CROI 2025 Abstract eBook

Abstract eBook

Poster Abstracts

virological assays to characterize antiviral potencies. Lead molecules were also studied in biophysical assays including X-ray crystallography and 2D-NMR to determine their mechanisms of action for viral intervention. Results: This chemical series demonstrates activity in biochemical and virological SARS-CoV-2 assays in vitro, with the most potent compound having a biochemical IC 50 of 271 nM and antiviral EC 50 of 33 nM. Two X-ray co-crystal structures revealed that these compounds engaged PLpro through a novel binding mode distinct from that of GRL0617, a known SARS-CoV/SARS-CoV-2 PLpro inhibitor that binds to the BL2-loop region of monomeric PLpro protein. Specifically, these compounds simultaneously engage the BL2-loop region of one PLpro monomer and a cryptic pocket between the Ubl/Thumb domain of another monomer inducing dimerization. This dimer-inducing mechanism of action was verified to be concentration-dependent in solution using analytical SEC and 1D-NMR suggesting these inhibitors act as molecular glues. Conclusions: There is a great interest in the discovery of inhibitors for SARS CoV-2 PLpro to complement currently available SARS-CoV-2 therapeutics. In this study, we report the discovery of a class of small molecule inhibitors that targets SARS-CoV-2 PLpro through the novel mechanism of PLpro dimerization. These compounds are proposed to mediate inhibition through the molecular glue-induced self-association of PLpro. This mechanism is different from those of other PLpro inhibitors which mediate inhibition through a single interaction with monomeric PLpro near the substrate binding pocket of the enzyme. Taken together, this class of inhibitors represents a novel and attractive chemical series for potent SARS-CoV-2 inhibition. SARS-CoV-2 Ensitrelvir Resistance-Associated Mutations in Phase III Randomized Clinical Trial Manish C. Choudhary 1 , Rinki Deo 1 , Annie F. Luetkemeyer 2 , Kara Chew 3 , Michael Hughes 4 , Linda J. Harrison 4 , Eric S. Daar 3 , Joseph J. Eron 5 , Simon Portsmouth 6 , Takeki Uehara 7 , Davey Smith 8 , Judith Currier 3 , Pavitra Roychoudhury 9 , Alexander L. Greninger 10 , Jonathan Li 1 , for the SCORPIO-HR/ACTIV 2d (ACTG A5407) Study Team 1 Brigham and Women's Hospital, Boston, MA, USA, 2 University of California San Francisco, San Francisco, CA, USA, 3 University of California Los Angeles, Los Angeles, CA, USA, 4 Harvard TH Chan School of Public Health, Boston, MA, USA, 5 University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, 6 Shionogi, Inc, Florham Park, NJ, USA, 7 Shionogi & Co, Ltd, Osaka, Japan, 8 University of California San Diego, La Jolla, CA, USA, 9 Washington DC VA Medical Center, Washington, DC, USA, 10 University of Washington, Seattle, WA, USA Background: Ensitrelvir, an oral main protease inhibitor targeting SARS-CoV-2, demonstrated robust antiviral activity in the phase 3 SCORPIO-HR/ACTIV-2d trial with a significant reduction in viral RNA levels and a higher percentage of negative viral cultures at Day 4 compared to placebo. In this exploratory analysis, we investigated emergence of resistance-associated mutations with ensitrelvir treatment. Methods: A total of 1,888 mITT participants (945 in the ensitrelvir group and 943 in the placebo group, all with Omicron infection) from the SCORPIO-HR/ ACTIV-2d trial who received ≥1 dose of study intervention within 3 days of symptom onset were included. Nasopharyngeal (NP) swabs were collected on days 1, 4, 8, and 16 for SARS-CoV-2 RNA levels by quantitative RT-PCR. Whole viral genome and targeted nsp5 gene sequencing were performed. Ensitrelvir resistance-associated mutations were defined as changes that reduced susceptibility by three-fold or more, or if found within 5 Angstroms of the active site. For the calculation of the frequency of treatment-emergent mutations, the denominator included all mITT participants regardless of sequence availability. Comparisons were by Wilcoxon rank sum tests. Results: Treatment-emergent mutations were more frequent in the ensitrelvir treated group compared to the placebo group (T25A/N: 0.4% (4/945) vs. 0% (0/943), p=0.12; M49L/I: 1.5% (14/945) vs. 0% (0/943), p<0.001). We also compared pre- and post-treatment SARS-CoV-2 RNA levels in those with successful sequencing at baseline and at least one follow-up time point. Ensitrelvir-treated participants with emergent mutations (n=18) showed higher RNA levels than ensitrelvir-treated participants without emergent mutations (n=255) both before treatment and on days 4 and 8: median (Q1, Q3) SARS-CoV 2 RNA levels pre-treatment: 8.2 (7.2, 8.3) vs. 7.3 (6.1, 8.1) log 10 copies/mL; day 4: 5.1 (4.4, 5.8) vs. 4.6 (3.9, 5.4) log 10 copies/mL; day 8: 5.4 (4.0, 6.1) vs. 1.7 log10 copies/mL (detected below lower limit of quantification [LLoQ]) (0.0, 2.7). Conclusions: Resistance-associated mutations emerged with ensitrelvir treatment, but was relatively infrequent and associated with higher pre treatment RNA levels. Protease inhibitors represent an important treatment

modality for COVID-19, but can be vulnerable to treatment-emergent mutations and additional monitoring is warranted. Patterns of Remdesivir Initiation in Immunocompromised Patients Hospitalized With COVID-19 Mark Berry 1 , Eunyoung Lee 1 , Valentina Shvachko 1 , Carrie Nielson 1 , Kathleen Hurwitz 2 , Nuvan Rathnayaka 2 , Rachel Faller 2 , Mazin Abdelghany 1 , M. Alan Brookhart 2 , Anand P. Chokkalingam 1 1 Gilead Sciences, Inc, Foster City, CA, USA, 2 Target RWE, Durham, NC, USA Background: Immunocompromised patients who are hospitalized with COVID-19 and initiate remdesivir (RDV) within the first 2 days of hospitalization have a lower risk of all-cause mortality than those who do not initiate RDV. However, it is unknown what proportions of patients with immunocompromising conditions (when stratified by age or the SARS-CoV-2 variant period) initiate RDV at different stages of hospitalization (ie, early, intermediate, late, or never). Methods: This was a retrospective observational cohort study using HealthVerity data, which includes US hospital chargemaster data and hospital, medical, and pharmacy claims. Patients with immunocompromising conditions aged ≥12 years who were hospitalized between May 2020 and December 2023 with a primary diagnosis of COVID-19 were evaluated by time of RDV initiation after hospital admission: 1-2 days (early), 3-7 days (intermediate), ≥8 days (late), or never; day 1 = day of admission. Analyses were stratified by age and variant period (initial wave: May 1, 2020-May 31, 2021; Delta: June 1, 2021 November 30, 2021; Omicron: December 1, 2021-December 3, 2023). Results: Among the 154,850 eligible patients identified, median (Q1, Q3) age was 71 (60, 80) years. Among the 54,238/154,850 (35%) patients who initiated RDV during hospitalization, 46,198/54,238 (85%) patients started RDV within 1-2 days of admission ( Table 1 ). Among those who received RDV in the hospital, the proportion of patients who initiated RDV within 1-2 days of hospitalization was comparable between those aged 12-64 and >65 years (15,767/17,992 [88%] and 30,431/36,246 [84%], respectively), as well as across the variant periods (initial wave: 18,359/22,261[82%]; Delta: 8608/9533 [90%]; Omicron: 19,231/22,444 [86%]). However, most (100,612/154,850 [65%]) patients never initiated RDV; this was also true among the subset of patients aged >65 years (65,926/102,172 [65%] did not initiate RDV) and those who had COVID-19 during the Omicron period (50,307/72,751 [69%] did not initiate RDV). Conclusions: While most patients with immunocompromising conditions who received RDV were treated within 1-2 days of hospital admission, the majority were never treated, suggesting an opportunity to prevent disease progression in one of the highest risk groups.

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Machine Learning Identifies Predictors of Delayed Remdesivir Use in Hospitalized COVID-19 Patients Anne-Maud Ferreira 1 , Cole Campton 1 , Zanthia Wiley 2 , Mark Berry 1 , Celine Der Torossian 1 , Anand P. Chokkalingam 1 , Bryan Downie 1 , Rikisha Gupta 1 1 Gilead Sciences, Inc, Foster City, CA, USA, 2 Emory University Hospital, Atlanta, GA, USA Background: COVID-19 remains a public health concern despite availability of effective interventions. Clinical studies have shown that remdesivir (RDV) reduces mortality, hospitalization, disease progression, and recovery time in individuals hospitalized with COVID-19. Current NIH guidelines recommend RDV treatment for patients at high risk of disease progression. This study of patients hospitalized for COVID-19 aimed to identify attributes linked with the likelihood of receiving delayed or no RDV treatment during the Omicron period.

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