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bioRxiv2024

Danicamtiv reduces myosin's working stroke but enhances contraction by activating the thin filament

Heart failure is a leading cause of death worldwide, and even with current treatments, the 5-year transplant-free survival rate is only [~]50-70%. As such, there is a need to develop new treatments for patients that improve survival and quality of life. Recently, there have been efforts to develop small molecules for heart failure that directly target components of the sarcomere, including cardiac myosin. One such molecule, danicamtiv, recently entered phase II clinical trials; however, its mechanism of action and direct effects on myosins mechanics and kinetics are not well understood. Using optical trapping techniques, stopped flow transient kinetics, and in vitro reconstitution assays, we found that danicamtiv reduces the size of cardiac myosins working stroke, and in contrast to studies in muscle fibers, we found that it does not affect actomyosin detachment kinetics at the level of individual crossbridges. We demonstrate that danicamtiv accelerates actomyosin association kinetics, leading to increased recruitment of myosin crossbridges and subsequent thin filament activation at physiologically-relevant calcium concentrations. Finally, we computationally model how the observed changes in mechanics and kinetics at the level of single crossbridges contribute to increased cardiac contraction and improved diastolic function compared to the related myotrope, omecamtiv mecarbil. Taken together, our results have important implications for the design of new sarcomeric-targeting compounds for heart failure. SIGNIFICANCE STATEMENTHeart failure is a leading cause of death worldwide, and there is a need to develop new treatments that improve outcomes for patients. Recently, the myosin-binding small molecule danicamtiv entered clinical trials for heart failure; however, its mechanism at the level of single myosin crossbridges is not well understood. We determined the molecular mechanism of danicamtiv and showed how drug-induced molecular changes can mechanistically increase heart contraction. Moreover, we demonstrate fundamental differences between danicamtiv and the related myosin-binding small molecule omecamtiv mecarbil that explain the improved diastolic function seen with danicamtiv. Our results have important implications for the design of new therapeutics for heart failure.

biophysics↗

bioRxiv2024

Combined inhibition of MDM2 and PARP lead to a synergistic anti-tumoral response in p53 wild-type rhabdomyosarcoma models

Targeting MDM2-p53 interaction to enhance p53 activity represents a promising antitumoral strategy for p53 wild-type pediatric tumors, including soft-tissue sarcomas. However, results from early-phase clinical trials in hematological and solid cancers have shown limited efficacy of MDM2 inhibitors, underscoring the necessity to explore more effective combinations with other agents. In this study, we provide results from a 22-drug combination screening demonstrating the therapeutic potential of combining siremadlin (MDM2 inhibitor) and olaparib (PARP inhibitor) for treating p53 wild-type rhabdomyosarcoma (p53 WT RMS). Cell survival, cell death, and apoptosis analysis revealed synergistic effects of combining siremadlin plus olaparib in vitro. The combination of both drugs led to a significant increase in p53 activity, as evidenced by p53 accumulation and K382 acetylation, along with an increased expression of bona fide p53 targets. Furthermore, treatment with both drugs resulted in significant reduction of tumor growth and increased mice overall survival when compared to single treatments and control in cell line-derived orthotopic xenograft models. Overall, our study demonstrates, for the first time, the synergistic effect of combining siremadlin plus olaparib in inhibiting p53 WT RMS tumor growth in vitro and in vivo. Our findings support the potential to study the combination of both drugs in clinical trials and warrants further investigation in other tumors with similar molecular features.

cancer biology↗

bioRxiv2018

Identifying individual risk rare variants using protein structure-guided local tests (POINT)

Rare variants are of increasing interest to genetic association studies because of their etiological contributions to human complex diseases. Due to the rarity of the mutant events, rare variants are routinely analyzed on an aggregate level. While aggregation analyses improve the detection of global-level signal, they are not able to pinpoint causal variants within a variant set. To perform inference on a localized level, additional information, e.g., biological annotation, is often needed to boost the information content of a rare variant. Following the observation that important variants are likely to cluster together on functional domains, we propose a protein structure guided local test (POINT) to provide variant-specific association information using structure-guided aggregation of signal. Constructed under a kernel machine framework, POINT performs local association testing by borrowing information from neighboring variants in the 3-dimensional protein space in a data-adaptive fashion. Besides merely providing a list of promising variants, POINT assigns each variant a p-value to permit variant ranking and prioritization. We assess the selection performance of POINT using simulations and illustrate how it can be used to prioritize individual rare variants in PCSK9 associated with low-density lipoprotein in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial data.\n\nAuthor summaryWhile it is known that rare variants play an important role in understanding associations between genotype and complex diseases, pinpointing individual rare variants likely to be responsible for association is still a daunting task. Due to their low frequency in the population and reduced signal, localizing causal rare variants often requires additional information, such as type of DNA change or location of variant along the sequence, to be incorporated in a biologically meaningful fashion that does not overpower the genotype data. In this paper, we use the observation that important variants tend to cluster together on functional domains to propose a new approach for prioritizing rare variants: the protein structure guided local test (POINT). POINT uses a genes 3-dimensional protein folding structure to guide aggregation of information from neighboring variants in the protein in a robust manner. We show how POINT improves selection performance over single variant tests and sliding window approaches. We further illustrate how it can be used to prioritize individual rare variants using the Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial data, finding five promising variants within PCSK9 in association with low-density lipoprotein, including three new mutations near the PCSK9-LDLR binding domain.

bioinformatics↗

bioRxiv2021

Topical TMPRSS2 inhibition prevents SARS-CoV-2 infection in differentiated primary human airway cells

BackgroundThere are limited effective prophylactic treatments for SARS-CoV-2 infection, and limited early treatment options. Viral cell entry requires spike protein binding to the ACE2 receptor and spike cleavage by TMPRSS2, a cell surface serine protease. Targeting of TMPRSS2 by either androgen blockade or direct inhibition is already in clinical trials in early SARS-CoV-2 infection. MethodsThe likely initial cells of SARS-CoV-2 entry are the ciliated cells of the upper airway. We therefore used differentiated primary human airway epithelial cells maintained at the air-liquid interface (ALI) to test the impact of targeting TMPRSS2 on the prevention of SARS-CoV-2 infection. ResultsWe first modelled the systemic delivery of compounds. Enzalutamide, an oral androgen receptor antagonist, had no impact on SARS-Cov-2 infection. By contrast, camostat mesylate, an orally available serine protease inhibitor, blocked SARS-CoV-2 entry. However, camostat is rapidly metabolised in the circulation in vivo, and systemic bioavailability after oral dosing is low. We therefore modelled local airway administration by applying camostat to the apical surface of the differentiated ALI cultures. We demonstrated that a brief exposure to topical camostat is effective at restricting SARS-CoV-2 viral infection. ConclusionThese experiments demonstrate a potential therapeutic role for topical camostat for pre- or post-exposure prophylaxis of SARS-CoV-2, which can now be evaluated in a clinical trial.

microbiology↗

bioRxiv2021

A molecular switch between mammalian MLL complexes dictates response to Menin-MLL inhibition

The chromatin adaptor Menin interacts with oncogenic fusion proteins encoded by MLL1-rearrangements (MLL1-r), and small molecules that disrupt these associations are currently in clinical trials for the treatment of leukemia. By integrating chromatin-focused and genome-wide CRISPR screens with genetic, pharmacological, and biochemical approaches in mouse and human systems, we discovered a molecular switch between the MLL1-Menin and MLL3/4-UTX chromatin modifying complexes that dictates response to Menin-MLL inhibitors. We show that MLL1-Menin safeguards leukemia survival by impeding binding of the MLL3/4-UTX complex at a subset of target gene promoters. Disrupting the interaction between Menin and MLL1 leads to UTX-dependent transcriptional activation of a tumor suppressor gene-program that is crucial for a therapeutic response in murine and human leukemia. We establish the therapeutic relevance of this mechanism by showing that CDK4/6 inhibitors allow re-activation of this tumor-suppressor program in Menin-inhibitor insensitive leukemia cells, mitigating treatment resistance. The discovery of a molecular switch between MLL1-Menin and MLL3/4-UTX complexes on chromatin sheds light on novel functions of these evolutionary conserved epigenetic mediators and is particularly relevant to understand and target molecular pathways determining response and resistance in ongoing phase 1/2 clinical trials.

cancer biology↗

bioRxiv2025

Preconditioning Matters: Enhancing or Impairing Antitumor Immunity with DC Vaccines

Preconditioning regimens are essential for the success of adoptive cell therapies like CAR T-cells due to effects on the T-cell response, yet they are underexplored and generally absent from cancer vaccine clinical trials. To address this gap, we evaluated the impact of various preconditioning strategies on dendritic cell (DC) vaccine efficacy in a murine tumor model. Mice bearing syngeneic KP tumors expressing ovalbumin received preconditioning with low-dose radiation (LD RT; whole body or tumor only), cyclophosphamide, paclitaxel, LD RT plus cyclophosphamide, or no preconditioning, followed by administration of antigen-loaded DC1s. Tumor growth, survival, and antigen-specific CD8+ T-cell responses were assessed. LD RT preconditioning, whether whole body or tumor-directed, significantly enhanced vaccine-induced antitumor CD8+ T-cell responses and improved survival compared to DC vaccine alone and all other groups. Cyclophosphamide preconditioning reduced vaccine efficacy and negated the benefits of LD RT, while paclitaxel had no significant effect. Notably, whole-body LD RT induced the strongest antigen-specific T-cell response. These findings demonstrate that, similar to CAR T-cell therapy, preconditioning regimens can significantly influence cancer vaccine outcomes. Rational selection of preconditioning agents may either maximize or minimize the therapeutic potential of DC cancer vaccines, and should be considered carefully in clinical trials.

immunology↗

bioRxiv2023

Chimeric oncolytic adenovirus evades neutralizing antibodies from human patients and exhibits enhanced anti-glioma efficacy in immunized mice

BACKGROUNDOncolytic adenoviruses, such as Delta-24-RGD, show promise as a potential breakthrough in treating patients with high-grade gliomas. However, their effectiveness against gliomas can be hindered by the presence of neutralizing antibodies. METHODSProduction of human neutralizing antibodies against adenoviruses was assessed in two cohorts of patients with malignant gliomas treated with Delta-24-RGD in a phase 1 clinical trial. Sera containing neutralizing antibodies were also obtained from mice immunized with intramuscular injections of wild-type Ad5. Chimeric adenovirus was constructed using molecular cloning, and its activity was assessed in vitro using quantitative PCR, western blot, and transmission electron microscopy. The therapeutic efficacy of the chimeric virus was tested in vivo using sera from patients previously treated with Delta-24-RGD and immunocompetent murine models of glioma. RESULTSExamination of sera from patients with malignant gliomas treated with Delta-24-RGD revealed that in the cohort treated with multiple injections of this oncolytic adenovirus, a higher percentage of patients developed neutralizing antibodies when compared to the patients treated with a single injection of Delta-24-RGD. Of note, long-term survival was only observed in patients who received a single injection. Delta-24-RGD-H43m, a chimeric oncolytic adenovirus engineered to overcome virus neutralization, demonstrated a potent anti-glioma effect both in vitro and in vivo. This chimeric virus showed resilience against anti-Ad5 neutralizing antibodies and conferred better therapeutic efficacy compared to Delta-24-RGD in mice with immunity against Ad5. Of further clinical relevance, Delta-24-RGD-H43m also evaded the inhibitory effects of sera from human patients treated with Delta-24-RGD. CONCLUSIONSThe development of neutralizing antibodies due to multiple virus injections was associated with lower frequency of long-term survivors in a clinical trial. The new chimeric virus shows increased resilience to inactivation by the sera of human patients compared to the parental virus. These findings lay the foundation for a novel oncolytic virus treatment approach targeting a significant percentage of glioma patients with prior exposure to adenovirus.

cancer biology↗

bioRxiv2025

SB 11285, a Novel Canonical Purine-Pyrimidine Cyclic Dinucleotide, is a Systemically Bioavailable STING Agonist for Cancer Immunotherapy

SummarySB 11285, a novel cell-permeable, canonical 3,5, purine-pyrimidine cyclic dinucleotide has been developed as a potent systemically bioavailable STING agonist currently in clinical trials. The stimulator of Interferon genes (STING) pathway, crucial for cytosolic DNA sensing and innate immunity, presents a promising avenue for novel cancer immunotherapies. Discussed here is the discovery and development of SB11285, a potent activator of the STING pathway, belonging to the canonical class of 3,5 purine-pyrimidine (PuPy) cyclic dinucleotides (CDNs). SB11285 exhibits superior potency and cell permeability compared to non-canonical 2,3-CDNs and demonstrates robust antitumor activity in in vivo syngeneic mouse tumor models, resulting in complete tumor regression, and durable immunological memory. Combination with checkpoint inhibitors and cytotoxic agents further enhances its efficacy. The anti-tumor effects of SB 11285 rely on the induction of CD8+ T cells, activated macrophages, and NK cells in the tumor microenvironment (TME), for efficient tumor killing and fostering profound and durable anti-tumor response. Our findings underscore the potential of functionalized canonical 3,5-Pu-Py CDNs, exemplified by SB11285, as safe and potent STING agonists for multiple routes of administration in cancer therapy. Currently, SB11285 administered intravenously (IV), is undergoing evaluation as the first systemically administered CDN analog in human clinical trials across various tumor types.

immunology↗

bioRxiv2020

Envelope Simulation: A New Adaptive Method for Dose Optimization/* Layout-provided Styles */div.standard { margin-bottom: 2ex;}

We present a flexible and general adaptive experimental design for dose finding clinical trials. This method can be applied in sterotypical settings such as determining a maximum tolerated dose, when the dose response relationship is complex, or when the response is an arbitrary quantitative measure. Our design generalizes dose finding methods such as the continual reassessment method (CRM), modified CRM, and estimation with overdose control (EWOC). Similar to those, our design requires a working mathematical model, which assures efficiency, low bias, and a higher fraction of dose selected near the optimum compared to purely operational designs. Unlike typical model based designs that always employ the same model, our method allows individual dose response models tailored to the circumstance. Simulations are also integral to our design allowing it to account for both known and unknown effects of dose on outcome. This method is applicable to general dose finding problems such as those encountered with modern targeted anti-cancer agents, immunotherapies, and titrations against biomarker outcome measures. The method can also support improvements in the design of the experiment being conducted by providing a platform for concurrent simulations to assess the influence of projected design points. Although we present the design in the context of clinical trials, it is equally applicable to experiments with non-human subjects.

cancer biology↗

bioRxiv2024

CCR5 antagonists as neuroprotective and stroke recovery enhancing agents: a preclinical systematic review and meta-analysis

C-C chemokine receptor type 5 (CCR5) antagonists may improve both acute stroke outcome and long-term recovery. Despite their evaluation in ongoing clinical trials, gaps remain in the evidence supporting their use. With a panel of patients with lived experiences of stroke, we performed a systematic review of animal models of stroke that administered a CCR5 antagonist and assessed infarct size or behavioural outcomes. MEDLINE, Web of Science, and Embase were searched. Article screening and data extraction were completed in duplicate. We pooled outcomes using random effects meta-analyses. We assessed risk of bias using the Systematic Review Centre for Laboratory Animal Experimentation (SYRCLE) tool and alignment with the Stroke Treatment Academic Industry Roundtable (STAIR) and Stroke Recovery and Rehabilitation Roundtable (SRRR) recommendations. Five studies representing 10 experiments were included. CCR5 antagonists reduced infarct volume (standard mean difference -1.02; 95% confidence interval -1.58 to -0.46) when compared to stroke-only controls. Varied timing of CCR5 administration (pre- or post-stroke induction) produced similar benefit. CCR5 antagonists significantly improved 11 of 16 behavioural outcomes reported. High risk of bias was present in all studies and critical knowledge gaps in the preclinical evidence were identified using STAIR/SRRR. CCR5 antagonists demonstrate promise; however, rigorously designed preclinical studies that better align with STAIR/SRRR recommendations and downstream clinical trials are warranted. Prospective Register of Systematic Reviews (PROSPERO CRD42023393438).

neuroscience↗

bioRxiv2018

An acute immune response underlies the benefit of cardiac adult stem cell therapy

Clinical trials using adult stem cells to regenerate damaged heart tissue continue to this day1-3 despite ongoing questions of efficacy and a lack of mechanistic understanding of the underlying biologic effect4-6. The rationale for these cell therapy trials is derived from animal studies that show a modest but reproducible improvement in cardiac function in models of cardiac ischemic injury7-9. Here we examined the mechanistic basis for cell therapy in mice after ischemia/reperfusion (I/R) injury, and while heart function was enhanced, it was not associated with new cardiomyocyte production. Cell therapy improved heart function through an acute sterile immune response characterized by the temporal and regional induction of CCR2+ and CX3CR1+ macrophages. Here we observed that intra-cardiac injection of 2 distinct types of progenitor cells, freeze/thaw-killed cells or a chemical inducer of the innate immune response similarly induced regional CCR2+ and CX3CR1+ macrophage accumulation and provided functional rejuvenation to the I/R-injured heart. Mechanistically, this selective macrophage response altered cardiac fibroblast activity and reduced border zone extracellular matrix (ECM) content and enhanced the mechanical properties of the injured area. The functional benefit of cardiac cell therapy is thus due to an acute inflammatory-based wound healing response that rejuvenates the mechanical properties of the infarcted area of the heart. Such results suggest a re-evaluation of strategies underlying cardiac cell therapy in current and planned human clinical trials.

cell biology↗

bioRxiv2021

Vandetanib Reduces Inflammatory Cytokines and Ameliorates COVID-19 in Infected Mice

The portfolio of SARS-CoV-2 small molecule drugs is currently limited to a handful that are either approved (remdesivir), emergency approved (dexamethasone, baricitinib) or in advanced clinical trials. We have tested 45 FDA-approved kinase inhibitors in vitro against murine hepatitis virus (MHV) as a model of SARS-CoV-2 replication and identified 12 showing inhibition in the delayed brain tumor (DBT) cell line. Vandetanib, which targets the vascular endothelial growth factor receptor (VEGFR), the epidermal growth factor receptor (EGFR), and the RET-tyrosine kinase showed the most promising results on inhibition versus toxic effect on SARS-CoV-2-infected Caco-2 and A549-hACE2 cells (IC50 0.79 M) while also showing a reduction of > 3 log TCID50/mL for HCoV-229E. The in vivo efficacy of vandetanib was assessed in a mouse model of SARS-CoV-2 infection and statistically significantly reduced the levels of IL-6, IL-10, TNF-, and mitigated inflammatory cell infiltrates in the lungs of infected animals but did not reduce viral load. Vandetanib rescued the decreased IFN-1{beta} caused by SARS-CoV-2 infection in mice to levels similar to that in uninfected animals. Our results indicate that the FDA-approved vandetanib is a potential therapeutic candidate for COVID-19 positioned for follow up in clinical trials either alone or in combination with other drugs to address the cytokine storm associated with this viral infection.

immunology↗

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↗

bioRxiv2021

SARS-CoV-2 preS dTM vaccine booster candidates increase functional antibody responses and cross-neutralization against SARS-CoV-2 variants of concern in non-human primates

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that partly evade neutralizing antibodies has raised concerns of reduced vaccine effectiveness and increased infection. We previously demonstrated in preclinical models and in human clinical trials that our SARS-CoV-2 recombinant spike protein vaccine adjuvanted with AS03 (CoV2 preS dTM-AS03) elicits robust neutralizing antibody responses in naive subjects. Here, the objective was to document the potency of various booster vaccine formulations in macaques previously vaccinated with mRNA or protein subunit vaccine candidates. We show that one booster dose of AS03-adjuvanted CoV2 preS dTM, D614 (parental) or B.1.351 (Beta), in monovalent or bivalent (D614 + B.1.351) formulations, significantly boosted pre-existing neutralizing antibodies and elicited high and stable cross-neutralizing antibodies covering the four known SARS-CoV-2 variants of concern (Alpha, Beta, Gamma and Delta) and, unexpectedly, SARS-CoV-1, in primed macaques. Interestingly, the non-adjuvanted CoV2 preS dTM B.1.351 vaccine formulation also significantly boosted and broadened the neutralizing antibody responses. Our findings show that these vaccine candidates used as a booster have the potential to offer cross-protection against a broad spectrum of variants. This has important implications for vaccine control of SARS-CoV-2 variants of concern and informs on the benefit of a booster with our vaccine candidates currently under evaluation in phase 2 and 3 clinical trials (NCT04762680 and NCT04904549).

immunology↗

bioRxiv2025

IL-1R1 Blockade Enhances CD40 Agonist-Mediated Immune Responses but Fails to Increase Efficacy or Mitigate Hepatotoxicity in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) has a poor survival rate and limited treatments. Agonistic CD40 antibodies are promising, but clinical trials have shown only modest efficacy and significant hepatotoxicity. We previously reported that IL-1 pathway blockade enhances agonistic CD40 antibody efficacy against melanoma by depleting polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs; CD11b+Ly6C+Ly6G+). Because PMN-MDSCs also cause liver toxicity, we investigated the impact of IL-1R1 blockade on the efficacy and toxicity of agonistic CD40 antibody therapy in PDAC. Agonistic CD40 antibody therapy induced immune activation and significantly prolonged survival in orthotopic PDAC-bearing mice. IL-1R1 blockade monotherapy downregulated innate and adaptive immune response and exacerbated tumor growth. Although combination therapy upregulated several immune-related pathways and boosted innate and adaptive immune responses. IL-1R1 blockade failed to improve the overall antitumor efficacy of agonistic CD40 antibody therapy and exacerbated liver toxicity. Ly6G+ cell depletion in mice reduced the efficacy of agonistic CD40 antibody therapy, suggesting that Ly6G immune cells (PMN-MDSCs or neutrophils) exhibit an antitumor rather than immunosuppressive role in PDAC. Our findings underscore the complex role of IL-1 signaling in modulating immune responses in PDAC and caution against pursuing IL-1R1 blockade, either as monotherapy or combined with agonistic CD40 antibodies, in clinical trials for PDAC.

cancer biology↗

bioRxiv2020

Stenoparib, an inhibitor of cellular poly (ADP-ribose) polymerase (PARP), blocks replication of the SARS-CoV-2 human coronavirus in vitro.

By late 2020, the coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2 has caused tens of millions of infections and over 1 million deaths worldwide. A protective vaccine and more effective therapeutics are urgently needed. We evaluated a new PARP inhibitor, stenoparib, which was recently advanced to Stage II clinical trials for treatment of ovarian cancer, for activity against human respiratory coronaviruses, including SARS-CoV-2, in vitro. Stenoparib exhibits dose-dependent suppression of SARS-CoV-2 multiplication and spread in Vero E6 monkey kidney and Calu-3 human lung adenocarcinoma cells. Stenoparib was also strongly inhibitory to the HCoV-NL63 human seasonal respiratory coronavirus. Compared to remdesivir, which inhibits viral replication downstream of cell entry, stenoparib impedes entry and post-entry processes as determined by time-of-addition (TOA) experiments. Moreover, a 10 M dosage of stenoparib - below the approximated 25.5 M half-maximally effective concentration (EC50), combined with 0.5 M remdesivir suppressed coronavirus growth by more than 90%, indicating a potentially synergistic effect for this drug combination. Stenoparib as a standalone or as part of combinatorial therapy with remdesivir should be a valuable addition to the arsenal against COVID-19. ImportanceNew therapeutics are urgently needed in the fight against COVID-19. Repurposing drugs that are either already approved for human use or are in advanced stages of the approval process can facilitate more rapid advances toward this goal. The PARP inhibitor stenoparib may be such a drug, as it is currently in Stage II clinical trials for the treatment of ovarian cancer and its safety and dosage in humans has already been established. Our results indicate that stenoparib possesses strong antiviral activity against SARS-CoV-2 and other coronaviruses in vitro. This activity appears to be based on multiple modes of action, where both pre-entry and post-entry viral replication processes are impeded. This may provide a therapeutic advantage over many current options that have a narrower target range. Moreover, our results suggest that stenoparib and remdesivir in combination may be especially potent against coronavirus infection.

microbiology↗

bioRxiv2024

The structural and mechanistic bases for the viral resistance to allosteric HIV-1 integrase inhibitor pirmitegravir

Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are investigational antiretroviral agents which potently impair virion maturation by inducing hyper-multimerization of IN and inhibiting its interaction with viral genomic RNA. The pyrrolopyridine-based ALLINI pirmitegravir (PIR) has recently advanced into Phase 2a clinical trials. Previous cell culture based viral breakthrough assays identified the HIV-1(Y99H/A128T IN) variant that confers substantial resistance to this inhibitor. Here, we have elucidated the unexpected mechanism of viral resistance to PIR. While both Tyr99 and Ala128 are positioned within the inhibitor binding V-shaped cavity at the IN catalytic core domain (CCD) dimer interface, the Y99H/A128T IN mutations did not substantially affect direct binding of PIR to the CCD dimer or functional oligomerization of full-length IN. Instead, the drug-resistant mutations introduced a steric hindrance at the inhibitor mediated interface between CCD and C-terminal domain (CTD) and compromised CTD binding to the CCDY99H/A128T + PIR complex. Consequently, full-length INY99H/A128T was substantially less susceptible to the PIR induced hyper-multimerization than the WT protein, and HIV-1(Y99H/A128T IN) conferred >150- fold resistance to the inhibitor compared to the WT virus. By rationally modifying PIR we have developed its analog EKC110, which readily induced hyper-multimerization of INY99H/A128T in vitro and was [~]14-fold more potent against HIV-1(Y99H/A128T IN) than the parent inhibitor. These findings suggest a path for developing improved PIR chemotypes with a higher barrier to resistance for their potential clinical use. IMPORTANCEAntiretroviral therapies save the lives of millions of people living with HIV (PLWH). However, evolution of multi-drug-resistant viral phenotypes is a major clinical problem, and there are limited or no treatment options for heavily treatment-experienced PLWH. Allosteric HIV-1 integrase inhibitors (ALLINIs) are a novel class of antiretroviral compounds which work by a unique mechanism of binding to the non-catalytic site on the viral protein and inducing aberrant integrase multimerization. Accordingly, ALLINIs potently inhibit both wild type HIV-1 and all drug-resistant viral phenotypes that have so far emerged against currently used therapies. Pirmitegravir, a highly potent and safe investigational ALLINI, is currently advancing through clinical trials. Here we have elucidated structural and mechanistic bases behind the emergence of HIV-1 integrase mutations in infected cell that confer resistance to pirmitegravir. In turn, our findings allowed us to rationally develop an improved ALLINI with substantially enhanced potency against the pirmitegravir resistant virus.

microbiology↗

bioRxiv2020

Biofilm development on urinary catheters promotes the appearance of viable but non-culturable (VBNC) bacteria

Catheter-associated urinary tract infections have serious consequences, both for patients and in impacting on healthcare resources. Much work has been carried out to develop an antimicrobial catheter. Although such developments have shown promise under laboratory conditions, none have demonstrated a clear advantage in clinical trials. Using a range of microbiological and advanced microscopy techniques, a detailed laboratory study comparing biofilm development on silicone, hydrogel latex and silver alloy coated hydrogel latex catheters was carried out. Biofilm development by Escherichia coli, Pseudomonas aeruginosa and Proteus mirabilis on three commercially available catheters was tracked over time. Samples were examined with episcopic differential interference contrast (EDIC) microscopy, culture analysis and staining techniques to quantify viable but non-culturable (VBNC) bacteria. Both qualitative and quantitative assessment found biofilms to develop rapidly on all three materials. EDIC microscopy revealed the rough surface topography of the materials. Differences between culture counts and quantification of total and dead cells demonstrated the presence of VBNC populations, where bacteria retain viability but are not metabolically active. The use of non-culture based techniques showed the development of widespread VBNC populations. These VBNC populations were more evident on silver alloy coated hydrogel latex catheters, indicating a bacteriostatic effect at best. The laboratory tests reported here, that detect VBNC bacteria, allow more rigorous assessment of antimicrobial catheters offering an explanation for why there is often minimal benefit to patients. IMPORTANCESeveral antimicrobial urinary catheter materials have been developed but, although laboratory studies may show a benefit, none have significantly improved clinical outcomes. The use of poorly designed laboratory testing and lack of consideration to the impact of VBNC populations may be responsible. While the presence of VBNC populations is becoming more widely reported, there remains a lack of understanding of the clinical impact or influence of exposure to antimicrobial products. This is the first study to investigate the impact of antimicrobial surface materials and the appearance of VBNC populations. This demonstrates how improved testing is needed prior to clinical trials uptake.

microbiology↗