Design and evaluation of a multiepitope vaccine for pancreatic cancer using immune-dominant epitopes derived from the signature proteome in expression datasets

Pancreatic cancer is a highly aggressive and often lethal malignancy with limited treatment options. Its late-stage diagnosis and resistance to conventional therapies make it a significant challenge in oncology. Immunotherapy, particularly cancer vaccines, has emerged as a promising avenue for treating pancreatic cancer. Multi-epitope vaccines, designed to target multiple epitopes derived from various antigens associated with pancreatic cancer, have gained attention as potential candidates for improving therapeutic outcomes. In this study, we have explored transcriptomics and protein expression databases to identify potential upregulated proteins in pancreatic cancer cells. After examining a total of 21,054 proteins from various databases, it was discovered that 143 proteins expressed differently in malignant and healthy cells. The CTL, HTL and BCE epitopes were predicted for the shortlisted proteins. 51,840 vaccine constructs were created by concatenating CTL, HTL, and B-cell epitopes in the respective sequences. The best 86 structures were selected from a set of 51,840 designs after they were analyzed for vaxijenicity, allergenicity, toxicity, and antigenicity scores. In further simulation of the immune response using constructs, it was found that 41417, 37961, and 40841 constructs could produce a strong immune response when injected. Further, it was found that construct 37961 showed stronger interaction and stability with TLR-9 as determined from the large-scale molecular dynamics simulations. Moreover, the 37961 construct has shown interactions with TLR-9 suggests its potential in inducing immune response. In addition, construct 37961 has shown 100% predicted solubility in the E. coli expression system. Overall, the study indicates the designed construct 37961 has the potential to induce an anti-tumor immune response and long-standing protection pending further studies.

CD36 Ectodomain Detects Apoptosis in Mammalian Cells

The cells that undergo apoptosis show phosphatidylserine (PS) on the cell membrane. The fluorescently labeled hCD36_ecto is staining and detecting apoptotic cells in a flow-based assay with several advantages over Annexin V. The human CD36 ectodomain (hCD36_ecto) is stable for a range of temperatures and experimental conditions and doesn't require Ca²⁺ for detecting apoptosis and specific towards PS compared to other lipids. The blocking with unlabeled hCD36_ecto reduces the staining of Annexin V-FITC for apoptotic cells, whereas R63A does not affect the binding of Annexin V- FITC to apoptotic cells. It indicates the role of CD36-PS interaction in detecting apoptotic cells. Dual-staining with hCD36_ecto-FITC/PI is universally detecting apoptosis in different nucleated cells or eryptosis in non-nucleated RBCs. Hence, our study highlights the utility of CD36 as a probe to detect apoptosis in mammalian cells. It might be a robust, economical reagent for the scientific community to facilitate their research.

Therapeutic Potentials of Scavenger Receptor CD36 Mediated Innate Immune Responses Against Infectious and Non-Infectious Diseases

CD36 is a multifunctional glycoprotein, expressed in different types of cells and known to play a significant role in the pathophysiology of the host. The structural studies revealed that the scavenger receptor consists of short cytosolic domains, two transmembrane domains, and a large ectodomain. The ectodomain serves as a receptor for a diverse number of endogenous and exogenous ligands. The CD36-specific ligands are involved in regulating the immune response during infectious and non-infectious diseases in the host. The role of CD36 in regulating the innate immune response during Pneumonia, Tuberculosis, Malaria, Leishmaniasis, HIV, and Sepsis in a ligand- mediated fashion. Apart from infectious diseases, it is also considered to be involved in metabolic disorders such as Atherosclerosis, Alzheimer's, cancer, and Diabetes. The ligand binding to scavenger receptor modulates the CD36 down-stream innate immune response, and it can be exploited to design suitable immuno-modulators. Hence, the current review focused on the role of the CD36 in innate immune response and therapeutic potentials of novel heterocyclic compounds as CD36 ligands during infectious and non-infectious diseases.

A dinitro-functionalized metal-organic framework featuring visual and fluorogenic sensing of H2S in living cells, human blood plasma and environmental samples

Here, we describe a new dinitro-functionalized Zr(iv) MOF (MOF = metal-organic framework) having a UiO-66 (UiO = University of Oslo) framework topology called UiO-66-(NO₂)₂ (1). It shows fluorescence turn-on behavior towards H₂S in simulated biological medium (HEPES buffer, pH = 7.4). By employing solvothermal conditions, 1 was successfully synthesized by reacting ZrCl₄, H₂BDC-(NO₂)₂ [H₂BDC-(NO₂)₂ = 2,5-dinitro-1,4-benzenedicarboxylic acid] ligand and benzoic acid with a molar ratio of 1 : 1 : 10 in DMF (DMF = N,N-dimethylformamide) at 130 °C for 24 h. The material was characterized by infrared spectroscopy, X-ray powder diffraction (XRPD) and thermogravimetric (TG) analyses. The compound not only displays highly sensitive fluorometric sensing of H₂S but also exhibits a visually detectable colorimetric change towards H₂S in daylight. Moreover, the high selectivity of 1' towards H₂S is retained even when several other biologically intrusive species co-exist in the sensing medium. The limit of detection (LOD) of the compound is 14.14 μM which lies in the range of the H₂S concentration found in biological systems. Fluorescence microscopy studies on J774A.1 cells revealed the efficacy of the probe for imaging H₂S in living cells. Moreover, this material can detect H₂S in human blood plasma (HBP) and monitor the sulfide concentration in real water samples. All these features clearly demonstrate that the material has huge potential for highly selective sensing of both extracellular and intracellular H₂S.

Selective and Sensitive Sensing of Hydrogen Peroxide by a Boronic Acid Functionalized Metal-Organic Framework and Its Application in Live-Cell Imaging

A new boronic acid functionalized Zr(IV) metal-organic framework having the capability of sensing H₂O₂ in live cells is reported. The Zr-MOF bears a UiO-66 structure and contains 2-boronobenzene-1,4-dicarboxylic acid (BDC-B(OH)₂) as a framework linker. The activated Zr-UiO-66-B(OH)₂ compound (called 1') is highly selective for the fluorogenic detection of H₂O₂ in HEPES buffer at pH 7.4, even in the presence of interfering ROS (ROS = reactive oxygen species) and other biologically relevant analytes. The fluorescent probe was found to display extraordinary sensitivity for H₂O₂ (detection limit 0.015 μM) in HEPES buffer, which represents a lower value in comparison to those of the MOF probes documented so far for sensing H₂O₂ using other analytical methods. Taking advantage of its high selectivity and sensitivity for H₂O₂ in HEPES buffer, the probe was successfully employed for the imaging of intracellular H₂O₂. Imaging studies with MDAMB-231 cells revealed the emergence of bright blue fluorescence after loading with probe 1' and subsequent treatment with H₂O₂ solution.

Mapping of phosphatidylserine recognition region on CD36 ectodomain

CD36-PS interaction is an important affair to identify and remove dead/aged cells to control inflammation. CD36 ectodomain was cloned, over-expressed in bacterial expression system and purified to homogeneity. The dot-blot analysis shows that the CD36_ecto selectively binds PS vesicles blotted on the nitrocellulose membrane. PS binds strongly to CD36_ecto with a dissociation constant K_D of 53.7 ± 0.48 μM. The stoichiometry of interaction between CD36 and PS is 1:2. The hCD36_ecto-PS thermogram revealed that the hydrophobic and salt bridge interactions play crucial role in their interactions. PS docked nicely into the predicted pharmacophoric site with a binding energy of 5.1 kcal/mol. Analysis of CD36-PS molecular model showed that the residues R63, R96, N118, D270 and E418 were forming hydrogen bonds with PS. Molecular dynamics simulations indicate that R63 mutation has disrupted the integrity of biophoric constituents, directly affecting the hydrogen bonding from R96, N118 and D270. ITC thermogram analysis of mutant protein with PS vesicles indicate complete loss of binding with R63A and very low affinity of PS vesicles with D270A. Dot blot analysis further confirmed the ITC results. These finding may help to design suitable agents mimicking PS biophore with potentials in diagnostics of apoptotic cells and cardiovascular intervention.

Extraordinary sensitivity for H2S and Fe(iii) sensing in aqueous medium by Al-MIL-53-N3 metal-organic framework: in vitro and in vivo applications of H2S sensing

An Al(iii) metal-organic framework (MOF) called Al-MIL-53-N₃ (1) was synthesized under solvothermal reaction conditions using Al(NO₃)₃·9H₂O and H₂BDC-N₃ (H₂BDC-N₃ = 2-azido-1,4-benzenedicarboxylic acid) ligand in a DMF/water (DMF = N,N-dimethylformamide) mixture. Phase purity was checked by performing X-ray powder diffraction, infrared spectroscopy and thermogravimetric analysis. Thermogravimetric analysis suggests that 1 is highly stable up to 300 °C under air atmosphere. The activated 1 (called 1') showed a very fast fluorescence response to H₂S (turn-on) and Fe(iii) ions (turn-off) in an aqueous medium with excellent sensitivity and selectivity even in the presence of other potentially intrusive analytes. In the presence of H₂S, the conversion of the azide moiety to amine is responsible for the fluorescence turn-on properties. On the other hand, the partial replacement of framework Al(iii) ions by Fe(iii) can be assigned for the selective detection behavior to Fe(iii) ions. The detection limits (90.47 nM for H₂S and 0.03 μM for Fe(iii) ions in water) of 1' are lower than those of the formerly reported MOF type of fluorescent sensors. The 1'-loaded J774A.1 macrophage cells are healthy and respond to intracellular H₂S to exhibit strong blue fluorescence, confirming its suitability to detect H₂S inside the cells. In addition, 1' can detect H₂S in human blood plasma (HBP) and sulfide ions in real water samples. These features make 1' a very promising candidate for the on-site sensing of Fe(iii) ions and the detection of intracellular and extracellular H₂S.

Rapid and highly sensitive detection of extracellular and intracellular H2S by an azide-functionalized Al(iii)-based metal–organic framework

Fast and highly sensitive sensing of both extracellular and intracellular H₂S by an Al(iii)-based CAU-10-N₃MOF is presented.

In silico approach towards lipase mediated chemoenzymatic synthesis of (S)-ranolazine, as an anti-anginal drug

An in silico modelling based biocatalytic approach for the synthesis of drugs and drug intermediates in enantiopure forms is a rationalized methodology over the organo-chemical routes.