Biology subjects

Gordon, C.

Publications and source records attributed to Gordon, C..

8 recordsLinked to original sources

bioRxiv2026

The nucleoside analog CMX521 inhibits coronavirus RNA-dependent RNA polymerase via a two-pronged mechanism

The SARS-CoV-2 pandemic has underscored the urgent need for broad-spectrum antivirals in pandemic preparedness efforts. Nucleoside analogs targeting viral polymerases are often considered in this context. Here, we employ ensemble biochemical assays and single-molecule magnetic tweezers to characterize the detailed mechanism of action of the adenosine analog CMX521 (developed through Phase 1 clinical studies), a broad-spectrum antiviral against caliciviruses and coronaviruses, against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). The triphosphate form of CMX521 is efficiently incorporated by RdRp, even against saturating ATP concentrations. Analog incorporation induces only a brief pause in nascent RNA synthesis. When embedded in the template strand, CMX521 causes the polymerase to stall [~]9 s on average due to impaired uridine opposite incorporation. Multiple CMX521 residues in the template strand completely inhibit polymerase elongation. When the coronavirus polymerase is associated with the viral helicase, CMX521 strongly promotes copy-back RNA synthesis suggesting a second inhibitory mechanism for CMX521. Collectively, our findings establish a two-pronged mode of coronavirus polymerase inhibition by CMX521.

microbiology↗

bioRxiv2025

Structural basis for selective remdesivir incorporation by SARS-CoV-2 RNA polymerase, and S759A resistance

Nucleoside analogs (NAs) have been successfully used to treat viral infections. dNTP analogs are primarily DNA chain terminators, while NTP analogs, such as remdesivir, can inhibit as delayed chain terminators or when in the template strand. Determining the frequency of remdesivir triphosphate (RTP) incorporation in the presence of the competing ATP can help in understanding different modes of viral RNA-dependent RNA polymerase (RdRp) inhibition by NTP analogs. We employed enzymatic assays, mass spectrometry, and cryo-EM to show that SARS-CoV-2 RdRp preferentially incorporates RTP, outcompeting 10-fold higher ATP concentration; however, successive RTP incorporations are less favoured when ATP is present. Structures of SARS-CoV-2 RdRp in this and previous studies demonstrate resilience of remdesivir:UMP base pair to translocation, explaining the reduced preference for conjugate incorporations. Together, the RTP versus ATP incorporation is driven by their relative concentration and structural rigidity of remdesivir:UMP, ultimately limiting the number of incorporated remdesivir in a fully synthesized RNA strand. The S759A mutant confers RTP resistance, and the structures of S759A RdRp catalytic complexes reveal that altered ribose-ring conformation and repositioning of the primer 3'-end nucleotide contribute to RTP resistance. These findings enhance our understanding of non-obligate NTP analogs and provide insight into S759A resistance mechanism.

biochemistry↗

bioRxiv2025

Cracking the egg: Isolation and discovery of distinct nonvesicular extracellular particles from Schistosoma mansoni eggs

Extracellular particles (EPs) derived from helminths are emerging as promising immunomodulatory agents, yet their heterogeneity challenges reproducible purification and characterisation. This study focused on purifying and characterising extracellular particles (EPs) from Schistosoma mansoni eggs using tangential flow filtration (TFF) and differential ultracentrifugation (dUC). Contrary to expectations, cryogenic transmission electron microscopy (cryoTEM) revealed that egg-derived EPs are nonvesicular (5-30 nm) nanoparticles (eggNPs) rather than membrane-bound extracellular vesicles. TFF demonstrated superior performance over dUC, yielding higher recovery (76.19% vs. 38.90%), greater purity, and lower endotoxin contamination. Despite limitations in standard protein quantification methods, enriched protein profiles and detection of S. mansoni tetraspanin-2 in TFF-purified eggNPs highlights their distinct molecular signatures. The study also identified contaminants in cryopreservation buffers, underscoring the need for optimised storage conditions. Compared to dUC, TFF preserved particle integrity, with cryoTEM images showing fewer aggregates and distinct EggNP morphology. This work proposes TFF as a scalable and reproducible method for isolating S. mansoni-derived eggNPs, providing a foundation for their exploration as immunomodulatory agents. These findings not only expand the understanding of helminth EPs but also emphasise their therapeutic potential, particularly in inflammatory and immune-dysregulation disorders.

molecular biology↗

bioRxiv2024

Protein Language Model Fitness Is a Matter of Preference

Leveraging billions of years of evolution, scientists have trained protein language models (pLMs) to understand the sequence and structure space of proteins aiding in the design of more functional proteins. Although they have shown ability to improve efficiency in engineering, it remains unclear if such models capture true biological patterns or artifacts of the training data. We aim to predict the circumstances in which pLMs can successfully perform zero-shot fitness estimation. Our work studies trends observed over hundreds of deep mutational scans across multiple different fitness objectives. We find that the likelihood, or abstractly, implicit preference of a certain protein sequence imbued during pretraining is predictive of fitness prediction capabilities. Both over-preferred and under-preferred wild type sequences harm performance. Using influence functions to causally understand how individual data points increase protein likelihoods, we find that there exists a power law tail due to sequence homology. Lastly, under-performance on low likelihood wild type proteins can be remedied by unsupervised finetuning. These findings that pLM zero-shot fitness estimation can be predicted by the likelihood of the engineered sequence can motivate and improve pLMs deployment in protein maturation campaigns.

bioinformatics↗

bioRxiv2022

Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome

THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 facilitates the formation of the Transcription Export complex (TREX) tetramer, composed of four THO monomers. The TREX tetramer supports mammalian mRNA processing that is distinct from yeast TREX dimer functions. Human and mouse TIDS model systems allow novel THOC6-dependent TREX tetramer functions to be investigated. Biallelic loss-of-function (LOF) THOC6 variants do not influence the expression and localization of TREX members in human cells, but our data suggests reduced binding affinity of ALYREF. Impairment of TREX nuclear export functions were not detected in cells with biallelic THOC6 LOF. Instead, mRNA mis-splicing was observed in human and mouse neural tissue, revealing novel insights into THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions that may inform TIDS neuropathology.

molecular biology↗

bioRxiv2022

Neural patterns differentiate traumatic from sad autobiographical memories in PTSD

For people with post-traumatic stress disorder (PTSD), recalling traumatic memories often displays as intrusions that differ profoundly from processing of regular negative memories. These mnemonic features fueled theories speculating a qualitative divergence in cognitive state linked with traumatic memories. Yet to date, little empirical evidence supports this view. Here, we examined neural activity of PTSD patients who were listening to narratives depicting their own memories. An inter-subject representational similarity analysis of cross-subject semantic content and neural patterns revealed a differentiation in hippocampal representation by narrative type: Semantically similar sad autobiographical memories elicited similar neural representations across participants. By contrast, within the same individuals, semantically thematically similar trauma memories were not represented similarly. Furthermore, we were able to decode memory type from hippocampal multivoxel patterns. Finally, individual symptom severity modulated semantic representation of the traumatic narratives in the posterior cingulate cortex. Taken together, these findings suggest that traumatic memories are a qualitatively divergent cognitive entity.

neuroscience↗

bioRxiv2021

Directed Evolution of Aptamer Discovery Technologies

ConspectusAlthough antibodies are a powerful tool for molecular biology and clinical diagnostics, there are many emerging applications for which nucleic acid-based aptamers can be advantageous. However, generating high-quality aptamers with sufficient affinity and specificity for biomedical applications is a challenging feat for most research laboratories. In this Account, we describe four techniques developed in our lab to accelerate the discovery of high quality aptamer reagents that can achieve robust binding even for challenging molecular targets. The first method is particle display, in which we convert solution-phase aptamers into aptamer particles that can be screened via fluorescence-activated cell sorting (FACS) to quantitatively isolate individual aptamer particles based on their affinity. This enables the efficient isolation of high-affinity aptamers in fewer selection rounds than conventional methods, thereby minimizing selection biases and reducing the emergence of artifacts in the final aptamer pool. We subsequently developed the multi-parametric particle display (MPPD) method, which employs two-color FACS to isolate aptamer particles based on both affinity and specificity, yielding aptamers that exhibit excellent target binding even in complex matrices like serum. The third method is a click chemistry-based particle display (click-PD) that enables the generation and high-throughput screening of "non-nattural" aptamers with a wide range of base modifications. We have shown that these base-modified aptamers can achieve robust affinity and specificity for targets that have proven challenging or inaccessible with natural nucleotide-based aptamer libraries. Lastly, we describe the non-natural aptamer array (N2A2) platform, in which a modified benchtop sequencing instrument is used to characterize base-modified aptamers in a massively parallel fashion, enabling the efficient identification of molecules with excellent affinity and specificity for their targets. This system first generates aptamer clusters on the flow-cell surface that incorporate alkyne-modified nucleobases, and then performs a click reaction to couple those nucleobases to an azide-modified chemical moiety. This yields a sequence-defined array of tens of millions of base-modified sequences, which can then be characterized in a high-throughput fashion. Collectively, we believe that these advancements are helping to make aptamer technology more accessible, efficient, and robust, thereby enabling the use of these affinity reagents for a wider range of molecular recognition and detection-based applications.

bioengineering↗

bioRxiv2020

A Shift from Value- to Saliency- Neural Encoding of Subjective Value in Combat Veterans with PTSD during Decision Making under Uncertainty

Military personnel engaged in combat are vulnerable to Posttraumatic Stress Disorder (PTSD), following traumatic experiences in the battlefield. Prior research has mostly employed fear-related paradigms to unravel neural underpinnings of fear dysregulation in individuals with PTSD. The ability to acquire and update fear responses depends critically on the individuals ability to cope with uncertainty, yet the role of individual uncertainty attitudes in the development of trauma-related psychopathology has hardly been examined. Here, we investigated the association between PTSD-related alterations and the subjective valuation of uncertain outcomes during decision-making. We used a monetary gambling paradigm inspired by behavioral economics in conjunction with fMRI and explored neural markers of both vulnerability and resilience to PTSD in a group of combat veterans. Behaviorally, PTSD symptom severity was associated with increased aversion to uncertainty. Neurally, activity in the ventromedial prefrontal cortex (vmPFC) during valuation of uncertain options was associated with PTSD symptoms, an effect which was specifically driven by numbing symptoms. Moreover, the neural encoding of the subjective value of those uncertain options was markedly different in the brains of veterans diagnosed with PTSD, compared to veterans who experienced trauma but did not develop PTSD. Most notably, veterans with PTSD exhibited enhanced representations of the saliency of rewards and punishments in the neural valuation system, especially in ventral striatum, compared with trauma-exposed controls. Our results point to a link between the function of the valuation system under uncertainty and the development and maintenance of PTSD symptoms, and stress the significance of studying reward processes in PTSD.

neuroscience↗