Integrative transcriptomic and genomic analyses unveil the IFI16 variants and expression as MASLD progression markers.

BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a broad and continuous spectrum of liver diseases ranging from fatty liver to steatohepatitis. The intricate interactions of genetic, epigenetic, and environmental factors in the development and progression of MASLD remain elusive. Here, we aimed to achieve an integrative understanding of the genomic and transcriptomic alterations throughout the progression of MASLD. APPROACH AND RESULTS: RNA-Seq profiling (n = 146) and whole-exome sequencing (n = 132) of MASLD liver tissue samples identified 3 transcriptomic subtypes (G1-G3) of MASLD, which were characterized by stepwise pathological and molecular progression of the disease. Macrophage-driven inflammatory activities were identified as a key feature for differentiating these subtypes. This subtype-discriminating macrophage interplay was significantly associated with both the expression and genetic variation of the dsDNA sensor IFI16 (rs6940, A>T, T779S), establishing it as a fundamental molecular factor in MASLD progression. The in vitro dsDNA-IFI16 binding experiments and structural modeling revealed that the IFI16 variant exhibited increased stability and stronger dsDNA binding affinity compared to the wild-type. Further downstream investigation suggested that the IFI16 variant exacerbated DNA sensing-mediated inflammatory signals through mitochondrial dysfunction-related signaling of the IFI16-PYCARD-CASP1 pathway. CONCLUSIONS: This study unveils a comprehensive understanding of MASLD progression through transcriptomic classification, highlighting the crucial roles of IFI16 variants. Targeting the IFI16-PYCARD-CASP1 pathway may pave the way for the development of novel diagnostics and therapeutics for MASLD.

The paradigm of immune escape by SARS-CoV-2 variants and strategies for repositioning subverted mAbs against escaped VOCs.

The perpetual emergence of SARS-CoV-2 variants is a serious issue that makes it difficult for the therapeutic antibodies and vaccines to end the COVID-19 pandemic. This article discusses the trend of increasing host fitness and immune escape by the virus and how to devise computational strategies for antibodies design and their affinity maturation against emerging SARS-CoV-2 variants.

Toll-like receptor-induced cytokines as immunotherapeutic targets in cancers and autoimmune diseases.

Immune cells of the myeloid and lymphoid lineages express Toll-like receptors (TLRs) to recognize pathogenic components or cellular debris and activate the immune system through the secretion of cytokines. Cytokines are signaling molecules that are structurally and functionally distinct from one another, although their secretion profiles and signaling cascades often overlap. This situation gives rise to pleiotropic cell-to-cell communication pathways essential for protection from infections as well as cancers. Nonetheless, deregulated signaling can have detrimental effects on the host, in the form of inflammatory or autoimmune diseases. Because cytokines are associated with numerous autoimmune and cancerous conditions, therapeutic strategies to modulate these molecules or their biological responses have been immensely beneficial over the years. There are still challenges in the regulation of cytokine function in patients, even in those who take approved biological therapeutics. In this review, our purpose is to discuss the differential expression patterns of TLR-regulated cytokines and their cell type specificity that is associated with cancers and immune-system-related diseases. In addition, we highlight key structural features and molecular recognition of cytokines by receptors; these data have facilitated the development and approval of several biologics for the treatment of autoimmune diseases and cancers.

USO1 isoforms differentially promote liver cancer progression by dysregulating the ER-Golgi network.

Alternative splicing of RNA transcripts plays an important role in cancer development and progression. Recent advances in RNA-seq technology have made it possible to identify alternately spliced events in various types of cancer; however, research on hepatocellular carcinoma (HCC) is still limited. Here, by performing RNA-seq profiling of HCC transcripts at isoform level, we identified tumor-specific and molecular subtype-dependent expression of the USO1 isoforms, which we designated as a normal form USO1-N (XM_001290049) and a tumor form USO1-T (NM_003715). The expression of USO1-T, but not USO1-N, was associated with worse prognostic outcomes of HCC patients. We confirmed that the expression of USO1-T promoted an aggressive phenotype of HCC, both in vitro and in vivo. In addition, structural modeling analyses revealed that USO1-T lacks an ARM10 loop encoded by exon 15, which may weaken the dimerization of USO1 and its tethering to GM130. We demonstrated that USO1-T ensured unstacking of the Golgi and accelerated the vesicles trafficking from endoplasmic reticulum (ER) to Golgi and plasma membrane in multiple liver cancer cells. ERK and GRASP65 were found to be involved in the USO1-T-mediated Golgi dysfunction. Conclusively, we provide new mechanophysical insights into the USO1 isoforms that differentially regulate the ER-Golgi network, promoting the heterogeneous HCC progression.

Endogenous Stem Cell-Based In Situ Tissue Regeneration Using Electrostatically Interactive Hydrogel with a Newly Discovered Substance P Analog and VEGF-Mimicking Peptide.

The use of chemoattractants to promote endogenous stem cell-based in situ tissue regeneration has recently garnered much attention. This study is the first to assess the endogenous stem cell migration using a newly discovered substance P (SP) analog (SP1) by molecular dynamics simulations as an efficient chemoattractant. Further, a novel strategy based on electrostatic interaction using cationic chitosan (Ch) and anionic hyaluronic acid (HA) to prepare an SP1-loaded injectable C/H formulation without SP1 loss is developed. The formulation quickly forms an SP1-loaded C/H hydrogel in situ through in vivo injection. The newly discovered SP1 is found to possess human mesenchymal stromal cells (hMSCs) migration-inducing ability that is approximately two to three times higher than that of the existing SP. The designed VEGF-mimicking peptide (VP) chemically reacts with the hydrogel (C/H-VP) to sustain the release of VP, thus inducing vasculogenic differentiation of the hMSCs that migrate toward the C/H-VP hydrogel. Similarly, in animal experiments, SP1 attracts a large number of hMSCs toward the C/H-VP hydrogel, after which VP induces vasculogenic differentiation. Collectively, these findings indicate that SP1-loaded C/H-VP hydrogels are a promising strategy to facilitate endogenous stem cell-based in situ tissue regeneration.

TPRG1-AS1 induces RBM24 expression and inhibits liver cancer progression by sponging miR-4691-5p and miR-3659.

BACKGROUND & AIMS: Noncoding RNAs (ncRNAs) play critical roles in hepatocellular carcinoma (HCC) progression. Here, by performing RNA-sequencing (RNA-Seq) profiling, we sought to identify novel ncRNAs that potentially drive the heterogeneous progression of liver cancers. METHODS: RNA-Seq profiles were obtained from 68 HCC specimens and 10 samples of adjacent non-tumour liver tissues. The functional significance of the potential driver ncRNAs was evaluated by cell experiments. RESULTS: TPRG1-AS1 was identified as a potential driver noncoding RNA that promotes heterogeneous liver cancer progression. TPRG1-AS1 induced tumour suppressor RNA-binding motif protein 24 (RBM24), suppressing tumour growth by activating apoptotic tumour cell death. In addition, we report that TPRG1-AS1 acts as a competing endogenous RNA (ceRNA) for RBM24, sponging miR-4691-5p and miR-3659 to interfere with their binding to RBM24. CONCLUSIONS: We suggest that TPRG1-AS1 is a novel ceRNA sponging miR-4691-5p and miR-3659, resulting in RBM24 expression and suppression of liver cancer growth. Our results provide new insights into the functions of ncRNAs in heterogeneous HCC progression.

Recent clinical trends in Toll-like receptor targeting therapeutics.

Toll-like receptors (TLRs) are germline-encoded receptors that are central to innate and adaptive immune responses. Owing to their vital role in inflammation, TLRs are rational targets in clinics; thus, many ligands and biologics have been reported to overcome the progression of various inflammatory and malignant conditions and support the immune system. For each TLR, at least one, and often many, drug formulations are being evaluated. Ligands reported as stand-alone drugs may also be reported based on their use in combinatorial therapeutics as adjuvants. Despite their profound efficacy in TLR-modulation in preclinical studies, multiple drugs have been terminated at different stages of clinical trials. Here, TLR modulating drugs that have been evaluated in clinical trials are discussed, along with their mode of action, suggestive failure reasons, and ways to improve the clinical outcomes. This review presents recent advances in TLR-targeting drugs and provides directions for more successful immune system manipulation.

Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2.

Half of the world population is infected by the Gram-negative bacterium Helicobacter pylori (H. pylori). It colonizes in the stomach and is associated with severe gastric pathologies including gastric cancer and peptic ulceration. The most virulent factor of H. pylori is the cytotoxin-associated gene A (CagA) that is injected into the host cell. CagA interacts with several host proteins and alters their function, thereby causing several diseases. The most well-known target of CagA is the tumor suppressor protein ASPP2. The subdomain I at the N-terminus of CagA interacts with the proline-rich motif of ASPP2. Here, in this study, we carried out alanine scanning mutagenesis and an extensive molecular dynamics simulation summing up to 3.8 µs to find out hot spot residues and discovered some new protein-protein interaction (PPI)-modulating molecules. Our findings are in line with previous biochemical studies and further suggested new residues that are crucial for binding. The alanine scanning showed that mutation of Y207 and T211 residues to alanine decreased the binding affinity. Likewise, dynamics simulation and molecular mechanics with generalized Born surface area (MMGBSA) analysis also showed the importance of these two residues at the interface. A four-feature pharmacophore model was developed based on these two residues, and top 10 molecules were filtered from ZINC, NCI, and ChEMBL databases. The good binding affinity of the CHEMBL17319 and CHEMBL1183979 molecules shows the reliability of our adopted protocol for binding hot spot residues. We believe that our study provides a new insight for using CagA as the therapeutic target for gastric cancer treatment and provides a platform for a future experimental study.

Oceans as a Source of Immunotherapy.

Marine flora is taxonomically diverse, biologically active, and chemically unique. It is an excellent resource, which offers great opportunities for the discovery of new biopharmaceuticals such as immunomodulators and drugs targeting cancerous, inflammatory, microbial, and fungal diseases. The ability of some marine molecules to mediate specific inhibitory activities has been demonstrated in a range of cellular processes, including apoptosis, angiogenesis, and cell migration and adhesion. Immunomodulators have been shown to have significant therapeutic effects on immune-mediated diseases, but the search for safe and effective immunotherapies for other diseases such as sinusitis, atopic dermatitis, rheumatoid arthritis, asthma and allergies is ongoing. This review focuses on the marine-originated bioactive molecules with immunomodulatory potential, with a particular focus on the molecular mechanisms of specific agents with respect to their targets. It also addresses the commercial utilization of these compounds for possible drug improvement using metabolic engineering and genomics.

Extraction of diverse polyphenols in relation with storage periods of Citrus paradisi CV. Shamber through HPLC-DAD technique using different solvent.

In this article, Citrus paradisi, (Shamber) an exceptional source of Vitamins A and C and full of nutrients, selected for extraction of diverse polyphenols including dietary flavonoids and essential flavonoids by HPLC-DAD technique using various solvents. These essential targeted compounds also analyze after keeping different storage periods and compare with fresh fruits for better efficacy of these compounds. The highest number of phenolic compounds including gallic acid, chlorogenic acid sinapic acid, ferulic acid, myricetin, quercetin, and kaempferol extracted in methanol solvent leading to the new compounds of tetra-O-methylscutellar and heptamethoxy flavone. The essential flavonoids determined by polyethersulfone filter and insoluble precipitation separated by the dimethyl sulfoxide. The results showed that the methanolic extraction exhibited higher essential flavonoids including nobiletin, sinensetin, tangeritin, and tetra-O-methylscutellarein and heptamethoxy flavone. The RP-HPLC analysis exposed the maximum number of nutritional flavonoids like naringin, hesperidin, total flavones, glycosyl. Moreover, it observed that dietary flavonoids and phenolic compounds of stored fruits were unaffected in 30 days of storage periods while minor variations were pragmatic during 60-90 days storage. The investigation revealed that C. paradisi proves to be the valuable resource of different phenolic compounds and flavonoids which are effective against various oxidative stresses in the human body.

Pharmacological studies of Adhatoda vasica and Calotropis procera as resource of bio-active compounds for various diseases.

Adhatoda vasica and Calotropis procera species were investigated as a resource for new diverse pharmacological agents including B complex, individual total phenolic compounds and antioxidants for curing and treatments of many infectious diseases in human through advanced analytical methods. These plants are abundant in Khyber Pukhtoon Khawa, Pakistan as well as in all over the world and famous for their unique medicinal importance. These herbaceous species are so far used for animals curing while current exploration of these species showed that these species are a precious resource of various compounds which can be employed in the formation of different drugs. The results showed that the leaf and flower extracts of Adhatoda vasica and leaf extract of Calotropis procera contained higher contents of bioactive compounds. The chemical analysis of the samples resulted in higher values of total phenolic compounds (71.32mg GAE/g), total antioxidants (651% DPPH inhibition), the enzyme catalase (4716µg/g), ash content (16.72%) and pH values in the Calotropis procera, whereas the total carotenoids (1987mg/100g), the enzymes, superoxide dismutase (4566µg/g) and peroxidase (1322µg/g) were higher in leaves of Adhatoda vasica. The flower extract of the Adhatoda vasica was rich in the flavonoids (0.87mg/100g) and organic matter (89.99%) as compared to Calotropis procera. The obtained data for each parameter was interpreted by applying Complete Randomized Design (CRD) along with factorial arrangements. The mean comparison was performed using LSD test at 5% probability level. The presence of these phytochemicals may lead to the conclusion that these herbal plants have the potential for formation of new drugs and can be used as herbal medicine for treatment of different cancer and viral diseases. These compounds are also useful in the treatment of the tumor.

Environment effects for earliness and grain yield traits in F1 diallel populations of maize (Zea mays L.).

BACKGROUND: Five maize inbred lines, 20 F1 diallel hybrids and two check genotypes were evaluated through genotype × environment interaction (GEI) and GGE biplot for earliness and yield traits at four locations. RESULTS: Genotype, environment and GEI showed highly significant differences for all the traits. In total sum of squares, environment and genotype played a primary role, followed by GEI. Larger effects of environment and genotype to total variation influence the earliness and yield traits. However, according to the GGE biplot, the first two principal components (PC1 and PC2) explained 95% of the variation caused by GEI. GGE biplot confirmed the differential response of genotypes across environments. F1 hybrid SWAJK-1 × FRHW-3 had better stability, with a good yield, and was considered an ideal genotype. F1 hybrid FRHW-2 × FRHW-1 showed more earliness at CCRI and Haripur, followed by PSEV3 × FRHW-2 and its reciprocal at Swat and Mansehra, respectively. F1 hybrids FRHW-1 × SWAJK-1, PSEV3 × SWAJK-1 and SWAJK-1 × FRHW-3 at Mansehra and Swat produced maximum grain yield, followed by SWAJK-1 × FRHW-1 and PSEV3 × FRHW-1 at Haripur and CCRI, respectively. CONCLUSION: Overall, maize genotypes showed early maturity in plain areas (CCRI and Haripur) but higher yield in hilly areas (Mansehra and Swat). © 2017 Society of Chemical Industry.

Interactions of ketoamide inhibitors on HCV NS3/4A protease target: molecular docking studies.

HCV infection in more than 200 million individuals worldwide is a principal health problem. Prior to the development of HCV protease inhibitor combination therapy, HCV infected patients were treated with pegylated interferon-α and ribavirin. The adverse side effects associated with this type of treatment may lead to the discontinuation of treatment in certain number of patients. Currently, the inhibitors of NS3/4A Protease were found promising candidates for the treatment of HCV infection. There are several inhibitors of HCV NS3/4A protease that are passing through clinical improvement showing good potency against HCV infections in a number of patients. To further recognize binding interactions and activity trend, the molecular docking studies were performed on a number of HCV NS3/4A protease ketoamide inhibitors via MOE docking protocol. The docking analysis resulted in the detection of important ligand interactions with respect to binding site of target protein and produced good correlation coefficient (r2 = 0.690) between docking score and biological activities. These molecular docking results should, in our view, contribute for further optimization of ketoamide derivatives as NS3/4A protease inhibitors.

Long Non-coding RNA TPRG1-AS1 Interacts With CLTC in Liver Cancer Cells.

BACKGROUND/AIM: Certain long non-coding RNAs (lncRNAs), identified as potential tumor suppressors, have shown potential in inhibiting tumor growth. Here, we investigated a novel mechanism involving the direct interaction between lncRNA TPRG1-AS1 and Clathrin Heavy Chain (CLTC) in the Epidermal Growth Factor (EGF) signaling pathway for its tumor-suppressive effects. MATERIALS AND METHODS: Our research revealed a direct physical interaction between TPRG1-AS1 and CLTC through RNA pulldown and RNA immunoprecipitation (RIP)-qPCR, which subsequently influenced the EGF signaling pathway. We confirmed phenotype changes by cell viability, sphere formation, and invasion. We confirmed the mechanism underlying these phenotypic changes through immunoblotting and immunocytochemistry. RESULTS: Firstly, we confirmed a reduction in the phenotype associated with the overexpression of TPRG1-AS1 (TPRG1-AS1oe) interacting with CLTC in the presence of EGF signaling. Next, it was observed that TPRG1-AS1oe suppressed EGF downstream signaling, specifically MAPK8 and MAPK14, in relation to CLTC. Moreover, we verified that overexpressed TPRG1-AS1 binds to CLTC and suppresses EGF downstream signaling using a custom HEX probe. CONCLUSION: Collectively our study uncovered a novel regulatory axis wherein TPRG1-AS1 interacts with CLTC, consequently attenuating EGF downstream signaling, particularly through the MAPK8 and MAPK14 pathways. These complex interactions ultimately lead to a reduction in the phenotype of liver cancer cells.

Identification of novel and potential inhibitors against the dengue virus NS2B/NS3 protease using virtual screening and biomolecular simulations.

Approximately 3.9 billion individuals are vulnerable to dengue infection, a prevalent cause of tropical diseases worldwide. Currently, no drugs are available for preventing or treating Flavivirus diseases, including Dengue, West Nile, and the more recent Zika virus. The highly conserved Flavivirus NS2B-NS3 protease, crucial for viral replication, is a promising therapeutic target. This study employed in-silico methodologies to identify novel and potentially effective anti-dengue small molecules. A pharmacophore model was constructed using an experimentally validated NS2B-NS3 inhibitor, with the Gunner Henry score confirming the model's validity. The Natural Product Activity and Species Source (NPASS) database was screened using the validated pharmacophore model, yielding a total of 60 hits against the NS2B-NS3 protease. Furthermore, the docking finding reveals that our newly identified compounds from the NPASS database have enhanced binding affinities and established significant interactions with allosteric residues of the target protein. MD simulation and post-MD analysis further validated this finding. The free binding energy was computed in terms of MM-GBSA analysis, with the total binding energy for compound 1 (-57.3 ± 2.8 and - 52.9 ± 1.9 replica 1 and 2) indicating a stronger binding affinity for the target protein. Overall, this computational study identified these compounds as potential hit molecules, and these findings can open up a new avenue to explore and develop inhibitors against Dengue virus infection.

RRM2 Is a CTNNB1 Transport Regulator Promoting Colon Cancer Progression.

BACKGROUND/AIM: The cytoplasmic retention and stabilization of CTNNB1 (ß-catenin) in response to Wnt is well documented in playing a role in tumor growth. Here, through the utilization of a multiplex siRNA library screening strategy, we investigated the modulation of CTNNB1 function in tumor cell progression by ribonucleoside-diphosphate reductase subunit M2 (RRM2). MATERIALS AND METHODS: We conducted a multiplex siRNA screening assay to identify targets involved in CTNNB1 nuclear translocation. In order to examine the effect of inhibition of RRM2, selected from the siRNA screening results, we performed RRM2 knockdown and assayed for colon cancer cell viability, sphere formation assay, and invasion assay. The interaction of RRM2 with CTNNB1 and its impact on oncogenesis was examined using immunoprecipitation, immunoblotting, immunocytochemistry, and RT-qPCR. RESULTS: After a series of screening and filtration steps, we identified 26 genes that were potentially involved in CTNNB1 nuclear translocation. All candidate genes were validated in various cell lines. The results revealed that siRNA-mediated knockdown of RRM2 reduces the nuclear translocation of CTNNB1. This reduction was accompanied by a decrease in cell count, resulting in a suppressive effect on tumor cell growth. CONCLUSION: High throughput siRNA screening is an attractive strategy for identifying gene functions in cancers and the interaction between RRM2 and CTNNB1 is an attractive drug target for regulating RRM2-CTNNB1-related pathways in cancers.

Regulatory pathways and therapeutic potential of PDE4 in liver pathophysiology.

Phosphodiesterase 4 (PDE4), crucial in regulating the cyclic adenosine monophosphate (cAMP) signaling pathway, significantly impacts liver pathophysiology. This article highlights the comprehensive effects of PDE4 on liver health and disease, and its potential as a therapeutic agent. PDE4's role in degrading cAMP disrupts intracellular signaling, increasing pro-inflammatory cytokines like tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). This contributes to liver inflammation in conditions such as hepatitis and non-alcoholic steatohepatitis (NASH). Additionally, PDE4 is a key factor in liver fibrosis, characterized by excessive extracellular matrix deposition. Inhibiting PDE4 shows promise in reducing liver fibrosis by decreasing the activation of hepatic stellate cells, which is pivotal in fibrogenesis. PDE4 also influences hepatocyte apoptosis a common feature of liver diseases. PDE4 inhibitors protect against hepatocyte apoptosis by raising intracellular cAMP levels, thus activating anti-apoptotic pathways. This suggests potential in targeting PDE4 to prevent hepatocyte loss. Moreover, PDE4 regulates hepatic glucose production and lipid metabolism, essential for liver function. Altering cAMP levels through PDE4 affects enzymes in these metabolic pathways, making PDE4 a target for metabolic disorders like type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). Since PDE4 plays a multifaceted role in liver pathophysiology, influencing PDE4's mechanisms in liver diseases could lead to novel therapeutic strategies. Still, extensive research is required to explore the molecular mechanisms and clinical potential of targeting PDE4 in liver pathologies.

Improving Access to Anti-HDV Testing: Development and Validation of an Affordable In-House ELISA Assay.

In certain low-income nations, the hepatitis Delta virus and hepatitis B virus (HBV) pose a serious medical burden, where the prevalence of hepatitis B surface antigen (HBsAg) is greater than 8%. Especially in rural places, irregular diagnostic exams are the main restriction and reason for underestimation. Utilizing serum samples from a Pakistani isolate, an internal ELISA for the quick identification of anti-HDV was created, and the effectiveness of the test was compared to a commercial diagnostic kit. HDV-positive serum samples were collected, and a highly antigenic domain of HDAg antigen was derived from them. This antigenic HDAg was expressed in a bacterial expression system, purified by Ni-chromatography, and confirmed by SDS-PAGE and Western blot analysis. The purified antigen was utilized to develop an in-house ELISA assay for anti-HDV antibody detection of the patient's serum samples at very low cost. Purified antigens and positive and negative controls can detect anti-HDV (antibodies) in ELISA plates. The in-house developed kit's efficiency was compared with that of a commercial kit (Witech Inc., USA) by the mean optical density values of both kits. No significant difference was observed (a P value of 0.576) by applying statistical analysis. The newly developed in-house ELISA is equally efficient compared to commercial kits, and these may be useful in regular diagnostic laboratories, especially for analyzing local isolates.

Analysis of dataset on reduction of high temperature stress by green net shade alleviate oxidative stress and augments the growth and vase life of gladiolus cut flower.

The study was conducted to investigate the effect of green net shade during staggered planting times on growth, biochemical, antioxidant enzymes and vase life of gladiolus cut flowers. The green net shade effectively reduces the internal temperature, particularly during extremely hot planting times. Under the green net shade conditions, high quality morphological and biochemical observations were observed during the months of March and April planting times. These included longer plant height, spike length, a higher number of leaves plant-1, larger leaf area, maximum spike diameter, greater number of florets spike-1, heavier flower diameter, higher fresh and dry weight, elevated photosynthetic rate, and reduced time taken for flowering. Additionally, chlorophyll contents and transpiration rate showed significant increases, while antioxidant enzyme activity (POD and CAT) was recorded at higher levels. This resulted in reduced electrolyte leakage and an extended vase life of the gladiolus cut flowers. Moreover, the application of green net shade conditions during the planting in May and June significantly enhanced the quality characteristics of gladiolus cut flowers. Effectiveness of green net shade is evident in reducing temperature of growing environment, leading to improved growth, alleviate oxidative stress, enhanced quality features and vase life of the gladiolus flowers.

Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping.

The emergence of new variants of the SARS-CoV-2 virus has posed a significant challenge in developing broadly neutralizing antibodies (nAbs) with guaranteed therapeutic potential. Some nAbs, such as Sotrovimab, have exhibited varying levels of efficacy against different variants, while others, such as Bebtelovimab and Bamlanivimab-etesevimab are ineffective against specific variants, including BQ.1.1 and XBB. This highlights the urgent need for developing broadly active monoclonal antibodies (mAbs) providing prophylactic and therapeutic benefits to high-risk patients, especially in the face of the risk of reinfection from new variants. Here, we aimed to investigate the feasibility of redirecting existing mAbs against new variants of SARS-CoV-2, as well as to understand how BQ.1.1 and XBB.1.5 can evade broadly neutralizing mAbs. By mapping epitopes and escape sites, we discovered that the new variants evade multiple mAbs, including FDA-approved Bebtelovimab, which showed resilience against other Omicron variants. Our approach, which included simulations, endpoint free energy calculation, and shape complementarity analysis, revealed the possibility of identifying mAbs that are effective against both BQ.1.1 and XBB.1.5. We identified two broad-spectrum mAbs, R200-1F9 and R207-2F11, as potential candidates with increased binding affinity to XBB.1.5 and BQ.1.1 compared to the reference (Wu01) strain. Additionally, we propose that these mAbs do not interfere with Angiotensin Converting Enzyme 2 (ACE2) and bind to conserved epitopes on the receptor binding domain of Spike that are not-overlapping, potentially providing a solution to neutralize these new variants either independently or as part of a combination (cocktail) treatment.