Biology subjects

Docken, S. S.

Publications and source records attributed to Docken, S. S..

3 recordsLinked to original sources

bioRxiv2026

A hERG Blocker Facilitates K+ Channel Current by Agonizing Pore Opening while Blocking

Many drugs that block voltage-gated K+ channels encoded by the human Ether-a-go-go-Related Gene (hERG) can cause long QT syndrome and life-threatening cardiac arrhythmias, yet the molecular mechanisms that determine this risk remain unclear. A process that may counteract arrhythmogenic hERG block, termed facilitation, is common to many clinically-approved hERG blockers including nifekalant, amiodarone, promethazine, imipramine, nortriptyline, haloperidol, verapamil, carvedilol, metoprolol, propranolol, quinidine, fluoxetine, and chlorpheniramine. Facilitation is an increase in hERG current, under certain conditions, due to these blockers. Here, we propose that an agonism-while-blocking mechanism undergirds facilitation. We focus on nifekalant, a Class III antiarrhythmic drug and exemplar hERG blocker that induces facilitation. We tested the hypothesis that nifekalant opens hERG channel gates while blocking, and that unblock of these open-yet-blocked channels results in supranormal hERG current. We develop rate-theory kinetic models to identify features of agonism-while-blocking that produce facilitation. We generate atomistic models that predict that nifekalant blocks the hERG conduction path while modulating the intracellular conduction gate. Voltage-clamp measurements reveal that agonism-while-blocking undergirds nifekalant block and facilitation. We speculate that this agonism-while-blocking mechanism contributes to the relative safety of hERG blockers that induce facilitation.

pharmacology and toxicology↗

bioRxiv2025

Dissecting the steps in early Simian Immunodeficiency Virus dissemination following mucosal and intravenous infection of rhesus macaques

In cases of HIV transmission, the typical delay from exposure to detectable viremia is approximately one week. This delay from exposure to viremia suggests that during initial expansion of virus from a limited number of founder lineages, there exists a period of low infected cell population. It is during this period of low infected cell population that the virus may be more vulnerable to clearance via primed immune responses targeting infected cells (e.g., antibody-dependent cellular cytotoxicity (ADCC) or CD8+ T cell killing/suppression). Potential future prophylactic harnessing of these immune mechanisms for early virally infected cell clearance will rely on an understanding of the earliest stages of viral replication and dissemination. The factors that dictate the rate of early viral spread, termed the dissemination bottleneck could include target-cell-mediated effects, the anatomical microenvironment, or the organ of the first infected cells. In this study, we use the barcoded Simian Immunodeficiency Virus (SIV) infection model to assess the contribution of various anatomical and cellular mechanisms to the SIV dissemination bottleneck. Viral, cellular, and anatomically-mediated heterogeneity in viral replication each introduce a degree of variability into the early phases of viral spread, and when multiple founder lineages are present, this variability in early growth results in a large distribution in lineage sizes. Therefore, we use a comparison of viral lineage size variability across multiple experimental SIV infection models to examine the relative contribution to the overall dissemination bottleneck of viral-mediated stochasticity of cellular infection (e.g., integration site), infected cell phenotype (e.g., activation state), anatomical variability, and initial viral spread within the genital tract. We estimate that inherent heterogeneity in viral production by infected cells corresponds to 23 to 44% of the dissemination bottleneck, but the majority (56 to 77%) arises from anatomical heterogeneity (presumably heterogeneity in how conducive local microenvironments are to viral replication). Author SummaryA brief window exists immediately following HIV transmission where low initial levels of virus and infected cells may be susceptible to immune clearance. A better understanding of the bottlenecks encountered by the virus during this window is necessary when designing therapies to clear HIV during this early period. We used a barcoded Simian Immunodeficiency Virus (SIV) infection model to track the early dissemination of multiple viral lineages after mucosal and intravenous inoculation. We observed up to 105-fold differences in lineage size between transmitted barcodes within a single animal two weeks after infection, suggesting very different trajectories of virial growth. By comparing lineage size diversity after mucosal and intravenous transmission and in vitro replication, we determined the contribution of anatomical and cellular mechanisms to the relative growth of different clonotypes. Although we expected that the processes of local dissemination may lead to greater lineage size diversity after mucosal transmission, this was not the case, and we saw no difference compared to intravenous transmission. We found that around a quarter of the diversity in clonotype size could be attributed to early cellular infection events, with the remainder likely attributable to differences in clonotype specific establishment and dissemination in vivo.

bioinformatics↗

bioRxiv2022

Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques

Transmitted/founder (TF) simian-human immunodeficiency viruses (SHIVs) express HIV-1 envelopes modified at position 375 to efficiently infect rhesus macaques while preserving authentic HIV-1 Env biology. TF SHIV.C.CH505 is an extensively characterized virus shown to recapitulate key features of HIV-1 immunobiology, including CCR5-tropism, a tier 2 neutralization profile, reproducible early viral kinetics, and authentic immune responses. SHIV.C.CH505 is used frequently in nonhuman primate studies of HIV, but viral loads after months of infection are variable and typically lower than those in people living with HIV. We hypothesized that additional mutations besides {Delta}375 might further enhance virus fitness without compromising essential components of CH505 Env biology. From sequence analysis of SHIV.C.CH505-infected macaques across multiple experiments, we identified a signature of envelope mutations associated with higher viremia. We then used short-term in vivo mutational selection and competition to identify a minimally adapted SHIV.C.CH505 with just five amino acid changes that substantially improve virus replication fitness in macaques. Next, we validated the performance of the adapted SHIV in vitro and in vivo and identified the mechanistic contributions of selected mutations. In vitro, the adapted SHIV shows improved virus entry, enhanced replication on primary rhesus cells, and preserved neutralization profiles. In vivo, the minimally adapted virus rapidly outcompetes the parental SHIV with an estimated growth advantage of 0.14 days-1 and persists through suppressive antiretroviral therapy to rebound at treatment interruption. Here, we report the successful generation of a well-characterized, minimally adapted virus, termed SHIV.C.CH505.v2, with enhanced replication fitness and preserved native Env properties that can serve as a new reagent for NHP studies of HIV-1 transmission, pathogenesis, and cure. Author SummaryThe power of the nonhuman primate model of HIV to predict outcomes in people living with HIV (PLWH) depends on authentic virus-host interactions. In pursuit of viruses that generate infection that mirrors the effects of HIV-1 in PLWH, we developed a minimally adapted version of a commonly used virus, SHIV.C.CH505, which has better fitness than the parental virus while retaining important biological properties. First, we studied virus sequences from SHIV.C.CH505-infected rhesus macaques to identify a signature of mutations common to animals with higher viral loads. We then tested viruses containing the various mutations in the lab and in animals to determine the most fit version and to identify the contribution of each mutation. Ultimately, we identified a minimally adapted version of SHIV.C.CH505 with just 5 amino acid substitutions that enhances virus replication and preserves CH505 envelope properties, including sensitivity to clinically relevant broadly neutralizing antibodies. This new virus, called SHIV.C.CH505.v2 replicates well in macaques over time and persists through antiretroviral therapy. SHIV.C.CH505.v2 could be an important component of nonhuman primate studies of HIV prevention, therapy, and cure.

microbiology↗