Our group discover bioactive compounds produce by plants and microbes, and study their biosynthetic pathways and mode-ofaction. To this end we develop and implement biochemical and cellular assays to screen organic extracts derived from plants, fungal fruiting bodies and fermentates of microorganisms for bioactivity. Once an interesting and novel bioactive compound has been identified we will study its biosynthetic pathway and determine its mode-of-action. We also investigate methods to turn on the expression of secondary metabolite biosynthetic gene clusters that are cryptic under standard laboratory cultivation conditions.
We manage the A*STAR Natural Product Library (NPL), which comprises of approximately 37,000 plant samples and 122,000 microbial strains, and their organic extracts (Figure 1). The genetic diversity within NPL is exceptional. With 57% of all known cultured fungal genera, over 67% of the world’s plant families and 70% of filamentous bacterial genera represented, the collection has been described as “the most diverse and comprehensive collection of plant and microbial samples in the world” (Prof Geoffrey A. Cordell, University of Illinois). This huge collection of plants and microbes serves as our rich and diverse resources for the discovery of bioactive compounds and industrial enzymes. To complement the traditional bioassay-guided compound discovery through extract screening, we are in the process of creating a genomic DNA library for our microbial strains. Work is also in progress to create a digital database for these microbial genomes to enable genome mining.
We collaborate closely with external partners in industry and academia to discover natural bioactive compounds for a wide variety of applications, ranging from pharmaceuticals, food ingredients, flavours and preservatives, to personal care products and cosmetics. We have developed and validated several cellular and biochemical assays with suitable technologies and formats for automated highthroughput screening in 384-well format. These include a cell-based transient transfection assay using a dual luciferase reporter system and an enzyme assay that is based on fluorescence resonance energy transfer. Most recently we have established a panel of highthroughput antimicrobial susceptibility assays against human pathogens and food spoilage microorganisms for antibiotics and natural preservatives discovery. Assay development is in progress for several enzymes relevant for the screening of active ingredients for cosmetics and functional food applications. All developed assays will be used to screen our extracts for the identification of bioactive compounds using bioassay-guided compound isolation approach. We have thus far identified >1,000 active extracts and isolated >100 active compounds.
Our bioactive compound discovery efforts are not limited to our own screening campaigns. We collaborated with Justin Tan and Roger Foo of GIS to screen for anticancer compounds (inhibitors of SALL4) and cardiac regeneration agents, respectively. Using the taste receptor assays developed by Biotrans we screen for natural taste modulators and flavour molecules.
To date more than 2,000 bioactive compounds have been isolated from NPL. As purification of these compounds from the crude mixture is a tedious and labour intensive process, to conserve the use of the purified materials we collaborate with Dr Hao Fan (Structure-based Ligand Discovery and Design) to in silico screen these compounds against molecular targets with structural information and perform experimental validation only on the in silico hits (Figure 2). We tested this approach on S. aureus sortase A enzyme and successfully identified two inhibitors that affected S. aureus biofilm formation (manuscript in preparation).
For new bioactive compounds with interesting activity profile we will embark on mode-of-action study in collaboration with Dr Prakash Arumugam (Chemical Gonomics), chemical screening (Dr Yoganathan Kanagasundaram, Natural Product Chemistry) to identify alternative producers and genome sequencing of their producers to understand their biosynthetic pathway (Frank & Birgit Eisenhaber, Gene Function Prediction/ANNOTATOR Group).
Microbial enzymes are widely used as biocatalysts in industries owing to their stability, catalytic activity, ease of production and optimization compared to plant and animal enzymes. Our collection of > 100,000 microbe is a rich resource for enzyme discovery for industrial applications, such as waste treatment, food processing, drug manufacturing, food flavour generation or diagnostics. An industrial collaboration to search for six different enzymes found numerous fungal strains showing at least one enzymatic activity of interest with sufficient production levels for follow-up studies. One of the enzymes has been successfully identified, cloned and expressed, and is being evaluated for product development. We are collaborating with Biotransformation Innovation Platform (https://www.a-star.edu.sg/biotrans) to screen for enzymes for food industry application. And we are collaborating with the Metabolic Engineering Research Laboratory (https://www.astar.edu.sg/merl) to discover and characterise tailoring enzymes from producers of bioactive compounds for possible application in advanced biomanufacturing.
We have accumulated the genome sequence data for more than 200 microbial strains from NPL, and the sequencing of another 2,000 strains is in progress. From the sequenced genomes putative biosynthetic gene clusters (BGCs) for secondary metabolites were identified using antiSMASH. Extracts derived from the sequenced strains are also tested for bioactivity. Putative biosynthetic gene clusters of bioactive compounds with interesting activity profile or structure will be identified, validated and engineered through our collaboration with Molecular Engineering Laboratory (https://www.a-star.edu.sg/mel) and Metabolic Engineering Research Laboratory.
A biodiversity study of 32 ascomycete strains isolated from St. John’s Island was undertaken to characterize the biosynthetic and antimicrobial potential of fungi from Singapore. Selected strains showing bioactivity were sequenced and analysed for putative biosynthetic gene clusters. The extracts derived from the fermentates of these bioactive strains were also analysed for secondary metabolite production. Comparison of their biosynthetic potential and the secondary metabolite profiles indicated the presence of silent or cryptic BGCs. We are applying the use of co-cultivation and chemical elicitors to activate the expression of these BGCs. Similar study was performed on approximately 300 strains of marine actinomycetes and endophytic fungi. We have also obtained permit from National Parks Board of Singapore to collect fungal fruiting bodies from parks and nature reserves to study their biosynthetic potential.
Ng Siew Bee joined the Bioinformatics Institute in 2014. She earned her Ph. D in Biochemistry from the Institute of Molecular and Cell Biology (IMCB) in Singapore. Siew Bee then embarked on her career in natural product research and drug discovery by joining the Centre for Natural Product Research (CNPR), IMCB. Initially she was involved in the development of new assays and subsequently was promoted to lead the High Throughput Screening group. When CNPR corporatized to form MerLion Pharmaceuticals Pte Ltd she was the Director of Discovery Biology (2002 – 2012), managing all assay development and screening activities, as well as leading the internal antibacterial discovery programme and supporting MerLion antibiotic development programmes. Prior to joining BII Siew Bee was an Adjunct Lecturer at the Singapore Polytechnic.
Siew Bee’s group studies the biology of natural products, in particular how they are made and what are their effects on biological systems. To this end they develop and implement biochemical and cellular assays to screen organic extracts derived from plants, fungal fruiting bodies and fermentates of microorganisms, for the discovery of naturally occurring bioactive secondary metabolites. Once an interesting and novel bioactive compound has been isolated and its structure elucidated, they identify and study its biosynthetic pathway. They also investigate methods to turn on the expression of secondary metabolite biosynthetic gene clusters that are cryptic under standard laboratory growth conditions.