A5012051565- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- Click Chemistry and Applications
- Peptidase Inhibition and Analysis
- Cell death mechanisms and regulation
- Gut microbiota and health
- RNA and protein synthesis mechanisms
- Chemical Synthesis and Analysis
- Advanced Proteomics Techniques and Applications
- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Metabolomics and Mass Spectrometry Studies
- RNA Interference and Gene Delivery
- Adenosine and Purinergic Signaling
- Mass Spectrometry Techniques and Applications
- Enzyme Structure and Function
- Ubiquitin and proteasome pathways
- Protease and Inhibitor Mechanisms
- Biochemical and Molecular Research
- Influenza Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- Protein Structure and Dynamics
- Protein Degradation and Inhibitors
- Biochemical and Structural Characterization
Scripps Research Institute
2015-2024
Scripps (United States)
2020-2021
Scripps Institution of Oceanography
2020-2021
Torrey Pines Institute For Molecular Studies
2020
University of California, San Francisco
2009-2012
Centro de Investigacion Principe Felipe
2011
UCSF Helen Diller Family Comprehensive Cancer Center
2010
Pennsylvania State University
2003
Yale University
2002
Cleveland Clinic Lerner College of Medicine
1998-1999
METLIN originated as a database to characterize known metabolites and has since expanded into technology platform for the identification of unknown other chemical entities. Through this effort it become comprehensive resource containing over 1 million molecules including lipids, amino acids, carbohydrates, toxins, small peptides, natural products, among classes. METLIN's high-resolution tandem mass spectrometry (MS/MS) database, which plays key role in process, data generated from both...
Targeting STING for cancer therapy Activation of the (stimulator interferon genes) protein by cyclic dinucleotide metabolites plays a critical role in antitumor immunity. The development synthetic agonists is therefore being pursued as strategy therapy, but inherent instability dinucleotides has limited current efforts. Pan et al. and Chin identified stable that act “closed” conformation similar to natural ligand, guanosine monophosphate–adenosine monophosphate (see Perspective Gajewski...
Sulfur fluoride exchange (SuFEx) has emerged as the new generation of click chemistry. We report here a SuFEx-enabled, agnostic approach for discovery and optimization covalent inhibitors human neutrophil elastase (hNE). Evaluation our ever-growing collection SuFExable compounds toward various biological assays unexpectedly revealed selective hNE inhibitor: benzene-1,2-disulfonyl fluoride. Synthetic derivatization initial hit led to more potent agent, 2-(fluorosulfonyl)phenyl fluorosulfate...
Optimization of small-molecule probes or drugs is a synthetically lengthy, challenging, and resource-intensive process. Lack automation reliance on skilled medicinal chemists cumbersome in both academic industrial settings. Here, we demonstrate high-throughput hit-to-lead process based the biocompatible sulfur(VI) fluoride exchange (SuFEx) click chemistry. A screening hit benzyl (cyanomethyl)carbamate (Ki = 8 μM) against bacterial cysteine protease SpeB was modified with SuFExable...
Small-Molecule Protease Activator Human proteases regulate numerous biological processes. Most are stored as inactive proenzymes that activated either by upstream processes or self-proteolysis. Wolan et al. (p. 853 ) have identified a small molecule activates the apoptotic procaspases-3 and -6. These caspases homodimers, compound probably competitively inhibits one active site, but stabilizes an on-state conformation promotes self-cleavage unoccupied site. It may thus be possible to find...
Abstract Macrocyclization is a broadly applied approach for overcoming the intrinsically disordered nature of linear peptides. Herein, it shown that dichloroacetone (DCA) enhances helical secondary structures when introduced between peptide nucleophiles, such as thiols, to yield an acetone‐linked bridge (ACE). Aside from stabilizing structures, ketone moiety embedded in linker can be modified with diverse molecular tags by oxime ligation. Insights into structure tether were obtained through...
There is significant interest in identifying and characterizing allosteric sites enzymes such as protein kinases both for understanding mechanisms well drug discovery. Here, we apply a site-directed technology, disulfide trapping, to interrogate structurally functionally how an site on the Ser/Thr kinase, 3-phosphoinositide-dependent kinase 1 (PDK1)—the PDK1-interacting-fragment (PIF) pocket—is engaged by activating peptide motif downstream substrate (PIFtides) small molecule fragments. By...
Abstract Diversity Oriented Clicking (DOC) is a unified click‐approach for the modular synthesis of lead‐like structures through application wide family click transformations. DOC evolved from concept achieving “diversity with ease” , by combining classic C−C π‐bond chemistry recent developments in connective SuFEx‐technologies. We showcase 2‐ S ubstituted‐ A lkynyl‐1‐ ulfonyl F luorides (SASFs) as new class hub concert diverse selection click‐cycloaddition processes. Through selective SASFs...
Transcriptional coregulators, which mediate chromatin-dependent transcriptional signaling, represent tractable targets to modulate tumorigenic gene expression programs with small molecules. Genetic loss-of-function studies have recently implicated the coactivator, ENL, as a selective requirement for survival of acute leukemia and highlighted an essential role its chromatin reader YEATS domain. Motivated by these discoveries, we executed screen nearly 300,000 molecules identified...
The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic central peripheral ganglia. GI also harbors a diverse microbiome, but interactions between ENS microbiome remain poorly understood. Here, we activate choline acetyltransferase (ChAT)-expressing or tyrosine hydroxylase (TH)-expressing gut-associated in mice to determine effects on intestinal microbial communities their metabolites as well host physiology. resulting multi-omics...
Cytokine-inducible nitric-oxide (NO) synthase (iNOS) contains an oxygenase domain that binds heme, tetrahydrobiopterin, and l-arginine, a reductase FAD, FMN, calmodulin, NADPH. Dimerization of two domains allows electrons to transfer from the flavins heme irons, which enables O<sub>2</sub> binding NO synthesis froml-arginine. In iNOS heterodimer comprised one full-length subunit partner, single transfers only hemes (Siddhanta, U., Wu, C., Abu-Soud, H. M., Zhang, J., Ghosh, D. K., Stuehr, J....
Tandem mass spectrometry based shotgun proteomics of distal gut microbiomes is exceedingly difficult due to the inherent complexity and taxonomic diversity samples. We introduce two new methodologies improve metaproteomic studies microbiome These methods include stable isotope labeling in mammals permit protein quantitation across mouse cohorts as well application activity-based probes enrich analyze both host microbial proteins with specific functionalities. used these technologies study...
Diversity Oriented Clicking (DOC) is a discovery method geared toward the rapid synthesis of functional libraries. It combines best attributes both classical and modern click chemistries. DOC strategies center upon chemical diversification core "SuFExable" hubs-exemplified by 2-Substituted-Alkynyl-1-Sulfonyl Fluorides (SASFs)-enabling modular assembly compounds through multiple reaction pathways. We report here range stereoselective Michael-type addition pathways from SASF hubs including...
Modulating enzyme function with small-molecule activators, as opposed to inhibitors, offers new opportunities for drug discovery and allosteric regulation. We previously identified a compound, called 1541, from high-throughput screen (HTS) that stimulates activation of proenzyme, procaspase-3, generate mature caspase-3. Here we further investigate the mechanism report surprising finding 1541 self-assembles into nanofibrils exceeding 1 μm in length. These particles are an unanticipated...
Cathepsin B is a cysteine protease that normally functions within acidic lysosomes for protein degradation, but in numerous human diseases, cathepsin translocates to the cytosol having neutral pH where enzyme activates inflammation and cell death. active at both 7.2 of 4.6 lysosomes. We evaluated hypothesis may possess pH-dependent cleavage preferences can be utilized design selective inhibitor by (1) analysis differential profiles compared using multiplex substrate profiling mass...
The gut microbiota plays an important yet incompletely understood role in the induction and propagation of ulcerative colitis (UC). Organism-level efforts to identify UC-associated microbes have revealed importance community structure, but less is known about molecular effectors disease. We performed 16S rRNA gene sequencing parallel with label-free data-dependent LC-MS/MS proteomics characterize stool microbiomes healthy (n = 8) UC 10) patients. Comparisons taxonomic composition between...
Cytokine-inducible nitric oxide synthase (iNOS) is a homodimeric enzyme that generates (NO) andl-citrulline from l-arginine (l-Arg) and O2. The N-terminal oxygenase domain (amino acids 1–498; iNOSox) in each subunit binds heme,l-Arg, tetrahydrobiopterin (H4B), the site of NO synthesis, responsible for dimeric interaction, which must occur to synthesize NO. In both cells purified systems, iNOS dimer assembly promoted by H4B, l-Arg, l-Arg analogs. We examined ability imidazole andN-substituted...
Caspases are required for essential biological functions, most notably apoptosis and pyroptosis, but also cytokine production, cell proliferation, differentiation. One of the well studied members this cysteine protease family includes executioner caspase-3, which plays a central role in Unfortunately, there exists dearth chemical tools to selectively monitor caspase-3 activity under complex cellular vivo conditions due its close homology with caspase-7. Commercially available activity-based...
Caspases are a family of cysteine-aspartyl proteases that well recognized for their essential roles in apoptosis and inflammation. Recently, caspases have also been linked to the promotion other biologically important phenomena, such as cellular differentiation proliferation. Dysregulation multifaceted indispensable activities has globally several diseases, including cancer neurodegenerative disorders; however, specific caspase members responsible these diseases yet be assigned....
Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database protein sequences. Existing computational analysis methods are limited in the size their sequence databases, which severely restricts proteomic sequencing depth and functional highly complex samples. The growing amount public high-throughput data will only exacerbate this problem. We designed broadly applicable metaproteomic method (ComPIL) that addresses limitations.