Decoding the effects of spike receptor binding domain mutations on antibody escape abilities of omicron variants.

Recent times witnessed an upsurge in the number of COVID19 cases which is primarily attributed to the emergence of several omicron variants, although there is substantial population vaccination coverage across the globe. Currently, many therapeutic antibodies have been approved for emergency usage. The present study critically evaluates the effect of mutations observed in several omicron variants on the binding affinities of different classes of RBD-specific antibodies using a combined approach of immunoinformatics and binding free energy calculations. Our binding affinity data clearly show that omicron variants achieve antibody escape abilities by incorporating mutations at the immunogenic hotspot residues for each specific class of antibody. K417N and Y505H point mutations are primarily accountable for the loss of class I antibody binding affinities. The K417N/Q493R/Q498R/Y505H combined mutant significantly reduces binding affinities for all the class I antibodies. E484A single mutation, on the other hand, drastically reduces binding affinities for most of the class II antibodies. E484A and E484A/Q493R double mutations cause a 33-38% reduction in binding affinity for an approved therapeutic monoclonal antibody. The Q498R RBD mutation observed across all the omicron variants can reduce ∼12% binding affinity for REGN10987, a class III therapeutic antibody, and the L452R/Q498R double mutation causes a ∼6% decrease in binding affinities for another class III therapeutic antibody, LY-CoV1404. Our data suggest that achieving the immune evasion abilities appears to be the selection pressure behind the emergence of omicron variants.

Singlet oxygen partition between the outer-, inner- and membrane-phases of photo/chemotherapeutic liposomes.

Liposomes carrying membrane-embedded porphyrin-phospholipid (PoP) are capable of chemo- and photo-therapeutic modes of action, which make them a potential candidate material for next-generation cancer treatments. This study examines singlet oxygen (1O2) production and release by PoP liposomes carrying either no chemotherapeutic cargo (EMPTY), or those carrying either doxorubicin (DOX) or irinotecan (IRT) chemotherapy drugs. Herein, we developed a strategy to quantify the fraction of 1O2 lifetime spent in the three distinct local liposomal environments by obtaining four key pieces of information for each system: average 1O2 deactivation rate constants (kΔ) for liposome suspensions in H2O and in D2O solvents, as well as the absolute and the apparent 1O2 production quantum yields (ΦΔ). Despite the characteristic differences in their photophysical behavior, namely in ΦΔ values, all three formulations of PoP liposomes were found to carry out 1O2 release in a similar manner. It was found that >80% of all sensitized 1O2 from the ensemble of PoP liposomes deactivates within the nanostructures themselves, with the largest portion (∼50%) deactivating in the lipid membrane specifically. Based on these findings, we conclude that the current design of the PoP liposomes is well suited for light-induced chemotherapeutic drug release. Importantly, the 1O2 partition quantification approach reported herein has potential to be a tool for characterizing nanoparticulate light-activated chemo- and phototherapeutic systems.

Loading and Releasing Ciprofloxacin in Photoactivatable Liposomes.

We demonstrate that ciprofloxacin can be actively loaded into liposomes that contain small amounts of porphyrin-phospholipid (PoP). PoP renders the liposomes photoactivatable, so that the antibiotic is released from the carrier under red light irradiation (665 nm). The use of 2 molar % PoP in the liposomes accommodated active loading of ciprofloxacin. Further inclusion of 2 molar % of an unsaturated phospholipid accelerated light-triggered drug release, with more than 90 % antibiotic release from the liposomes occurring in less than 30 seconds. With or without laser treatment, ciprofloxacin PoP liposomes inhibited the growth of Bacillus subtilis in liquid media, apparently due to uptake of the liposomes by the bacteria. However, when liposomes were first separated from smaller molecules with centrifugal filtration, only the filtrate from laser-treated liposomes was bactericidal, confirming effective release of active antibiotic. These results establish the feasibility of remote loading antibiotics into photoactivatable liposomes, which could lead to opportunities for enhanced localized antibiotic therapy.

Chemophototherapeutic Ablation of Doxorubicin-Resistant Human Ovarian Tumor Cells.

Porphyrin-phospholipid (PoP) liposomes loaded with Doxorubicin (Dox) have been demonstrated to be an efficient vehicle for chemophototherapy (CPT). Multidrug resistance (MDR) of cancer cells is a problematic phenomenon in which tumor cells develop resistance to chemotherapy. Herein, we report that Dox-resistant tumor cells can be ablated using our previously described formulation termed long-circulating Dox loaded in PoP liposomes (LC-Dox-PoP), which is a PEGylated formulation containing 2 mol. % of the PoP photosensitizer. In vitro studies using free Dox and LC-Dox-PoP showed that human ovarian carcinoma A2780 cells were more susceptible to Dox compared to the corresponding Dox-resistant A2780-R cells. When CPT was applied with LC-Dox-PoP liposomes, effective killing of both nonresistant and resistant A2780 cell lines was observed. An in vivo study to assess the efficiency of LC-Dox-PoP showed effective tumor shrinkage and prolonged survival of athymic nude mice bearing subcutaneous Dox-resistant A2780-R tumor xenografts when they were irradiated with a red laser. Biodistribution analysis demonstrated enhanced tumoral drug uptake in Dox-resistant tumors with CPT, suggesting that increased drug delivery was sufficient to induce ablation of resistant tumor cells.

Folate-Targeted Nanoliposomal Chemophototherapy.

Light-responsive liposomes have been developed for the on-demand release of drugs. However, efficient delivery of chemotherapeutic drugs to tumor for cancer theranostics remains a challenge. Herein, folic acid (FA), an established ligand for targeted drug delivery, was used to decorate light-sensitive porphyrin-phospholipid (PoP) liposomes, which were assessed for FA-targeted chemophototherapy (CPT). PoP liposomes and FA-conjugated PoP liposomes were loaded with Doxorubicin (Dox), and physical properties were characterized. In vitro, FA-PoP liposomes that were incubated with FA receptor-overexpressing human KB cancer cells showed increased uptake compared to non-targeted PoP liposomes. Dox and PoP contributed towards chemophototherapy (CPT) in vitro, and PoP and FA-PoP liposomes induced cell killing. In vivo, mice bearing subcutaneous KB tumors treated with PoP or FA-PoP liposomes loaded with Dox, followed by 665 nm laser treatment, had delayed tumor growth and improved survival. Dox delivery to tumors increased following laser irradiation for both PoP and FA-PoP liposomes. Thus, while Dox-FA-PoP liposomes were effective following systemic administration and local light irradiation in this tumor model, the FA targeting moiety did not appear essential for anti-tumor responses.

Topical Drug Delivery of Concentrated Cabazitaxel in an α-Tocopherol and DMSO Solution.

Topical chemotherapy approaches are relevant for certain skin cancer treatments. This study observes that cabazitaxel (CTX), a broad-spectrum second-generation taxane cytotoxic agent, can be dissolved in α-tocopherol at high concentrations exceeding 100 mg mL-1 . 2D nuclear magnetic resonance (NMR) analysis and molecular dynamics (MD) are used to study this phenomenon. The addition of 30% dimethyl sulfoxide (DMSO) to the α-tocopherol/CTX solution improves its working viscosity and enhances CTX permeation through human skin in vitro (over 5 µg cm-2 within 24 h), while no detectable drug permeates when CTX is dissolved in α-tocopherol alone. In a transepidermal water loss assay, the barrier impairment induced by CTX in 30% DMSO in α-tocopherol, but not in pure DMSO, is reversible 8 h after the formulation removal from the skin surface. Antitumor efficacy of the topical CTX formulation is evaluated in nude mice bearing A431 human squamous carcinoma skin cancer xenografts. With topical application of concentrated CTX solutions (75 mg mL-1 ), tumor growth is significantly suppressed compared to lower concentration groups (0, 25, or 50 mg mL-1 CTX). Taken together, these findings show that topical delivery of CTX using a DMSO and α-tocopherol solvent warrants further study as a treatment for skin malignancies.

Decoding molecular factors shaping human angiotensin converting enzyme 2 receptor usage by spike glycoprotein in lineage B beta-coronaviruses.

Acquiring the human ACE2 receptor usage trait enables the coronaviruses to spill over to humans. However, the origin of the ACE2 usage trait in coronaviruses is poorly understood. Using a multi-disciplinary approach combining evolutionary bioinformatics and molecular dynamics simulation, we decode the principal driving force behind human ACE2 receptor recognition in coronaviruses. Genomic content, evolutionary divergence, and codon usage bias analysis reveal that SARS-CoV2 is evolutionarily divergent from other human ACE2-user CoVs, indicating that SARS-CoV2 originates from a different lineage. Sequence analysis shows that all the human ACE2-user CoVs contain two insertions in the receptor-binding motif (RBM) that directly interact with ACE2. However, the insertion sequences in SARS-CoV2 are divergent from other ACE2-user CoVs, implicating their different recombination origins. The potential of mean force calculations reveals that the high binding affinity of SARS-CoV2 RBD to human ACE2 is primarily attributed to its ability to form a higher number of hydrogen bonds than the other ACE2-user CoVs. The adaptive branch-site random effects likelihood method identifies positive selection bias across the ACE2 user CoVs lineages. Recombination and selection forces shape the spike evolution in human ACE2-using beta-CoVs to optimize the interfacial hydrogen bonds between RBD and ACE2. However, these evolutionary forces work within the constraints of nucleotide composition, ensuring optimum codon adaptation of the spike (S) gene within the host cell.

Immune checkpoint blockade enhances chemophototherapy in a syngeneic pancreatic tumor model.

Pancreatic cancer (PaCa) suffers from poor treatment options for locally advanced cases. Chemophototherapy (CPT) is an emerging anti-tumor modality, and porphyrin-phospholipid liposomes have been shown to be versatile drug carriers for CPT in preclinical rodent models. Here we show that in the syngeneic subcutaneous KPC PaCa tumor model, exhausted CD8+ T cells are localized in the tumor, and that CPT is enhanced in combination with immune checkpoint blockade (ICB). Addition of ICB using anti-programmed cell death 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) antibodies resulted in ablation of medium-sized, established KPC tumors (∼200 mm3) without recurrence for over 100 days. Mice rejected subsequent tumor re-challenge. Flow cytometry and tumor slice analysis following injection of a fluorescently labeled anti-PD-1 antibody showed that CPT improved antibody delivery to the tumor microenvironment. Treatment of large established tumors (∼400 mm3) using with CPT and ICB induced appreciable tumor regression and delay in regrowth. Taken together, these data demonstrate the utility of combining CPT with immunotherapies.

Single-treatment tumor ablation with photodynamic liposomal irinotecan sucrosulfate.

Irinotecan (IRI) loaded actively into PEGylated liposomes via a sucrosulfate gradient has been approved recently to treat advanced pancreatic cancer. In this study, a similar liposomal composition was developed that includes a low mole fraction (1 mol.%) of porphyrin-phospholipid (PoP), a photosensitizer that stably incorporates into liposomes, to confer light-triggered IRI release. IRI-loaded PoP liposomes containing ammonium sucrosulfate (ASOS) as a complexing agent were more stable in serum compared to liposomes employing the more conventional ammonium sulfate. Without irradiation, PoP IRI liposomes released less than 5% IRI during 8 h of incubation in bovine serum at 37 °C, but released over 90% of the drug within minutes of exposure to red light (665 nm) irradiation. A single treatment with IRI-PoP liposomes and light exposure (15 mg/kg IRI with 250 J/cm2) resulted in tumor eradication in mice bearing either MIA PaCa-2 tumors or low-passage patient-derived tumor xenografts that recapitulate characteristics of the clinical disease. Analogous monotherapies of IRI or photodynamic therapy were ineffective in controlling tumor growth. Enhanced drug uptake could be visualized within laser-treated tumors by direct in situ imaging of irinotecan. Biodistribution analysis of IRI, its active metabolite (SN-38), and major metabolite (SN-38 G) showed that laser treatment significantly increased tumor accumulation of all IRI-derived molecular species. A pharmacokinetic model that hypothesized tumor vasculature permeabilization as the primary reason underlying the increased drug deposition accounted for the enhanced drug influx into tumors.

Two Laser Treatments Can Improve Tumor Ablation Efficiency of Chemophototherapy.

Chemophototherapy is an emerging tumor ablation modality that can improve local delivery of chemotherapeutic agents. Long circulating doxorubicin (Dox) in porphyrin-phospholipid (PoP) liposomes (LC-Dox-PoP) has previously been developed as an effective chemophototherapy agent. In the present study, we observed that in mice, LC-Dox-PoP showed enhanced accumulation in human pancreatic tumor xenografts even with suboptimal light doses, as assessed by fluorometric analysis of tissue homogenates and microscopic imaging of Dox and PoP in tumor slices. A second laser treatment, at a time point in which tumors had greater drug accumulation as a result of the first laser treatment, induced potent tumor ablation. Efficacy studies were carried out in two human pancreatic cancer subcutaneous mouse tumor models; MIA PaCa-2 or low-passage patient derived pancreatic cancer xenografts. A single treatment of 3 mg/kg LC-Dox-PoP and an initial 150 J/cm2 laser treatment 1 h after drug administration, followed by second laser treatment of 50 J/cm2 8 h after drug administration, was more effective than a single laser treatment of 200 J/cm2 at either of those time points. Thus, this study presents proof-of-principle and rationale for using two discrete laser treatments to enhance the efficacy of chemophototherapy.

Phylogenomics Analysis of SARS-CoV2 Genomes Reveals Distinct Selection Pressure on Different Viral Strains.

We are witnessing a tremendous outbreak of a novel coronavirus (SARS-CoV2) across the globe. Upon exposure to different population and changing environment, the viral strain might experience different mutational bias that leads to genetic diversity among the viral population. Also, the diversification can be influenced by distinct selection pressure on different viral genomes. We have carried out a comparative genomic analysis of 82 SARS-CoV2 genomes. We have evaluated their evolutionary divergence, substitution pattern, and rates. Viral genomes under distinct selection pressure have been identified. Sites that experience strong selection pressure also have been identified. Our result shows that the translational preference of a few codons is strongly correlated with the mutational bias imposed by genome compositional constraint and influenced by natural selection. Few genomes are evolving with a higher mutational rate with a distinct signature of nucleotide substitution in comparison to others. Four viral strains are under the effect of purifying selection, while nine SARS-CoV2 genomes are under strong positive selection bias. Site analysis indicates a strong positive selection pressure on two codon positions at 3606th and 8439th positions. Our study elucidates adaptation of few SARS-CoV2 viral strain during the outbreak shaping by natural selection and genomic compositional constraints.

Liposomal formulations of photosensitizers.

Photodynamic therapy (PDT) is a clinical ablation modality to treat cancers and other diseases. PDT involves administration of a photosensitizer, followed by irradiation of target tissue with light. As many photosensitizers are small and hydrophobic, solubilization approaches and nanoscale delivery vehicles have been extensively explored. Liposomes and lipid-based formulations have been used for the past 30 years, and in some cases have been developed into well-defined commercial PDT products. This review provides an overview of common liposomal formulation strategies for photosensitizers for PDT and also photothermal therapy. Furthermore, research efforts have examined the impact of co-loading therapeutic cargo along with photosensitizers within liposomes. Additional recent approaches including imaging, overcoming hypoxia, upconversion and activatable liposomal formulations are discussed.