Molecular Mechanism Of Interaction Research Articles

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer–RBD interaction, demonstrating the aptamer’s potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer–RBD for possible antiviral therapy but also introduces a computational method to study aptamer–protein interactions.

New lactate- and pyruvate-containing polysaccharide and rhamnomannan with xylose residues from the cell wall of Rathayibacter oskolensis VKM Ac-2121T

The cell wall of endophytic strain Rathayibacter oskolensis VKM Ac-2121T (family Microbacteriaceae, class Actinomycetes) was found to contain neutral and acidic glycopolymers. The neutral polymer is a block-type rhamnomannan partially should be substitutied by xylose residues, [→2)-α-[β-D-Xylp-(1→3)]-D-Manp-(1→3)-α-D-Rhap-(1→]∼30 [→2)-α-D-Manp-(1→3)-α-D-Rhap-(1→]∼45. The acidic polymer has branched chain, bearing lactate and pyruvate residues, →4)-α-D-[S-Lac-(2―3)-α-L-Rhap-(1→3)]-D-Manp-(1→3)-α-D-[4,6-R-Pyr]-D-Galp-(1→3)-β-D-Glcp-(1→. The structures of both glycopolymers were not described in the Gram-positive bacteria to date. The glycopolymers were studied by chemical and NMR spectroscopic methods. The results of this study provide new data on diversity of bacterial glycopolymers and may prove useful in the taxonomy of the genus Rathayibacter and for understanding the molecular mechanisms of interaction between plants and plant endophytes.

Tributyl(hexyl)phosphonium chloride as a new leveler for microvia copper superconformal electronic plating

A phosphorus-containing new compound of tributyl(hexyl)phosphonium chloride (TBHP), but not the commonly used nitrogen-containing heterocycles and quaternary ammonium salts, is successfully applied for the superconformal copper filling of microvia in acid sulfate electroplating bath for the application of electronic industry. The molecular interaction mechanisms of TBHP combined with suppressor (polyethylene glycol, PEG) and accelerator (bis-(sodium sulfopropyl)-disulfide, SPS) are investigated in detail. Galvanostatic measurements at platinum rotation disk electrode indicate that the leveler of TBHP among with the suppressor and accelerator behaves the key characters of inhibition and convection-dependent adsorption during copper ions electroreduction for the bottom-up filling of microvia. Cyclic voltammetry measurements and in-situ FTIR spectroscopy further reveal that TBHP synergistically interacts with the suppressor to inhibit copper ions electroreduction at the mouth of microvia; while TBHP competes for adsorption with the accelerator, behaving as TBHP gradually replaced by the accelerator at the bottom. Based on the sufficient theoretical supports, the practical copper electroplating is conducted for the verification of microvia void free filling. In the developed novel copper plating formula containing TBHP, PEG and SPS, the void free filling is successfully achieved and the filling percentage (FP) is high in 95.5%.

Mechanism of Interfacial Molecular Interactions Reveals the Intrinsic Factors for the Highly Enhanced Sensing Performance of Ag-Loaded Co3O4.

The noble metal-loaded strategy can effectively improve the gas-sensing performances of metal oxide sensors. However, the gas-solid interfacial interactions between noble metal-loaded sensing materials and gaseous species remain unclear, posing a significant challenge in correlating the physical and chemical processes during gas sensing. In this study, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and in situ Raman spectroscopy were conducted to collaboratively investigate the interfacial interactions involved in the ethanol gas-sensing processes over Co3O4 and Ag-loaded Co3O4 sensors. In situ DRIFTS revealed differences in the compositions and quantities of sensing reaction products, as well as in the adsorption-desorption interactions of surface species, among Co3O4 and Ag-loaded Co3O4 materials. In parallel, in situ Raman spectroscopy demonstrated that the ethanol atmosphere can modulate the electron scattering of Ag-loaded Co3O4 materials but not of raw Co3O4. In situ experimental results revealed the intrinsic reason for the highly enhanced sensing performances of the Ag-loaded Co3O4 sensors toward ethanol gas, including a decreased optimal working temperature (from 250 to 150 °C), an improved gas response level (from 24 to 257), and accelerated gas recovery dynamics. This work provides an effective platform to investigate the interfacial interactions of sensing processes at the molecular level and further advances the development of high-performance gas sensors.

Heterocellular Adhesion in Cancer Invasion and Metastasis: Interactions between Cancer Cells and Cancer-Associated Fibroblasts.

Cancer invasion is a requisite for the most malignant progression of cancer, that is, metastasis. The mechanisms of cancer invasion were originally studied using in vitro cell culture systems, in which cancer cells were cultured using artificial extracellular matrices (ECMs). However, conventional culture systems do not precisely recapitulate in vivo cancer invasion because the phenotypes of cancer cells in tumor tissues are strongly affected by the tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) are the most abundant cell type in the TME and accelerate cancer progression through invasion, metastasis, therapy resistance, and immune suppression. Thus, the reciprocal interactions between CAFs and cancer cells have been extensively studied, leading to the identification of factors that mediate cellular interactions, such as growth factors, cytokines, and extracellular vesicles. In addition, the importance of direct heterocellular adhesion between cancer cells and CAFs in cancer progression has recently been elucidated. In particular, CAFs are directly associated with cancer cells, allowing them to invade the ECM and metastasize to distant organs. In this review, we summarize the recent progress in understanding the molecular and cellular mechanisms of the direct heterocellular interaction in CAF-led cancer invasion and metastasis, with an emphasis on gastric cancer.

Co-clustering of EphB6 and ephrinB1 in trans restrains cancer cell invasion

EphB6 is an understudied ephrin receptor tyrosine pseudokinase that is downregulated in multiple types of metastatic cancers. Unlike its kinase-active counterparts which autophosphorylate and transmit signals upon intercellular interaction, little is known about how EphB6 functions in the absence of intrinsic kinase activity. Here, we unveil a molecular mechanism of cell-cell interaction driven by EphB6. We identify ephrinB1 as a cognate ligand of EphB6 and show that in trans interaction of EphB6 with ephrinB1 on neighboring cells leads to the formation of large co-clusters at the plasma membrane. These co-clusters exhibit a decreased propensity towards endocytosis, suggesting a unique characteristic for this type of cell-cell interaction. Using lattice light-sheet microscopy, 3D structured illumination microscopy and cryo-electron tomography techniques, we show that co-clustering of EphB6 and ephrinB1 promotes the formation of double-membrane tubular structures between cells. Importantly, we also demonstrate that these intercellular structures stabilize cell–cell adhesion, leading to a reduction in the invasive behavior of cancer cells. Our findings rationalize a role for EphB6 pseudokinase as a tumor suppressor when interacting with its ligands in trans.

Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers.

Chimeric RNAs, which can arise from gene recombination at the DNA level or non-canonical splicing events at the RNA level, have been identified as important roles in human tumors. Dysregulated gene expression caused by somatic mutations and altered splicing patterns of oncogenes or tumor suppressor genes can contribute to the development of tumors. Therefore, investigating the formation mechanism of chimeric RNAs via somatic mutations is critical for understanding tumor pathogenesis. This project is the first to propose studying the association between somatic single nucleotide variants and chimeric RNAs, identifying around 2900 somatic SNVs affecting chimeric RNAs in pan-cancer level. The somatic SNVs on chimeric RNAs were commonly observed in various types of tumor tissues, providing a valuable resource for future study. Additionally, these SNVs show distinct tumor specificity, and those with high frequency had a significant impact on the survival time of patients with tumors. Further research revealed that somatic SNVs associated with chimeric RNA (chiR-SNVs) were typically found within 10 nt of the junction site of chimeric RNAs and had a particularly significant effect on chimeric RNAs from different chromosomes. The enrichment analysis revealed that chiR-SNVs were significantly overrepresented in oncogenes and genes related to RNA binding proteins involved in RNA splicing, which could imply that chiR-SNVs may disrupt the process of RNA splicing and induce the occurrence of chimeric RNAs. This study sheds light on the potential molecular interaction mechanism between somatic SNVs and chimeric RNAs, which opens up a new avenue for researching disease pathway and tumorigenesis development.

The Plasmodium vivax MSP1P-19 is involved in binding of reticulocytes through interactions with the membrane proteins band3 and CD71

The parasite Plasmodium vivax preferentially invades human reticulocytes. Its merozoite surface protein 1 paralog (PvMSP1P), particularly the 19-kDa C-terminal region (PvMSP1P-19), has been shown to bind to reticulocytes and this binding can be inhibited by antisera obtained by PvMSP1P-19 immunization. The molecular mechanism of interactions between PvMSP1P-19 and reticulocytes during P. vivax invasion, however, remains unclear. In this study, we analyzed the ability of MSP1P-19 to bind to different concentrations of reticulocytes and confirmed its reticulocyte preference. LC-MS analysis was used to identify two potential reticulocyte receptors, band3 and CD71, that interact with MSP1P-19. Both PvMSP1P-19 and its sister taxon Plasmodium cynomolgi MSP1P-19 (PcMSP1P-19) were found to bind to the extracellular loop (loop 5) of band3, where the interaction of MSP1P-19 with band3 was chymotrypsin-sensitive. Antibodies against band3-P5, CD71, and MSP1P-19 reduced the binding activity of PvMSP1P-19 and PcMSP1P-19 to reticulocytes, while MSP1P-19 proteins inhibited P. falciparum invasion in vitro in a concentration-dependent manner. To sum up, identification and characterization of the reticulocyte receptor is important for understanding the binding of reticulocytes by MSP1P-19.

Synthesis of gold nanoparticles using plum waste extract with green solvents

The current study focuses on the synthesis of gold nanoparticles (AuNPs) using the plum peel extract obtained by deep eutectic solvent (DES) (Betaine-Urea and Choline chloride-Urea). Formation mechanism of DESs and molecular interactions between components has been studied using quantum chemical methods. DESs have been used for obtaining extracts from plum peel. It has been established that the reducing ability of extracts obtained using DESs is higher (489–580 mg ASE/g extract) than when using a traditional aqueous-alcohol solution (336 mg ASE/g extract). Gold nanoparticles were characterized by UV–vis spectroscopy, FTIR, and SEM-XRD analysis. The size of AuNPs was found to be 5–10 nm as per the particle size analyzer, and the zeta potential is − 46 to 47 mV. The scavenging ability of the sample solution to ABTS radical was determined by ABTS radical scavenging test. The AuNPs synthesized by extracting Cl-U exhibited significant antioxidant potential against ABTS•+, with an IC50 of 110 mg/mL. For the first time in a cosmetic product, AgNPs synthesized by plum peel extract in a deep eutectic solvent was used. The creams were evaluated for their organoleptic characteristics, physicochemical properties, and in vitro antibacterial activity against Escherichia coli and Bacillus subtilis. Results show that the cream with 0.5% AuNp increases the value of moisturizer for the skin.

Molecular mechanism of muscarinic acetylcholine receptor M3 interaction with Gq

Muscarinic acetylcholine receptor M3 (M3) and its downstream effector Gq/11 are critical drug development targets due to their involvement in physiopathological processes. Although the structure of the M3-miniGq complex was recently published, the lack of information on the intracellular loop 3 (ICL3) of M3 and extensive modification of Gαq impedes the elucidation of the molecular mechanism of M3-Gq coupling under more physiological condition. Here, we describe the molecular mechanism underlying the dynamic interactions between full-length wild-type M3 and Gq using hydrogen-deuterium exchange mass spectrometry and NanoLuc Binary Technology-based cell systems. We propose a detailed analysis of M3-Gq coupling through examination of previously well-defined binding interfaces and neglected regions. Our findings suggest potential binding interfaces between M3 and Gq in pre-assembled and functionally active complexes. Furthermore, M3 ICL3 negatively affected M3-Gq coupling, and the Gαq AHD underwent unique conformational changes during M3-Gq coupling.

Abstract 5524: Identification of PAEP as an immune activity modulator to mediate the immune resistance in tumor metastasis

Abstract Most cancer-related deaths are associated with the complex phenotypic behavior of metastasis, a process in which tumor cells spread from their initial site to distant sites. To successfully metastasize, the tumor cell will be required to make numerous adjustments and survive a series of stages involving intravasation, circulation in the blood or lymph system, extravasation, and growth at distant organs, and overcome the challenges of immunosurveillance. The tumor microenvironment is the ecosystem that surrounds and feeds the tumor. The molecular mechanism by which the metastatic tumors survive and escape from immune attack in the tumor microenvironment remains unclear. To study the molecular mechanism of interaction between metastatic tumors and the immune system in metastasis, we established immune-resistant metastatic models. We identified that PAEP, a progestogen-associated endometrial protein, is significantly upregulated in immune-resistant metastatic tumors compared with non-immune-resistant tumors. PAEP is a glycoprotein that inhibits cell immune function and plays an essential role in the pregnancy process. To examine the function of PAEP in tumor metastasis, we first introduced PAEP into non-immune resistant and poorly metastatic melanoma and rhabdomyosarcoma (RMS) cells. We found that overexpression of PAEP significantly promotes tumor metastatic potential of both melanoma and RMS cells in immunocompetent mice. Interestingly, there was no difference in metastasis between the control and overexpression groups in immunodeficient mice. These data suggest that PAEP may mediate tumor metastasis relating to host immunity. To further confirm the function of PAEP in tumor metastasis, we use CRISPR/Cas9 technology to knockout endogenous PAEP and will test the metastatic potential in different hosts. We will also investigate the molecular mechanisms using RNA sequencing and Digital Spatial Profiling (DSP) to analyze the metastatic samples. Our study will uncover a new mechanism for how tumors survive in the microenvironment and identify a novel target for the treatment of metastatic diseases. Citation Format: Rand Gabriel M. Buenaventura, Weiping Chen, Shuling Zhang, Beverly Mock, Glenn Merlino, Yanlin Yu. Identification of PAEP as an immune activity modulator to mediate the immune resistance in tumor metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5524.

Computational study on the inhibition mechanism of cyclodextran against GTF-SI from Streptococcus mutans focusing on the glucan-binding domain

Glucosyltransferases (GTFs) from Streptococcus mutans (S. mutans) are enzymes that synthesize glucan, a polymer that forms a biofilm causing dental caries. Cyclodextran (CI), which contains a ring structure formed from D-glucose by α-1,6 glycoside linkage, has been reported to strongly inhibit GTFs. In contrast, cyclodextrin, formed by α-1,4 glycoside linkage, has almost no inhibitory activity. In this study, we examined the inhibition mechanism of CI through computational chemistry, focusing on the glucan-binding domain of GTF-SI, which is one of GTFs produced by S. mutans. Analysis using molecular dynamics simulation and fragment molecular orbital method demonstrated a clear difference in the molecular interaction mechanism between α-1,6- and α-1,4-linked oligosaccharides. The calculated affinity of α-1,6-linked oligosaccharides was higher than that of α-1,4-linked oligosaccharides. Additionally, geometry optimization based on density functional theory revealed that three amino acids—Q1282, K1284, and S1302—play an essential role in the binding with α-1,6-linked oligosaccharides. These results successfully explain the inhibition mechanism of CI.

The postbiotic sodium butyrate synergizes the antiproliferative effects of dexamethasone against the AGS gastric adenocarcinoma cells.

A growing body of literature underlines the fundamental role of gut microbiota in the occurrence, treatment, and prognosis of cancer. In particular, the activity of gut microbial metabolites (also known as postbiotics) against different cancer types has been recently reported in several studies. However, their in-depth molecular mechanisms of action and potential interactions with standard chemotherapeutic drugs remain to be fully understood. This research investigates the antiproliferative activities of postbiotics- short-chain fatty acid (SCFA) salts, specifically magnesium acetate (MgA), sodium propionate (NaP), and sodium butyrate (NaB), against the AGS gastric adenocarcinoma cells. Furthermore, the potential synergistic interactions between the most active SCFA salt-NaB and the standard drug dexamethasone (Dex) were explored using the combination index model. The molecular mechanisms of the synergy were investigated using reactive oxygen species (ROS), flow cytometry and biochemometric and liquid chromatography-mass spectrometry (LC-MS)-driven proteomics analyses. NaB exhibited the most significant inhibitory effect (p < 0.05) among the tested SCFA salts against the AGS gastric cancer cells. Additionally, Dex and NaB exhibited strong synergy at a 2:8 ratio (40 μg/mL Dex + 2,400 μg/mL NaB) with significantly greater inhibitory activity (p < 0.05) compared to the mono treatments against the AGS gastric cancer cells. MgA and NaP reduced ROS production, while NaB exhibited pro-oxidative properties. Dex displayed antioxidative effects, and the combination of Dex and NaB (2,8) demonstrated a unique pattern, potentially counteracting the pro-oxidative effects of NaB, highlighting an interaction. Dex and NaB individually and in combination (Dex:NaB 40:2400 μg/mL) induced significant changes in cell populations, suggesting a shift toward apoptosis (p < 0.0001). Analysis of dysregulated proteins in the AGS cells treated with the synergistic combination revealed notable downregulation of the oncogene TNS4, suggesting a potential mechanism for the observed antiproliferative effects. These findings propose the potential implementation of NaB as an adjuvant therapy with Dex. Further investigations into additional combination therapies, in-depth studies of the molecular mechanisms, and in vivo research will provide deeper insights into the use of these postbiotics in cancer, particularly in gastric malignancies.

Characterization and application of active human α2,6-sialyltransferases ST6GalNAc V and ST6GalNAc VI recombined in Escherichia coli

Eukaryotic sialyltransferases play key roles in many physiological and pathological events. The expression of active human recombinant sialyltransferases in bacteria is still challenging. In the current study, the genes encoding human N-acetylgalactosaminide α2,6-sialyltransferase V (hST6GalNAc V) and N-acetylgalactosaminide α2,6-sialyltransferase VI (hST6GalNAc VI) lacking the N-terminal transmembrane domains were cloned into the expression vectors, pET-32a and pET-22b, respectively. Soluble and active forms of recombinant hST6GalNAc V and hST6GalNAc VI when coexpressed with the chaperone plasmid pGro7 were successfully achieved in Escherichia coli. Further, lactose (Lac), Lacto-N-triose II (LNT II), lacto-N-tetraose (LNT), and sialyllacto-N-tetraose a (LSTa) were used as acceptor substrates to investigate their activities and substrate specificities. Unexpectedly, both can transfer sialic acid onto all those substrates. Compared with hST6GalNAc V expressed in the mammalian cells, the recombinant two α2,6-sialyltransferases in bacteria displayed flexible substrate specificities and lower enzymatic efficiency. In addition, an important human milk oligosaccharide disialyllacto-N-tetraose (DSLNT) can be synthesized by both human α2,6-sialyltransferases expressed in E. coli using LSTa as an acceptor substrate. To the best of our knowledge, these two active human α2,6-sialyltransferases enzymes were expressed in bacteria for the first time. They showed a high potential to be applied in biotechnology and investigating the molecular mechanisms of biological and pathological interactions related to sialylated glycoconjugates.

Prognostic significance of T lymphocyte subgroups (CD4 and CD8) in lung cancer patients after neoadjuvant chemotherapy

ObjectiveThe basis for current and future lung cancer immunotherapy depends on our knowledge of molecular mechanisms of interactions between tumor and immune system cells. Interactions that occur between different intratumoral populations of the same cells are important. In our study, we aimed to evaluate relationship between the clinical and prognostic features and T lymphocyte subgroups of patients with lung tumors after neoadjuvant treatment.MethodsA total of 72 patients were included in our study, including study group, 39 of whom received neoadjuvant chemotherapy. Clinical/radiological/pathological findings of patients and CD4/CD8 staining rates in peritumoral/intratumoral areas were recorded.ResultsOur study revealed significantly lower intratumoral CD4 + T cell density and lower intratumoral CD4/CD8 ratio in primary tumor after neoadjuvant therapy (respectively, 0.012 and 0.016). Considering tumor types, when control-study groups were compared, inflammation was statistically significant only in adenocarcinoma subtype; intratumoral CD4/CD8 ratio was statistically significant only in squamous-cell carcinoma subtype (respectively, p = 0.0008 and p = 0.0139). When CD4 + T lymphocytes and CD8 + T lymphocytes and CD4/CD8 ratio were compared between control and study groups in low-stage patients according to clinical stages, only intratumoral CD4 + T lymphocyte values and intratumoral CD4/CD8 ratio were significant (respectively, p = 0.0291 ve p = 0.0154).ConclusionAll cell types of innate and adaptive intratumoral immunity can affect lung cancer tissues simultaneously, and these interactions have a very complex structure. Understanding the tumor microenvironment and the different roles of associated cancer immune cells may lead to the discovery of new targets for immunological therapies and increased survival times in lung cancer.

Molecular mechanism for the interaction of natural products with ionic liquids: Insights from MD and DFT study

Ionic liquids (ILs) as a class of green sustainable solvents, have been widely studied and used for the extraction, separation, recovery, and catalytic conversion of natural products (NPs). It is well known that elucidating the dynamic interaction behavior and mechanism of NPs in ILs can help rationally design efficient IL solvent systems at the molecular level. However, the interaction mechanism of rutin molecules and ILs is still unclear. In this contribution, an exhaustive theoretical study of dynamic interaction behavior and mechanism of rutin in six imidazolium-based IL systems is presented for the first time by combining molecular dynamics (MD) simulations with density functional theory (DFT) calculations. Meanwhile, the synergistic effect of cation and anion on rutin-IL complexes stability is deeply investigated by the frontier molecular orbital (FMO), electrostatic potential (ESP), radial distribution functions (RDF), averaged non-covalent interaction (aNCI) and non-covalent interaction (NCI). The final result provides a comprehensive molecular mechanism of interaction between rutin and ILs. The combination of various nonbonded forces (such as H-bond, van der Waals, repulsion and cation-π stacking) between molecules determines the stability of rutin-IL complexes. In addition, the structure, size and functional groups of ILs play a decisive role in promoting the formation of nonbonded forces. Our work shows that avoiding substituents with steric hindrance and electron-withdrawing effect in anions, considering the symmetry of the alkyl chain of imidazolium cations, and enhancing the cooperation between anions and cations is a promising pathway to develop a new and efficient ILs solvent systems for the NPs extraction, recovery, separation, detection, and catalytic conversion.

Molecular Mechanisms of the Stripe Rust Interaction with Resistant and Susceptible Wheat Genotypes.

Rust fungi cause significant damage to wheat production worldwide. In order to mitigate disease impact and improve food security via durable resistance, it is important to understand the molecular basis of host-pathogen interactions. Despite a long history of research and high agricultural importance, still little is known about the interactions between the stripe rust fungus and wheat host on the gene expression level. Here, we present analysis of the molecular interactions between a major wheat pathogen-Puccinia striiformis f. sp. tritici (Pst)-in resistant and susceptible host backgrounds. Using plants with durable nonrace-specific resistance along with fully susceptible ones allowed us to show how gene expression patterns shift in compatible versus incompatible interactions. The pathogen showed significantly greater number and fold changes of overexpressed genes on the resistant host than the susceptible host. Stress-related pathways including MAPK, oxidation-reduction, osmotic stress, and stress granule formation were, almost exclusively, upregulated in the resistant host background, suggesting the requirement of the resistance-countermeasure mechanism facilitated by Pst. In contrast, the susceptible host background allowed for broad overrepresentation of the nutrient uptake pathways. This is the first study focused on the stripe rust pathogen-wheat interactions, on the whole transcriptome level, from the pathogen side. It lays a foundation for the better understanding of the resistant/susceptible hosts versus pathogenic fungus interaction in a broader sense.

The Diverse Nature of the Molecular Interactions That Govern the COV-2 Variants' Cell Receptor Affinity Ranking and Its Experimental Variability.

A critical determinant of infectivity and virulence of the most infectious and or lethal variants of concern (VOCs): Wild Type, Delta and Omicron is related to the binding interactions between the receptor-binding domain of the spike and its host receptor, the initial step in cell infection. It is of the utmost importance to understand how mutations of a viral strain, especially those that are in the viral spike, affect the resulting infectivity of the emerging VOC, knowledge that could help us understand the variant virulence and inform the therapies applied or the vaccines developed. For this sake, we have applied a battery of computational protocols of increasing complexity to the calculation of the spike binding affinity for three variants of concern to the ACE2 cell receptor. The results clearly illustrate that the attachment of the spikes of the Delta and Omicron variants to the receptor originates through different molecular interaction mechanisms. All our protocols unanimously predict that the Delta variant has the highest receptor-binding affinity, while the Omicron variant displays a substantial variability in the binding affinity of the spike that relates to the structural plasticity of the Omicron spike-receptor complex. We suggest that the latter result could explain (at least in part) the variability of the in vitro binding results for this VOC and has led us to suggest a reason for the lower virulence of the Omicron variant as compared to earlier strains. Several hypotheses have been developed around this subject.

Siponimod Attenuates Neuronal Cell Death Triggered by Neuroinflammation via NFκB and Mitochondrial Pathways.

Multiple sclerosis (MS) is the most common autoimmune demyelinating disease of the central nervous system (CNS), consisting of heterogeneous clinical courses varying from relapsing-remitting MS (RRMS), in which disability is linked to bouts of inflammation, to progressive disease such as primary progressive MS (PPMS) and secondary progressive MS (SPMS), in which neurological disability is thought to be linked to neurodegeneration. As a result, successful therapeutics for progressive MS likely need to have both anti-inflammatory and direct neuroprotective properties. The modulation of sphingosine-1-phosphate (S1P) receptors has been implicated in neuroprotection in preclinical animal models. Siponimod/BAF312, the first oral treatment approved for SPMS, may have direct neuroprotective benefits mediated by its activity as a selective (S1P receptor 1) S1P1 and (S1P receptor 5) S1P5 modulator. We showed that S1P1 was mainly present in cortical neurons in lesioned areas of the MS brain. To gain a better understanding of the neuroprotective effects of siponimod in MS, we used both rat neurons and human-induced pluripotent stem cell (iPSC)-derived neurons treated with the neuroinflammatory cytokine tumor necrosis factor-alpha (TNF-α). Cell survival/apoptotic assays using flow cytometry and IncuCyte live cell analyses showed that siponimod decreased TNF-α induced neuronal cell apoptosis in both rat and human iPSCs. Importantly, a transcriptomic analysis revealed that mitochondrial oxidative phosphorylation, NFκB and cytokine signaling pathways contributed to siponimod's neuroprotective effects. Our data suggest that the neuroprotection of siponimod/BAF312 likely involves the relief of oxidative stress in neuronal cells. Further studies are needed to explore the molecular mechanisms of such interactions to determine the relationship between mitochondrial dysfunction and neuroinflammation/neurodegeneration.

Identification of characteristic aroma compounds of Longjing tea and their molecular mechanisms of interaction with olfactory receptors using molecular docking

Identification of characteristic aroma compounds of Longjing tea and their molecular mechanisms of interaction with olfactory receptors using molecular docking