Biology subjects

Vuong, W.

Publications and source records attributed to Vuong, W..

6 recordsLinked to original sources

bioRxiv2026

Modulation of the human cathelicidin dimerization interface separates antimicrobial activity from mammalian membrane disruption

The human CAMP gene product LL-37 is a prototypical cationic host defense peptide with potent activity against gram-negative bacteria. The development of LL-37 and other membrane-active host defense peptides as antibiotics, however, is limited in part by their activity against mammalian membranes. To better understand the structural features underlying LL-37 functions, we reconceived of LL-37 as a small protein and systematically ablated the sidechain content of entire surfaces while preserving helical character. This approach revealed that selected modifications within surface m4 retain wild-type levels of activity against gram-negative bacteria while disrupting activity against mammalian membranes by >100-fold. Separation of antimicrobial and mammalian membrane activities mapped primarily to residues I24 and L28, and was attributable to a combination of disrupted oligomerization and decreased hydrophobic content within the dimerization interface. Modulation of the LL-37 dimerization interface thus constitutes a rational pathway by which to engineer derivatives with improved therapeutic potential.

biochemistry↗

bioRxiv2025

PSMtags improve peptide sequencing and throughput in sensitive proteomics

Mass spectrometry-based proteomics enables comprehensive characterization of protein abundance, function, and interactions. Label-free approaches are simple to implement but challenging to scale to thousands of samples per day. Multiplexed techniques, such as plexDIA, can address these limitations but remain restricted by the lack of mass tags optimized for data-independent acquisition (DIA) workflows. Here, we present a systematic approach screening a library of 576 compounds that identifies several small molecules that, when conjugated to peptides, improve their detection and sequence identification by mass spectrometry. The lead molecule, PSMtag, substantially increases the detection of fragment b-ions, which increases the confidence of sequence identification and enhances de novo sequencing. PSMtags allow 9-plexDIA, using only stable isotopes of carbon, oxygen and nitrogen. As a result, it allows simultaneously increasing proteome coverage and sample throughput for plexDIA workflows without compromising quantitative accuracy. We demonstrate 240 samples-per-day with 9-plexDIA, while acquiring 28,359 protein data points in the same time label-free methods acquire 4,340. Our approach constitutes an expandable framework for designing mass tags to overcome existing limitations in multiplexed proteomics and provides plexDIA reagents capable of analyzing over 1,000 samples per day when using 10 minute runs. By facilitating higher throughput and improved identification, this innovation holds significant potential for accelerating proteomic studies across diverse biological and clinical applications.

bioengineering↗

bioRxiv2025

Separability of antibacterial and membranolytic activity in the human host defense peptide LL-37

The human CAMP gene product LL-37 is thought to exert direct antimicrobial activity against gram-negative bacteria via membrane disruption. In the course of structure-activity relationship studies of LL-37 aimed at developing peptidomimetic antibiotics, however, we incidentally noted mutations in LL-37 that globally inhibit membrane disruption in both mammalian and gram-negative bacterial cells. Despite their diminished capacity for membranolysis, these variants retained full antibacterial activity against gram-negative bacteria. While testing LL-37 and derivatives thereof against clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis, we further noted unusually high rates of elevated minimum inhibitory concentrations for LL-37. Further evaluation of these clinical isolates revealed that they are fully permeabilized by LL-37 without being killed. Thus, we have identified variants of LL-37 that kill gram-negative bacteria without permeabilizing, and gram-negative bacteria that are permeabilized by LL-37 without being killed. This may suggest the existence of one or more mechanisms other than membrane disruption by which LL-37 can kill gram-negative bacteria, which may open up new avenues for antibiotic development based on the naturally evolved, non-membrane targets of human host defense peptides.

microbiology↗

bioRxiv2021

N-Terminal finger stabilizes the reversible feline drug GC376 in SARS-CoV-2 Mpro

The main protease (Mpro, also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drugs properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar Ki values with the Mpro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 Mpro. The comparison of a new X-ray crystal structure of Mpro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 Mpro, and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the Mpro, which facilitates coordination of the drugs P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.

biophysics↗

bioRxiv2020

Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication

The COVID-19 pandemic, attributed to the SARS-CoV-2 coronavirus infection, resulted in millions infected worldwide and an immediate need for antiviral treatments. The main protease (Mpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide and subsequent viral replication. Feline infectious peritonitis, a fatal infection in cats caused by a coronavirus, was successfully treated previously with a dipeptide-based protease inhibitor. Here we show this drug, GC376, and its analog GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of the SARS-CoV and SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 in cell culture, with EC50 values near one micromolar and little to no toxicity. These protease inhibitors are soluble, non-toxic, and bind reversibly. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals (cats). The work here lays the framework for their use in human trials for the treatment of COVID-19.

biochemistry↗

bioRxiv2018

Electrophysiological correlates of hyperoxia during resting-state EEG in awake human subjects

Recreational use of concentrated oxygen has increased. Claims have been made that hyperoxic breathing can help reduce fatigue, increase alertness, and improve attentional capacities; however, few systematic studies of these potential benefits exist. Here we examined the effects of short-term (15 minute) hyperoxia on resting-states in awake human subjects by measuring spontaneous EEG activity between normoxic and hyperoxic situations, using a within-subjects design for both eyes-opened and eyes-closed conditions. We also measured respiration rate, heart rate, and blood oxygen saturation levels to correlate basic physiological changes due to the hyperoxic challenge with any brain activity changes. Our results show that breathing short term 100% oxygen led to increased blood-oxygen saturation levels, decreased heart rate, and a slight, but non-significant, decrease in breathing rate. Changes of brain activity were apparent, including decreases in low-alpha (7-10 Hz), high-alpha (10-14 Hz), beta (14-30 Hz), and gamma (30-50 Hz) frequency ranges during eyes-opened hyperoxic conditions. During eyes-closed hyperoxia, increases in the delta (0.5-3.5 Hz) and theta (3.5-7 Hz) frequency range were apparent together with decreases in the beta range. Hyperoxia appeared to accentuate the decrease of low alpha and gamma ranges across the eyes-opened and closed conditions suggesting that it modulated brain state itself. As decreased alpha during eyes-opened conditions has been associated with increased attentional processing and selective attention, and increased delta and theta during eyes-closed condition are typically associated with the initiation of sleep, our results suggest a state-specific and perhaps opposing influence of short-term hyperoxia.

neuroscience↗