A5015133560- Microbial Natural Products and Biosynthesis
- Metabolomics and Mass Spectrometry Studies
- Marine Sponges and Natural Products
- Analytical Chemistry and Chromatography
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Antibiotic Resistance in Bacteria
- Vibrio bacteria research studies
- Bacterial biofilms and quorum sensing
- Mass Spectrometry Techniques and Applications
- Computational Drug Discovery Methods
- Plant-Derived Bioactive Compounds
- Malaria Research and Control
- RNA and protein synthesis mechanisms
- Crystallization and Solubility Studies
- X-ray Diffraction in Crystallography
- Cell Image Analysis Techniques
- Synthetic Organic Chemistry Methods
- Spectroscopy and Chemometric Analyses
- Antimicrobial Peptides and Activities
- Microbial Metabolism and Applications
- Trypanosoma species research and implications
- Chemical Synthesis and Analysis
- Plant biochemistry and biosynthesis
- Molecular spectroscopy and chirality
Simon Fraser University
2016-2025
Burnaby Hospital
2018-2021
University of California, Santa Cruz
2009-2018
Scripps Institution of Oceanography
2007-2015
University of California, San Diego
2009-2015
Instituto de Investigaciones Científicas y Servicios de Alta Tecnología
2006-2015
University of California System
2015
University of British Columbia
2002-2012
University of the Pacific
2011
Pacific University
2011
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among variety populations. It paves way to studying biological systems on large scale by using chemical and genetic perturbations. The general workflow this technology involves image acquisition with microscopy subsequent processing analysis. Here, we introduce steps required create high-quality image-based (i.e., morphological) profiles from collection images. We recommend techniques...
A major goal in natural product discovery programs is to rapidly dereplicate known entities from complex biological extracts. We demonstrate here that molecular networking, an approach organizes MS/MS data based on chemical similarity, a powerful complement traditional dereplication strategies. Successful with networks requires spectra of the mixture along standards, synthetic compounds, or well-characterized organisms, preferably organized into robust databases. This can accommodate...
Abstract Fueled by the explosion of (meta)genomic data, genome mining specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played central role through analysis Biosynthetic Gene Clusters (BGCs). Thousands candidate BGCs from microbial genomes been identified stored in public databases. Interpreting function novelty predicted requires comparison with well-documented set known...
Significance Natural products research seems to be at a critical juncture in terms of its relevance modern biological science. We have evaluated this landscape chemical diversity ask key questions, including the following. How has rate discovery new natural progressed over past 70 y? Has product structural novelty changed as function time? novel declined recent years? Does exploring taxonomic space afford an advantage compound discovery? Is it possible estimate how close we are describing...
Despite rapid evolution in the area of microbial natural products chemistry, there is currently no open access database containing all microbially produced product structures. Lack availability these data preventing implementation new technologies science. Specifically, development computational strategies for compound characterization and identification are being hampered by lack a comprehensive known compounds against which to compare experimental data. The creation an access,...
Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role the discovery novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these are often organised into gene clusters (BGCs). In 2015, we defined Minimum Information about Biosynthetic Gene cluster (MIBiG): standardised format describes minimally required information to...
Within the natural products field there is an increasing emphasis on study of compounds from microbial sources. This has been fuelled by interest in central role that microorganisms play mediating both interspecies interactions and host-microbe relationships. To support chemistry produced we released Natural Products Atlas, a database known structures, 2019. paper reports release new version which includes full RESTful application programming interface (API), website framework, expanded 8128...
Abstract Spectral matching of MS 2 fragmentation spectra has become a popular method for characterizing natural products libraries but identification remains challenging due to differences in properties between instruments and the low coverage current spectral reference libraries. To address this bottleneck we present Structural similarity Network Annotation Platform Mass Spectrometry (SNAP-MS) which matches chemical grouping Natural Products Atlas mass spectrometry features from molecular...
Two new modified cyclic hexapeptides, venturamides A (1) and B (2), were isolated from the marine cyanobacterium Oscillatoria sp. by antimalarial bioassay-guided fractionation. The isolation of 1 2 represents first example identification cyanobacterial peptides with selective activity. planar structures determined 1D 2D NMR analyses and, in case venturamide (1), comparison literature data for a previously reported synthetic compound. absolute configuration amino acid residues was hydrolysis...
Investigation of a Symploca sp. from Papua New Guinea has led to the isolation symplocamide A (1), potent cancer cell cytotoxin, which also inhibits serine proteases with 200-fold greater inhibition chymotrypsin over trypsin. The complete stereostructure was determined by detailed NMR and MS analysis as well chiral HPLC component amino acid residues. presence several unusual structural features in provides new insights into pharmacophore model for protease selectivity this drug class may...
As part of a continuing program to identify novel treatments for neglected parasitic diseases, the Panama International Cooperative Biodiversity Group (ICBG) has been investigating antimalarial potential secondary metabolites from Panamanian marine cyanobacteria. From over 60 strains cyanobacteria evaluated in our biological screens, organic extract Schizothrix species tropical reef near Piedras Gallinas (Caribbean coast Panama) showed potent initial activity against W2 chloroquine-resistant...
As part of the Panama International Cooperative Biodiversity Groups (ICBG) project, two new (2, 4) and known (1, 3) linear alkynoic lipopeptides have been isolated from a Panamanian strain marine cyanobacterium Lyngbya majuscula. Carmabin A (1), dragomabin (2), dragonamide (3) showed good antimalarial activity (IC50 4.3, 6.0, 7.7 μM, respectively), whereas nonaromatic analogue, B (4), was inactive. The planar structures all four compounds were determined by NMR spectroscopy in combination...
Traditional natural products discovery using a combination of live/dead screening followed by iterative bioassay-guided fractionation affords no information about compound structure or mode action until late in the process. This leads to high rates rediscovery and low probabilities finding compounds with unique biological and/or chemical properties. By integrating image-based phenotypic HeLa cells high-resolution untargeted metabolomics analysis, we have developed new platform, termed...
Cutimycin, a thiopeptide antibiotic produced by the skin commensal Cutibacterium acnes , reduces Staphylococcus colonization of human hair follicles.
Abstract The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites other biologically derived chemicals. NMR spectroscopy has long been viewed as ‘gold standard’ structure determination novel products metabolites. also widely used in product dereplication characterization biofluid mixtures (metabolomics)....
Few tools exist in natural products discovery to integrate biological screening and untargeted mass spectrometry data at the library scale. Previously, we reported Compound Activity Mapping as a strategy for predicting compound bioactivity profiles directly from primary results on extract libraries. We now present NP Analyst, an open online platform that accepts bioassay of almost any type, is compatible with major instrument manufacturers via mzML format. In addition, Analyst will accept...
Leishmaniasis is a debilitating disease caused by protozoan parasites of the genus Leishmania, which affects an estimated 12 million people worldwide. The discovery new lead compounds for leishmaniasis therefore pressing concern global health programs. organic extract Panamanian collection marine cyanobacterium Lyngbya majuscula showed strong in vitro activity two complementary screens against tropical parasite Leishmania donovani, causative agent visceral leishmaniasis. Chromatographic...