds will also be acquired to populate the A*STAR NPRL MS/MS database for future annotation.

    Figure 2
    Figure 2: Schematic of Phase II: automated large-scale fractionation, purification & structure elucidation;

    Following are some examples of research projects in my laboratory.

    With the bioassay-guided purification platform, we isolated a new anthracimycin derivative, anthracimycin BII-2619, with methyl group at C-8 and none at C-2, from Nocardiopsis kunsanensis and providing validation evidence to its biosynthetic gene cluster identified by genomic mining strategies (SiewBee/Frank/Birgit, BII)2.

    We also discovered a new antifungal cyclic lipodepsipeptide from a fungal strain in a black sea cucumber near the coastal area of Raffles Marina Clubhouse, Singapore. The amino acid residues sequence and absolute configurations were first determined by acid/basic hydrolysis and derivatization with FDAA, followed by LCMS/MS analysis, and finally confirmed by cross validation with the predicted biosynthetic gene cluster (in collaboration with SiewBee/Frank/Birgit’s team, manuscript submitted).

    In addition, we had undertaken LC-MS analysis and compounds purification, which provided useful insights into the characterization of new notonesomycin A analogues biosynthetic gene cluster from A793 by gene disruption experiments (Shawn Hoon, Wong Fong Tian and Zhang Mingzi, MERL and MEL).

    In collaboration with Prakash/Siew Bee’s team, we have isolated hypoculoside, a new glycosidic amino alcohol lipid from the fungus Acremonium sp. F2434 and determined its structure by 2D-NMR spectroscopy. Hypoculoside has antifungal, antibacterial and cytotoxic activities. Chemogenomic profiling analysis of hypoculoside in budding yeast indicated that it is two-fold more toxic to several vesicular trafficking mutants in comparison to the wild type strain. Interestingly, the sugar residue in hypoculoside is essential for its toxicity3. Besides in-house biological assays in NPB, we also support various research groups in A*STAR, such as discovery of SALL4 inhibitors (Justin Tan, GIS, manuscript submitted) and supply of compounds for chemogenomics (Prakash, BII) and Sortase Inhibitor (Hao Fan, BII).

    Through our cross functional collaboration project with Prof Ganesan (NUH-NUS-BII), we had identified two bioactives with distinct functions from pineapples. Serotonin was found to have uterotonic effect (induced contraction)4 whereas citric acid and a less polar fraction form a synergistic effect to product potent tocolytic activity (suppressed the oxytocin-induced contraction)5.

    We have also attracted industrial partners who have committed into collaborative research programmes or confidential contract research on a fee for service basis. We had identified 12 compounds from 15 edible plants that could be potentially used as functional ingredient in food/consumer product for an International Food Company.

  3. Chemometrics (Differential Metabolomics Analysis)
  4. Our group performs two strategies for the examination of metabolites: 1) targeted metabolomics (hypothesis-driven), or 2) untargeted metabolomics (unbiased approach, hypothesis generating). Multivariate statistical methods such as PCA, tests of significance, Venn diagram and Hierarchical clustering etc. are used to perform data analysis to distinguish the metabolites which have been significantly altered in samples. Identities of known metabolites can be confirmed by matching their fragmentation patterns with tandem mass spectral libraries. For unknown compounds which lack ready standards, purification and structure elucidation is undertaken to efficiently confirm their identities.

    Using the QTOF HRMS, our highly versatile discovery platform has found wide applications in both in-house and other research groups. We conducted analysis ranging from evaluation of effects of fungal co-cultivation and gene disruption on actinomycetes (NPB), strains selection and process optimization for production of target chemical classes (BioTrans), tentative identification of bacterial peptidoglycan fragments followed by isolation for antibody production (Wang Yue, IMCB). We are also expanding our analytics capability into answering biochemical questions. In collaboration with IMCB groups, we supported the metabolomics study on the effect of gene knock-out mice mutations lead to Glutaric Aciduria Type 3 (Sebastian/Frank BII and Philipp, IMCB, manuscript submitted) and tumour cells (Wee Wei, IMCB).

    We had also ventured into the area of lipidomics where we performed lipid profiling on Nocodazole treated and control cells. Our results validated the accumulation of neutral lipids in cells post slippage 6.

    We are involved in the metabolites profiling and identification for the study of Modes-of-Action (MoA) of chemicals using the Toxicity MoA Discovery (ToxMAD) Platform HBMSIAF-PP (Lit Hsin, BII). In addition, we will generate and profile using high resolution LCMS on 8000 extracts with the aim to discover alkaloids producing strains and characterise bioactive alkaloid compounds (An Integrative Approach to Build a Microbial Alkaloid Production Platform for Biotechnology, CRP-19).

Natural Product Chemistry Members

Dr. Yoganathan KANAGASUNDARAM
Principal Investigator
 
  Biography Details
NameTitle
Dr. KANAGASUNDARAM YoganathanPrincipal Investigator
Dr. CHING Kuan ChiehPostdoctoral Fellow
Dr. NGE Choy EngPostdoctoral Fellow
Ms. Amanda SNG Xin YiResearch Officer
Ms. SEOW Chwee San, DeborahResearch Officer
Ms. YANG Lay KienResearch Officer
No Publications

The primary focus of my group is to explore the chemical diversity of A*STAR Natural Product Library (A*STAR NPL) plants and microbes as a source of new natural products derived compounds, enzymes and drug candidates to advance our knowledge of the nature and the development of new pharmaceuticals, agrochemicals, functional foods, flavourings, cosmetics and personal care sectors. The strategy in my group involves two possible approaches.

  1. Bio-assay Guided Purification. Rapid dereplication workflow for prioritisation of active crude extracts to reduce discovery timeline, followed by efficient purification and structure elucidation to identify active constituents.
  2. Chemometrics (Differential Metabolomics Analysis). Targeted and untargeted metabolomics workflow incorporating multivariate statistical methods as discovery tools for new metabolites discovery and functional genomics.

Platforms for Natural Product Metabolites Discovery

  1. Bio-assay Guided Purification
  2. Since 1993, the Natural Product Collection has been used for the discovery of small organic bioactive molecules. This is accomplished through the high throughput screening of the extracts through biochemical or cellular assays to identify biological activities of interest. Once active extracts have been identified, they will be subjected to a two-phase chemical characterization process. Phase I entailing dereplication and Phase II comprising of fractionation, compounds isolation and structure elucidation.

    Phase 1, Dereplication

    The purpose of bio-assay guided dereplication characterisation is to rapidly identify known compounds which account for the activity observed in a particular extract. This is achieved by simultaneously analyzing the extract mixtures by analytical HPLC coupled to a high-resolution mass spectrometry and collecting 38 fractions directly into a deep well microtiter format block for biological testing. A schematic of the process and the equipment used at Natural Product Chemistry Laboratory is shown in Figure 1.

    Figure 1
    Figure 1: Schemaic of Phase 1 analytical chemistry: dereplication

    Compounds observed within the active fractions are matched against HRMS/MS database. We have also computed an accurate mass libraries (HR-MS) where the high-resolution MS data are “coupled” with the Dictionary of Natural Products or Chemspider search, to enable dereplication of compounds not represented in the NPL database and detection of target compounds (new compounds) for isolation.

    Phase 2, Fractionation & Structure Elucidation

    Phase II analysis involves fractionation and structure elucidation of the purified active compounds is shown in Figure 2. Fractions of sufficient purity and amount will then be further analysed using HR-MS/MS and 2D-NMR techniques, as appropriate, to confirm compound identity or to solve novel structures. Tandem mass spectral data of novel compounds will also be acquired to populate the A*STAR NPRL MS/MS database for future annotation.

    Figure 2
    Figure 2: Schematic of Phase II: automated large-scale fractionation, purification & structure elucidation;

    Following are some examples of research projects in my laboratory.

    With the bioassay-guided purification platform, we isolated a new anthracimycin derivative, anthracimycin BII-2619, with methyl group at C-8 and none at C-2, from Nocardiopsis kunsanensis and providing validation evidence to its biosynthetic gene cluster identified by genomic mining strategies (SiewBee/Frank/Birgit, BII)2.

    We also discovered a new antifungal cyclic lipodepsipeptide from a fungal strain in a black sea cucumber near the coastal area of Raffles Marina Clubhouse, Singapore. The amino acid residues sequence and absolute configurations were first determined by acid/basic hydrolysis and derivatization with FDAA, followed by LCMS/MS analysis, and finally confirmed by cross validation with the predicted biosynthetic gene cluster (in collaboration with SiewBee/Frank/Birgit’s team, manuscript submitted).

    In addition, we had undertaken LC-MS analysis and compounds purification, which provided useful insights into the characterization of new notonesomycin A analogues biosynthetic gene cluster from A793 by gene disruption experiments (Shawn Hoon, Wong Fong Tian and Zhang Mingzi, MERL and MEL).

    In collaboration with Prakash/Siew Bee’s team, we have isolated hypoculoside, a new glycosidic amino alcohol lipid from the fungus Acremonium sp. F2434 and determined its structure by 2D-NMR spectroscopy. Hypoculoside has antifungal, antibacterial and cytotoxic activities. Chemogenomic profiling analysis of hypoculoside in budding yeast indicated that it is two-fold more toxic to several vesicular trafficking mutants in comparison to the wild type strain. Interestingly, the sugar residue in hypoculoside is essential for its toxicity3. Besides in-house biological assays in NPB, we also support various research groups in A*STAR, such as discovery of SALL4 inhibitors (Justin Tan, GIS, manuscript submitted) and supply of compounds for chemogenomics (Prakash, BII) and Sortase Inhibitor (Hao Fan, BII).

    Through our cross functional collaboration project with Prof Ganesan (NUH-NUS-BII), we had identified two bioactives with distinct functions from pineapples. Serotonin was found to have uterotonic effect (induced contraction)4 whereas citric acid and a less polar fraction form a synergistic effect to product potent tocolytic activity (suppressed the oxytocin-induced contraction)5.

    We have also attracted industrial partners who have committed into collaborative research programmes or confidential contract research on a fee for service basis. We had identified 12 compounds from 15 edible plants that could be potentially used as functional ingredient in food/consumer product for an International Food Company.

  3. Chemometrics (Differential Metabolomics Analysis)
  4. Our group performs two strategies for the examination of metabolites: 1) targeted metabolomics (hypothesis-driven), or 2) untargeted metabolomics (unbiased approach, hypothesis generating). Multivariate statistical methods such as PCA, tests of significance, Venn diagram and Hierarchical clustering etc. are used to perform data analysis to distinguish the metabolites which have been significantly altered in samples. Identities of known metabolites can be confirmed by matching their fragmentation patterns with tandem mass spectral libraries. For unknown compounds which lack ready standards, purification and structure elucidation is undertaken to efficiently confirm their identities.

    Using the QTOF HRMS, our highly versatile discovery platform has found wide applications in both in-house and other research groups. We conducted analysis ranging from evaluation of effects of fungal co-cultivation and gene disruption on actinomycetes (NPB), strains selection and process optimization for production of target chemical classes (BioTrans), tentative identification of bacterial peptidoglycan fragments followed by isolation for antibody production (Wang Yue, IMCB). We are also expanding our analytics capability into answering biochemical questions. In collaboration with IMCB groups, we supported the metabolomics study on the effect of gene knock-out mice mutations lead to Glutaric Aciduria Type 3 (Sebastian/Frank BII and Philipp, IMCB, manuscript submitted) and tumour cells (Wee Wei, IMCB).

    We had also ventured into the area of lipidomics where we performed lipid profiling on Nocodazole treated and control cells. Our results validated the accumulation of neutral lipids in cells post slippage 6.

    We are involved in the metabolites profiling and identification for the study of Modes-of-Action (MoA) of chemicals using the Toxicity MoA Discovery (ToxMAD) Platform HBMSIAF-PP (Lit Hsin, BII). In addition, we will generate and profile using high resolution LCMS on 8000 extracts with the aim to discover alkaloids producing strains and characterise bioactive alkaloid compounds (An Integrative Approach to Build a Microbial Alkaloid Production Platform for Biotechnology, CRP-19).

Natural Product Chemistry Members

Dr. Yoganathan KANAGASUNDARAM
Principal Investigator
 
  Biography Details
NameTitle
Dr. KANAGASUNDARAM YoganathanPrincipal Investigator
Dr. CHING Kuan ChiehPostdoctoral Fellow
Dr. NGE Choy EngPostdoctoral Fellow
Ms. Amanda SNG Xin YiResearch Officer
Ms. SEOW Chwee San, DeborahResearch Officer
Ms. YANG Lay KienResearch Officer
No Publications