A5006663325- Bacterial Genetics and Biotechnology
- Bacterial biofilms and quorum sensing
- Bacteriophages and microbial interactions
- Tuberculosis Research and Epidemiology
- Click Chemistry and Applications
- Monoclonal and Polyclonal Antibodies Research
- HIV Research and Treatment
- Toxoplasma gondii Research Studies
- Biochemical and Molecular Research
- Antibiotic Resistance in Bacteria
- Pneumocystis jirovecii pneumonia detection and treatment
- Mechanisms of cancer metastasis
- Antimicrobial Peptides and Activities
- Computational Drug Discovery Methods
- Biosensors and Analytical Detection
- Cancer Research and Treatments
- Mycobacterium research and diagnosis
- Cancer Mechanisms and Therapy
- Chromatin Remodeling and Cancer
- Mosquito-borne diseases and control
- SARS-CoV-2 and COVID-19 Research
- Drug Solubulity and Delivery Systems
- Biochemical and Structural Characterization
- Computational Physics and Python Applications
- Biotin and Related Studies
Stanford University
2018-2021
California Institute of Technology
2012-2019
University of Massachusetts Amherst
2008-2010
Summary Here we describe the application of a new click chemistry method for fluorescent tracking protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non‐canonical amino acid tagging ( BONCAT ), is based on vivo incorporation L ‐azidohomoalanine AHA surrogate l ‐methionine, followed by labelling ‐containing cellular proteins azide‐alkyne chemistry. was evaluated with range phylogenetically and physiologically diverse archaeal...
Two proteases produced by the SARS-CoV-2 virus, main protease and papain-like protease, are essential for viral replication have become focus of drug development programs treatment COVID-19. We screened a highly focused library compounds containing covalent warheads designed to target cysteine identify new lead scaffolds both Mpro PLpro proteases. These efforts identified small number hits no viable protease. Of as inhibitors purified recombinant only two inhibited infectivity in cellular...
The heterogeneity of cellular microenvironments in tumors severely limits the efficacy most cancer therapies. We have designed a microfluidic device that mimics microenvironment gradients present will enable development more effective Tumor cell masses were formed within micron-scale chambers exposed to medium perfusion on one side create linear nutrient gradients. optical accessibility PDMS and glass enables quantitative transmitted fluorescence microscopy all regions masses. Time-lapse was...
Tuberculosis (TB) is a top-ten cause of death worldwide. Successful treatment often limited by insufficient diagnostic capabilities, especially at the point care in low-resource settings. The ideal must be fast, cheap, and require minimal clinical resources while providing high sensitivity, selectivity, ability to differentiate live from dead bacteria. We describe here development luminescent, affordable sensor Hip1 (FLASH) for detecting monitoring drug susceptibility Mycobacterium...
Biofilm infections exhibit high tolerance against antibiotic treatment. The study of biofilms is complicated by phenotypic heterogeneity; biofilm subpopulations differ in their metabolic activities and responses to antibiotics. Here, we describe the use bio-orthogonal noncanonical amino acid tagging (BONCAT) method enable selective proteomic analysis a Pseudomonas aeruginosa subpopulation. Through controlled expression mutant methionyl-tRNA synthetase, targeted BONCAT labeling cells regions...
Significance Pathogens that are dormant or growing slowly play important roles in chronic infections, but studying how cells adapt to these conditions is difficult experimentally. This work demonstrates time-selective analysis of cellular protein synthesis, using bioorthogonal noncanonical amino acid tagging (BONCAT), can provide the sensitivity needed identify factors slow-growth physiology. We identified Pseudomonas aeruginosa , a previously uncharacterized transcriptional regulator...
Target-anchored monovalent degraders are more drug-like than their bivalent counterparts, Proteolysis Targeting Chimeras (PROTACs), while offering greater target specificity control the E3 ligase-anchored degraders, also known as molecular glues. However, discovery has typically been serendipitous, and rules governing identification remain unclear. This study focused on intentional of SMARCA2/A4 using a library based bromodomain-binding ligands. Compound G-6599 emerged lead candidate,...
<title>Abstract</title> Target-anchored monovalent degraders are more drug-like than their bivalent counterparts, Proteolysis Targeting Chimeras (PROTACs), while offering greater target specificity control the E3 ligase-anchored degraders, also known as molecular glues. However, discovery has typically been serendipitous, and rules governing identification remain unclear. This study focused on intentional of SMARCA2/A4 using a library based bromodomain-binding ligands. Compound G-6599...
Interest in covalent drug discovery has surged recent years, following the high-profile FDA approvals of inhibitors that target BTK and KRAS G12C. High-throughput screening by intact protein mass spectrometry is a popular method for identifying lead matter from fragment libraries. While technique proven its capacity to confirm binding, it does not provide binding site information on own. Follow-up assays identify sites can be time- resource-intensive, potentially extending hit confirmation...
Transcriptional activity from a specified promoter can provide useful marker for the physiological state of cell. Here we introduce method selective tagging proteins made in cells which promoters are active. Tagged be modified with affinity reagents enrichment or fluorescent dyes visualization. The allows state-selective analysis proteome, whereby synthesized predetermined states identified. approach is demonstrated by proteome-wide labeling bacterial upon activation PBAD and SoxRS regulon...
Lon is a widely conserved housekeeping protease found in all domains of life. Bacterial involved recovery from various types stress, including tolerance to fluoroquinolone antibiotics, and linked pathogenesis number organisms. However, detailed functional studies have been limited by the lack selective, cell-permeant inhibitors. Here, we describe use positional scanning libraries hybrid peptide substrates profile primary sequence specificity bacterial Lon. In addition identifying optimal...
Botulinum neurotoxins (BoNTs) are the most potent toxins known to man and a significant threat as weapons of bioterrorism. BoNTs contain metalloprotease domain that blocks neurotransmitter release in nerve terminals, resulting descending, flaccid paralysis with 5-10% mortality rate. Existing treatment options cannot access or neutralize toxin following its endocytosis, so there is clear need develop novel therapies. Numerous substrate-based zinc-chelating small-molecule inhibitors have been...
Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies model organisms doubling rapidly. We previously identified a small protein unknown function, SutA, screen proteins synthesized Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes gene expression, including upregulation the ribosomal genes. Here, using biochemical structural methods, we...
ABSTRACT Two proteases produced by the SARS-CoV-2 virus, M pro and PL , are essential for viral replication have become focus of drug development programs treatment COVID-19. We screened a highly focused library compounds containing covalent warheads designed to target cysteine identify new lead scaffolds both proteases. These efforts identified small number hits protease no viable protease. Of as inhibitors purified recombinant protease, only two inhibited infectivity in cellular infection...
Abstract Tuberculosis (TB) is a top-ten cause of death worldwide. Successful treatment often limited by insufficient diagnostic capabilities, especially at the point care in low-resource settings. The ideal must be fast, cheap, and require minimal clinical resources while providing high sensitivity, selectivity, ability to differentiate live from dead bacteria. We describe here development Fast, Luminescent, Affordable Sensor Hip1 (FLASH) for diagnosis monitoring drug sensitivity...
Abstract Lon is a widely-conserved housekeeping protease found in all domains of life. Bacterial involved the recovery from various types stress, including tolerance to fluoroquinolone antibiotics, and linked pathogenesis number organisms. However, detailed functional studies have been limited by lack selective, cell-permeable inhibitors. Here we describe use positional scanning libraries hybrid peptide substrates profile primary sequence specificity bacterial Lon. In addition identifying...
Summary The increasing incidence of antibiotic-resistant Mycobacterium tuberculosis infections is a global health threat necessitating the development new antibiotics. Serine hydrolases (SHs) are promising class targets because their importance for synthesis mycobacterial cell envelope. We screened library small molecules containing serine-reactive electrophiles and identified narrow spectrum inhibitors M. tuberculous growth. Using these lead molecules, we performed competitive...
ABSTRACT Though bacteria in nature are often nutritionally limited and growing slowly, most of our understanding core cellular processes such as transcription comes from studies a handful model organisms doubling rapidly under nutrient-replete conditions. We previously identified small protein unknown function, called SutA, global screen proteins synthesized Pseudomonas aeruginosa growth arrest (Babin BM , et al. (2016) SutA is bacterial factor expressed during slow . PNAS 113(5):E597-605)....