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Sinha, Anupama

Publications and source records attributed to Sinha, Anupama.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Computationally restoring the potency of a clinical antibody against Omicron

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs and revealed how quickly viral escape can curtail effective options. When the SARS-CoV-2 Omicron variant emerged in 2021, many antibody drug products lost potency, including Evusheld and its constituent, cilgavimab. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign and renew the efficacy of COV2-2130 against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and subsequent variants of concern, and provides protection in vivo against the strains tested: WA1/2020, BA.1.1 and BA.5. Deep mutational scanning of tens of thousands of pseudovirus variants reveals that 2130-1-0114-112 improves broad potency without increasing escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Our computational approach does not require experimental iterations or pre-existing binding data, thus enabling rapid response strategies to address escape variants or lessen escape vulnerabilities.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Therapeutic efficacy of a potent anti-Venezuelan equine encephalitis virus antibody is contingent on Fc effector function

The development of specific, safe, and potent monoclonal antibodies (Abs) has led to novel therapeutic options for infectious disease. In addition to preventing viral infection through neutralization, Abs can clear infected cells and induce immunomodulatory functions through engagement of their crystallizable fragment (Fc) with complement proteins and Fc receptors on immune cells. Little is known about the role of Fc effector functions of neutralizing Abs in the context of encephalitic alphavirus infection. To determine the role of Fc effector function in therapeutic efficacy against Venezuelan equine encephalitis virus (VEEV), we compared the potently neutralizing anti-VEEV human IgG F5 (hF5) Ab with intact Fc function (hF5-WT) or containing the loss of function Fc mutations L234A and L235A (hF5-LALA) in the context of VEEV infection. We observed significantly reduced binding to complement and Fc receptors, as well as differential in vitro kinetics of Fc-mediated cytotoxicity for hF5-LALA compared to hF5-WT. The in vivo efficacy of hF5-LALA was comparable to hF5-WT at -24 and + 24 h post infection, with both Abs providing high levels of protection. However, when hF5-WT and hF5-LALA were administered + 48 h post infection, there was a significant decrease in the therapeutic efficacy of hF5-LALA. Together these results demonstrate that optimal therapeutic Ab treatment of VEEV, and possibly other encephalitic alphaviruses, requires neutralization paired with engagement of immune effectors via the Fc region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Whole‐Cell MALDI‐ToF MS Coupled with Untargeted Metabolomics Facilitates Investigations of Microbial Chemical Interactions

Abstract The emergence of drug‐resistant pathogens necessitates the development of new countermeasures. In this regard, the introduction of probiotics to directly attack or competitively exclude pathogens presents a useful strategy. Application of this approach requires an understanding of how a probiotic and its target pathogen interact. A key means of probiotic‐pathogen interaction involves the production of small molecules called natural products (NPs). Here, we report the use of whole‐cell matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐ToF) mass spectrometry to characterize NP production by candidate probiotics (mouse airway microbiome isolates) when co‐cultured with the respiratory pathogen Burkholderia . We found that a Bacillus velezensis strain inhibits growth of and elicits NP production by Burkholderia thailandensis . Dereplication of known NPs detected in the metabolome of this B. velezensis strain suggests that a previously unannotated bioactive compound is involved. Thus, we present the use of whole‐cell MALDI as a broadly applicable method for screening the NP composition of microbial co‐cultures; this can be combined with other ‐omics methods to characterize probiotic‐pathogen and other microbe‐microbe interactions.

Aiosa, Nicole↗
DOE OSTI2022

Metabolomics Analysis of Bacterial Pathogen Burkholderia thailandensis and Mammalian Host Cells in Co-culture

The Tier 1 HHS/USDA Select Agent Burkholderia pseudomallei is a bacterial pathogen that is highly virulent when introduced into the respiratory tract and intrinsically resistant to many antibiotics. Transcriptomic- and proteomic-based methodologies have been used to investigate mechanisms of virulence employed by B. pseudomallei and Burkholderia thailandensis, a convenient surrogate; however, analysis of the pathogen and host metabolomes during infection is lacking. Changes in the metabolites produced can be a result of altered gene expression and/or post-transcriptional processes. Thus, metabolomics complements transcriptomics and proteomics by providing a chemical readout of a biological phenotype, which serves as a snapshot of an organism’s physiological state. However, the poor signal from bacterial metabolites in the context of infection poses a challenge in their detection and robust annotation. In this work, we coupled mammalian cell culture-based metabolomics with feature-based molecular networking of mono- and co-cultures to annotate the pathogen’s secondary metabolome during infection of mammalian cells. These methods enabled us to identify several key secondary metabolites produced by B. thailandensis during infection of airway epithelial and macrophage cell lines. Additionally, the use of in silico approaches provided insights into shifts in host biochemical pathways relevant to defense against infection. Using chemical class enrichment analysis, for example, we identified changes in a number of host-derived compounds including immune lipids such as prostaglandins, which were detected exclusively upon pathogen challenge. Taken together, our findings indicate that co-culture of B. thailandensis with mammalian cells alters the metabolome of both pathogen and host and provides a new dimension of information for in-depth analysis of the host–pathogen interactions underlying Burkholderia infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Nanoparticle Mediated Delivery of Therapeutic mRNA for Protection Against Lung Damage

Medical countermeasures (MCMs) based on messenger ribonucleic acid (mRNA) are promising due to their programmability, targeting precision and specificity, predictable physicochemical properties, and amenability to scalable manufacture. However, safe and effective delivery vehicles are needed, especially for targeting the lung. We developed a generalized approach to nanoparticle-mediated mRNA delivery to lung, and used it to evaluate candidate therapies. In initial studies, reporter mRNA was delivered using lipid-coated mesoporous silica nanoparticles (LC-MSNs) and lipid nanoparticles (LNPs), the latter with greater consistency. Then, mRNA encoding known protein therapies were delivered using LNPs. These formulations showed some toxicity in mice with lung damage, but those with IL-1RA, sACE2-Ig, and ANGPT1 mRNA were modestly therapeutic on balance. Our work advances the state of the art for mRNA delivery to lung, and provides a foundation for evaluating and characterizing mRNA-based lung therapies, including three that appear to be exceptionally promising.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Photocatalytic Material Surfaces for SARS-CoV-2 Virus Inactivation

Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) can be spread through close contact or through fomite mediated transmission. This study details the fabrication and analysis of a photocatalyst surface which can rapidly inactivate SARS-COV-2 to limit spread of the virus by fomite mediated transmission. The surface being developed at Sandia for this purpose is a minimally hazardous Ag-Ti0 2 nanomaterial which is engineered to have high photocatalytic activity. Initial results at Sandia California in a BSL-2 safe surrogate virus- Vesicular Stomatitis Virus (VSV) show a significant difference between the photocatalyst material under exposure to visible light than controls. Additionally, UV-A light (365 nm) was found to eliminate SARS-COV-2 after 9 hours on all tested surfaces with irradiance of 15 mW/cm 2 equivalent to direct circumsolar irradiance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sandia's Research in Support of COVID-19 Pandemic Response: Materials Science

Sandia Materials Science Investment Area contributed to the SARS-CoV-2 virus and COVID-19 disease which represent the most significant pandemic threat in over 100 years. We completed a series of 7, short duration projects to provide innovative materials science research and development in analytical techniques to aid the neutralization of COVID-19 on multiple surfaces, approaches to rapidly decontaminate personal protective equipment, and pareto assessment of construction materials for manufacturing personal protective equipment. The developed capabilities and processes through this research can help US medical personnel, government installations and assets, first responders, state and local governments, and multiple federal agencies address the COVID-19 Pandemic.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Supercritical CO2 sterilization of N95 Masks

A preliminary investigation of the use of supercritical carbon dioxide for treating of 3M 1860 N95 masks was undertaken to evaluate a potential route to low-cost, scalable, sterilization of personal protective equipment for multiple reuse in hospital settings. Upon entering the supercritical regime, the normally distinct liquid and gaseous phases of CO 2 merge into a single homogeneous phase that has density, short-range order, and solvation capacity of a liquid, but the volume-filling and permeation properties that of a gas. This enables supercritical CO2 to function as a vehicle for delivery of biocidal agents such peracetic acid into microporous structures. The potentially adverse effect of a liquid-to-gas phase transition on mask filter media is avoided by conducting cleaning operations above 31 C, the critical temperature for carbon dioxide. A sample of fifteen 3M 1860 N95 masks was subjected to ten consecutive cycles of supercritical CO 2 cleaning to determine its effect on mask performance. These 15 masks, along with 5 control samples then underwent a battery of standardized tests at the CDC NIOSH NPPTL research facility in Pittsburgh, PA. The data from these tests strongly suggest (but do not prove) that supercritical carbon dioxide do not damage 3M 1860 N95 masks. Additional tests conducted during this project confirmed the compatibility of supercritical CO 2 with ventilator tubing that, like N95 masks, has been in short supply during portions of the COVID-19 pandemic and cannot be sterilized by conventional means. Finally, a control experiment was also conducted to examine the effect of supercritical CO 2 on a BSL-2 surrogate virus, vesicular stomatitis virus (VSV), Indiana serotype strain. In the absence of biocidal additives, supercritical CO 2 exhibited no measurable lethality against VSV. This surrogate virus experiment suggests that a biocidal additive such as peracetic acid will be necessary to achieve required sterilization metrics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗