A cheminformatics and network pharmacology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors.

Background: Mycobacterium tuberculosis (Mtb) carbonic anhydrases (CAs) are critical enzymes that regulate pH by converting CO2 to HCO3 -, essential for Mtb's survival in acidic environments. Inhibiting γ-CAs presents a potential target for novel antituberculosis drugs with unique mechanisms of action. Objective: This study aimed to explore the biological connections underlying Mtb pathogenesis and investigate the mechanistic actions of antituberculosis compounds targeting the Cas9 protein. Methods: We employed homology modeling and virtual screening to identify compounds with high binding affinities for Cas9 protein. This study used the homology modeling approach employing high-quality AlphaFold DB models for γ-CA. Furthermore, the systems biology approach was used for analyzing the integrated modelling of compounds, integrating data on genes, pathways, phenotypes, and molecular descriptors. Single-cell RNA sequencing was also conducted to profile gene expression. Results: Three compounds, F10921405, F08060425, and F14437079, potentially binding to Cas9 protein, have been identified. F10921405 and F08060425 showed significant overlap in their effects on pathways related to the immune response, while F14437079 displayed distinct mechanistic pathways. Expression profiling revealed high levels of genes such as PDE4D, ROCK2, ITK, MAPK10, and SYK in response to F1092-1405 and F0806-0425, and MMP2 and CALCRL in response to F1443-7079. These genes, which play a role in immune modulation and lung tissue integrity, are essential to fight against Mtb. Conclusion: The molecular relationship and pathways linked to the mentioned compounds give the study a holistic perspective of targeting Mtb, which is essential in designing specific therapeutic approaches. Subsequent research will involve experimental validation to demonstrate the efficacy of the promising candidates in Mtb infections.

Exploring the globoid cell leukodystrophy protein network and therapeutic interventions.

Globoid cell leukodystrophy is a severe rare disorder characterized by white matter degradation, resulting in a progressive loss of physical and mental abilities and has extremely limited therapeutic interventions. Therefore, this study aimed to delve into the Globoid cell leukodystrophy associated intricate network of differentially expressed genes (p < 0.05, |Fc|> 1) to identify potential druggable targets and possible therapeutic interventions using small molecules. The disease-associated neuronal protein circuit was constructed and analyzed, identifying 53 nodes (minimum edge cutoff 1), among which five (FOS, FOSB, GDNF, GFRA1, and JUN) were discerned as potential core protein nodes. Although our research enumerates the potential small molecules to target various protein nodes in the proposed disease network, we particularly underscore T-5224 to inhibit c-Jun activity as JUN was identified as one of the pivotal elements within the disease-associated neuronal protein circuit. The evaluation of T-5224 binding energy (- 11.0 kcal/mol) from docking study revealed that the compound to exhibit a notable affinity towards Jun/CRE complex. Moreover, the structural integrity of complex was affirmed through comprehensive molecular dynamics simulations, indicating a stable hydrophilic interaction between T-5224 and the Jun/CRE complex, thereby enhancing protein compactness and reducing solvent accessibility. This binding energy was further substantiated by free binding analysis, revealing a substantial thermodynamics complex state (- 448.00 ± 41.73 kJ/mol). Given that this investigation is confined to a computational framework, we additionally propose a hypothetical framework to ascertain the feasibility of inhibiting the Jun/CRE complex with T-5224 against Globoid cell leukodystrophy, employing a combination of in vitro and in vivo methodologies as a prospective avenue of this study.

Advancements in Nano-Mandoor Bhasma: Unravelling the Particle Size-Ascorbic Acid Synergy for Enhanced Iron Bioavailability for Anemia Treatment.

Mandoor Bhasma (MB) medicine, based on classical Indian Ayurveda, was size- and surface-modified to improve its therapeutic efficiency for treating iron-deficient anemia. Physical grinding reduced the size of MB to the nanoparticle (nano-MB) range without changing its chemical composition, as measured by particle size distribution. The surface of nano-MB was modified with ascorbic acid (nano-AA-MB) and confirmed using scanning electron microscopy and Fourier transformed infrared spectroscopy. Enhanced iron dissolution from the surface-modified nano-AA-MB under neutral-to-alkaline pH conditions, and in the intestinal region of the simulated gastrointestinal tract (GIT) digestion model was determined using inductively coupled plasma mass spectroscopy. GIT digestae of MB microparticles and nano-AA-MB were found to be biocompatible in human colon epithelial (Caco-2) cells, with the latter showing threefold higher iron uptake. Subsequently, a dose-dependent increase in cellular ferritin protein was observed in the nano-AA-MB digestae-treated Caco-2 cells, indicating the enhanced bioavailability and storage of dissolved iron. Overall, the study showed that reducing the size of centuries-old traditional Mandoor Bhasma medicine to nanoscale, and its surface-modification with ascorbic acid would help in enhancing its therapeutic abilities for treating iron-deficient anemia.

Multifaceted targets of cannabidiol in epilepsy: Modulating glutamate signaling and beyond.

Cannabidiol has been reported to interact with broad-spectrum biological targets with pleiotropic pharmacology including epilepsy although a cohesive mechanism is yet to be determined. Even though some studies propose that cannabidiol may manipulate glutamatergic signals, there is insufficient evidence to support cannabidiol direct effect on glutamate signaling, which is important in intervening epilepsy. Therefore, the present study aimed to analyze the epilepsy-related targets for cannabidiol, assess the differentially expressed genes with its treatment, and identify the possible glutamatergic signaling target. In this study, the epileptic protein targets of cannabidiol were identified using the Tanimoto coefficient and similarity index-based targets fishing which were later overlapped with the altered expression, epileptic biomarkers, and genetically altered proteins in epilepsy. The common proteins were then screened for possible glutamatergic signaling targets with differentially expressed genes. Later, molecular docking and simulation were performed using AutoDock Vina and GROMACS to evaluate binding affinity, ligand-protein stability, hydrophilic interaction, protein compactness, etc. Cannabidiol identified 30 different epilepsy-related targets of multiple protein classes including G-protein coupled receptors, enzymes, ion channels, etc. Glutamate receptor 2 was identified to be genetically varied in epilepsy which was targeted by cannabidiol and its expression was increased with its treatment. More importantly, cannabidiol showed a direct binding affinity with Glutamate receptor 2 forming a stable hydrophilic interaction and comparatively lower root mean squared deviation and residual fluctuations, increasing protein compactness with broad conformational changes. Based on the cheminformatic target fishing, evaluation of differentially expressed genes, molecular docking, and simulations, it can be hypothesized that cannabidiol may possess glutamate receptor 2-mediated anti-epileptic activities.

In silico design and evaluation of a multiepitope vaccine targeting the nucleoprotein of Puumala orthohantavirus.

The Puumala orthohantavirus is present in the body of the bank vole (Myodes glareolus). Humans infected with this virus may develop hemorrhagic fever accompanying renal syndrome. In addition, the infection may further lead to the failure of an immune system completely. The present study aimed to propose a possible vaccine by employing bioinformatics techniques to identify B and T-cell antigens. The best multi-epitope of potential immunogenicity was generated by combining epitopes. Additionally, the linkers EAAAK, AAY, and GPGPG were utilized in order to link the epitopes successfully. Further, C-ImmSim was used to perform in silico immunological simulations upon the vaccine. For the purpose of conducting expression tests in Escherichia coli, the chimeric protein construct was cloned using Snapgene into the pET-9c vector. The designed vaccine showed adequate results, evidenced by the global population coverage and favorable immune response. The developed vaccine was found to be highly effective and to have excellent population coverage in a number of computer-based assessments. This work is fully dependent on the development of nucleoprotein-based vaccines, which would constitute a significant step forward if our findings were used in developing a global vaccination to combat the Puumala virus.

Twenty-eight days of repeated dose sub-acute toxicological evaluation of polyherbal Ayurvedic medicine BPGrit in Sprague-Dawley rats.

A pre-clinical toxicological evaluation of herbal medicines is necessary to identify any underlying health-associated side effects, if any. BPGrit is an Ayurveda-based medicine prescribed for treating hypertensive conditions. High-performance liquid chromatography-based analysis revealed the presence of gallic acid, ellagic acid, coumarin, cinnamic acid, guggulsterone E, and guggulsterone Z in BPGrit. For sub-acute toxicity analysis of BPGrit, male and female Sprague-Dawley rats were given repeated oral gavage at 100, 300, and 1000 mg/kg body weight/day dosages for 28 days, followed by a 14-day recovery phase. No incidences of mortality, morbidity, or abnormal clinical signs were observed in BPGrit-treated rats throughout the study period. Also, the body weight and food consumption habits of the experimental animals did not change during the study duration. Hematological, biochemical, and histopathological analysis did not indicate any abnormal changes occurring in the BPGrit-treated rats up to the highest tested dose of 1000 mg/kg body weight/day. Finally, the study established the "no-observed-adverse-effect level" for BPGrit at >1000 mg/kg body weight/day in Sprague-Dawley rats.

Cellular senescence in lung cancer: Molecular mechanisms and therapeutic interventions.

Lung cancer stands as the primary contributor to cancer-related fatalities worldwide, affecting both genders. Two primary types exist where non-small cell lung cancer (NSCLC), accounts for 80-85% and SCLC accounts for 10-15% of cases. NSCLC subtypes include adenocarcinoma, squamous cell carcinoma, and large cell carcinoma. Smoking, second-hand smoke, radon gas, asbestos, and other pollutants, genetic predisposition, and COPD are lung cancer risk factors. On the other hand, stresses such as DNA damage, telomere shortening, and oncogene activation cause a prolonged cell cycle halt, known as senescence. Despite its initial role as a tumor-suppressing mechanism that slows cell growth, excessive or improper control of this process can cause age-related diseases, including cancer. Cellular senescence has two purposes in lung cancer. Researchers report that senescence slows tumor growth by constraining multiplication of impaired cells. However, senescent cells also demonstrate the pro-inflammatory senescence-associated secretory phenotype (SASP), which is widely reported to promote cancer. This review will look at the role of cellular senescence in lung cancer, describe its diagnostic markers, ask about current treatments to control it, look at case studies and clinical trials that show how senescence-targeting therapies can be used in lung cancer, and talk about problems currently being faced, and possible solutions for the same in the future.

Livogrit prevents Amiodarone-induced toxicity in experimental model of human liver (HepG2) cells and Caenorhabditis elegans by regulating redox homeostasis.

Treatment with cationic amphiphilic drugs like Amiodarone leads to development of phospholipidosis, a type of lysosomal storage disorder characterized by excessive deposition of phospholipids. Such disorder in liver enhances accumulation of drugs and its metabolites, and dysregulates lipid profiles, which subsequently leads to hepatotoxicity. In the present study, we assessed pharmacological effects of herbal medicine, Livogrit, against hepatic phospholipidosis-induced toxicity. Human liver (HepG2) cells and in vivo model of Caenorhabditis elegans (N2 and CF1553 strains) were used to study effect of Livogrit on Amiodarone-induced phospholipidosis. In HepG2 cells, Livogrit treatment displayed enhanced uptake of acidic pH-based stains and reduced phospholipid accumulation, oxidative stress, AST, ALT, cholesterol levels, and gene expression of SCD-1 and LSS. Protein levels of LPLA2 were also normalized. Livogrit treatment restored Pgp functionality which led to decreased cellular accumulation of Amiodarone as observed by UHPLC analysis. In C. elegans, Livogrit prevented ROS generation, fat-6/7 gene overexpression, and lysosomal trapping of Amiodarone in N2 strain. SOD-3::GFP expression in CF1553 strain normalized by Livogrit treatment. Livogrit regulates phospholipidosis by regulation of redox homeostasis, phospholipid anabolism, and Pgp functionality hindered by lysosomal trapping of Amiodarone. Livogrit could be a potential therapeutic intervention for amelioration of drug-induced phospholipidosis and prevent hepatotoxicity.

Integration of network pharmacology, molecular docking, and simulations to evaluate phytochemicals from Drymaria cordata against cervical cancer.

Introduction: Cervical cancer is prevalent among women worldwide. It is a type of cancer that occurs in the cells of the cervix, the lower part of the uterus. Mostly, it is observed in developing nations due to limited access to screening tools. Natural products with anticancer properties and fewer side effects have gained attention. Therefore, this study evaluates the potential of Drymaria cordata as a natural source for treating cervical cancer. Methodology: Phytocompounds present in Drymaria cordata were screened for their molecular properties and drug-likeness. The selected compounds were studied using systems biology tools such as network pharmacology, molecular docking, and molecular dynamics simulations, including MMGBSA studies. Results: Through network pharmacology, molecular docking, and molecular dynamics simulations, quercetin 3-O-ß-d-glucopyranosyl-(1→2)-rhamnopyranoside was identified as a hit compound targeting HRAS and VEGFA proteins. These proteins were found to be responsible for the maximum number of pathway modulations in cervical cancer. Conclusion: Drymaria cordata exhibits potential for treating cervical cancer due to the presence of quercetin 3-O-ß-d-glucopyranosyl-(1→2)-rhamnopyranoside. Further validation of these findings through in vitro and in vivo studies is required.

Assessing the potential of Psidium guajava derived phytoconstituents as anticholinesterase inhibitor to combat Alzheimer's disease: an in-silico and in-vitro approach.

Acetylcholinesterase (AChE) inhibitors play a crucial role in the treatment of Alzheimer's disease. These drugs increase acetylcholine levels by inhibiting the enzyme responsible for its degradation, which is a vital neurotransmitter involved in memory and cognition. This intervention intermittently improves cognitive symptoms and augments neurotransmission. This study investigates the potential of Psidium guajava fruit extract as an acetylcholinesterase (AChE) inhibitor for Alzheimer's disease treatment. Molecular characteristics and drug-likeness were analyzed after HR-LCMS revealed phytocompounds in an ethanolic extract of Psidium guajava fruit. Selected phytocompounds were subjected to molecular docking against AChE, with the best-docked compound then undergoing MD simulation, MMGBSA, DCCM, FEL, and PCA investigations to evaluate the complex stability. The hit compound's potential toxicity and further pharmacokinetic features were also predicted. Anticholinesterase activity was also studied using in vitro assay. The HR-LCMS uncovered 68 compounds. Based on computational analysis, Fluspirilene was determined to have the highest potential to inhibit AChE. It was discovered that the Fluspirilene-AChE complex is stable and that Fluspirilene has a high binding affinity for AChE. Extract of Psidium guajava fruit significantly inhibits AChE (88.37% at 200 µg/ml). It is comparable to the standard AChE inhibitor Galantamine. Fluspirilene exhibited remarkable binding to AChE. Psidium guajava fruit extract demonstrated substantial AChE inhibitory activity, indicating its potential for Alzheimer's treatment. The study underscores natural sources' significance in drug discovery.Communicated by Ramaswamy H. Sarma.

Neuroprotection by Polyherbal Medicine Divya-Medha-Vati Against Scopolamine-Induced Cognitive Impairment Through Modulation of Oxidative Stress, Acetylcholine Activity, and Cell Signaling.

Alzheimer disease is associated with cognitive impairments and neuronal damages. In this study, Scopolamine, a model drug used for the generation of Alzheimer-like symptoms induced cognitive dysfunction in C57BL/6 mice. It also elevated acetylcholine esterase (AcHE) activity, and reduced antioxidant (superoxide dismutase and catalase) activity in cortex tissue. Scop reduced neuronal density and increased pyknotic neurons in hippocampus tissue. In mouse neuroblastoma (Neuro2a) cells, Scop triggered a dose-dependent loss of cell viability and neurite outgrowth reduction. Scop-treated Neuro2a cells showed oxidative stress and reduction in mRNA expression for brain-derived neurotrophic factor (BDNF), nerve growth factor-1 (NGF-1), and Synapsin-1 (SYN-1) genes. Mice treated with Divya-Medha-Vati (DMV), an Ayurvedic polyherbal medicine showed protection against Scop-induced cognitive impairment (Morris Water Maze Escape Latency, and Elevated Plus Maze Transfer Latency). DMV protected against Scop-induced AcHE activity, and loss of antioxidant activities in the mice brain cortex while sustaining neuronal density in the hippocampus region. In the Neuro2a cells, DMV reduced Scop-induced loss of cell viability and neurite outgrowth loss. DMV protected the cells against induction of oxidative stress and promoted mRNA expression of BDNF, NGF-1, and SYN-1 genes. Phytochemical profiling of DMV showed the presence of Withanolide A, Withanolide B, Bacopaside II, Jujubogenin, Apigenin, Gallic acid, Caffeic acid, and Quercetin that are associated with antioxidant and neurostimulatory activities. In conclusion, the study showed that Divya-Medha-Vati was capable of promoting neuronal health and inhibiting Alzheimer-like cognitive dysfunction through enhanced antioxidant activities and modulation of neuronal activities.

Netting into the Sophoretin pool: An approach to trace GSTP1 inhibitors for reversing chemoresistance.

Chemoresistance, a significant challenge in cancer treatment, is often associated with the cellular glutathione-related detoxification system. The GSTP1 isoenzyme (glutathione S-transferases) plays a critical role in the cytoplasmic inactivation of anticancer drugs. This suggests the identification of GSTP1 inhibitors to combat chemoresistance. We screened Sophoretin (also called quercetin) derivatives for molecular properties, pharmacokinetics, and toxicity profiles. Following that, we conducted molecular docking and simulations between selected derivatives and GSTP1. The best-docked complex, GSTP1-quercetin 7-O-ß-D-glucoside, exhibited a binding affinity of -8.1 kcal/mol, with no predicted toxicity and good pharmacokinetic properties. Molecular dynamics simulations confirmed the stability of this complex. Quercetin 7-O-ß-D-glucoside shows promise as a lead candidate for addressing chemoresistance in cancer patients, although further experimental studies are needed to validate its efficacy and therapeutic potential.

Computational pharmacology profiling of borapetoside C against melanoma.

Melanoma,also known as a 'black tumor', begins in the melanocytes when cells (that produce pigment) grows out of control. Immunological dysregulation, which raises the risk for multiple illnesses, including melanoma, may be influenced by stress tiggered through viral infection, long term effects of ultraviolet radiation, environmental pollutants etc. Borapetoside C is one of the phytoconstituents from Tinospora crispa, and its biological source has been reported for its antistress property. Network pharmacology and KEGG pathway analysis of borapetoside C-regulated proteins were conducted to identify the hub genes involved in melanoma development. Further, a molecular docking was performed between borapetoside C and targets involved in melanoma. Further, the top 3 complexes were selected based on the binding energy to conduct molecular dynamics simulations to evaluate the stability of ligand-protein complex followed by principal component analysis and dynamic cross-correlation matrix. In addition, borapetoside C was also screened for its pharmacokinetics and toxicity profile. Network Pharmacology studies and KEGG pathway analysis revealed 8 targets involved in melanoma. Molecular docking between borapetoside C and targets involved in melanoma identified 3 complexes with minimum binding i.e. borapetoside C- MAP2K1, MMP9, and EGFR. Further, molecular dynamics simulations showed a stable complex of borapetoside C with MMP9 and EGFR. The present study suggested that borapetoside C may target MMP9 and EGFR to possess an anti-melanoma property. This finding can be useful in developing a novel therapeutic agent against melanoma from a natural source.Communicated by Ramaswamy H. Sarma.

Targeting Melanoma with a phytochemical pool: Tailing Makisterone C.

BACKGROUND AND OBJECTIVE: According to World Health Organization, melanoma claims the lives of about 48000 people worldwide each year. The purpose of this study was to identify potential phytochemical pool from Diplazium esculentum against proteins that contribute to melanoma development. METHODS: The research was carried to locate potentially bioactive molecules and conduct a theoretical analysis of active ingredients from DE to impact melanoma. Network pharmacology, pharmacokinetics, protein network interaction, gene enrichment, survival, and infiltration analysis were conducted. Furthermore, molecular docking and molecular dynamics simulation was carried out for makisterone C-MAPK1, MAPK3, and AKT1 complexes. RESULTS: The potential phytochemical pool were identified (stigmast-5-en-3-ol, esculentic acid, rutin, and makisterone C) and based on network pharmacology and molecular docking studies, makisterone-C was proposed to be the most promising ingredient. Furthermore, the investigation revealed 14 genes as critical "hubs" involved in combating melanoma that are manipulated by the above-mentioned 4 active ingredients and modulate multiple signaling in melanoma development. CONCLUSION: This study insights into the potential anti-melanoma effects of phytochemical pool from Diplazium esculentum using network pharmacology analysis, molecular docking, and simulation tailing makisterone C as a lead moiety and suggests the need for makisterone C further evaluation in intervening melanoma progression.

The marijuana-schizophrenia multifaceted nexus: Connections and conundrums towards neurophysiology.

Delta-9-tetrahydrocannabinol, a component of marijuana, interacts with cannabinoid receptors in brain involved in memory, cognition, and emotional control. However, marijuana use and schizophrenia development is a complicated and contentious topic. As a result, more investigation is needed to understand this relationship. Through the functional enrichment analysis, we report the delta-9-tetrahydrocannabinol to manipulate the homeostatic biological process and molecular function of different macromolecules. Additionally, using molecular docking and subsequent processing for molecular simulations, we assessed the binding ability of delta-9-tetrahydrocannabinol with the estrogen-related protein, dopamine receptor 5, and hyaluronidase. It was found that delta-9-tetrahydrocannabinol may have an impact on the brain's endocannabinoid system and may trigger the schizophrenia progression in vulnerable people. Delta-9-tetrahydrocannabinol may interfere with the biological function of 18 proteins linked to schizophrenia and disrupt the synaptic transmission (dopamine, glutamine, and gamma-aminobutyric acid). It was discovered that it may affect lipid homeostasis, which is closely related to membrane integrity and synaptic plasticity. The negative control of cellular and metabolic processes, fatty acids binding /activity, and the manipulated endocannabinoid system (targeting cannabinoid receptors) were also concerned with delta-9-tetrahydrocannabinol. Hence, this may alter neurotransmitter signaling involved in memory, cognition, and emotional control, showing its direct impact on brain physiological processes. This may be one of the risk factors for schizophrenia development which is also closely tied to some other variables such as frequency, genetic vulnerability, dosage, and individual susceptibility.

Exploiting Mass Spectrometry to Unlock the Mechanism of Nanoparticle-Induced Inflammasome Activation.

Nanoparticles (NPs) elicit sterile inflammation, but the underlying signaling pathways are poorly understood. Here, we report that human monocytes are particularly vulnerable to amorphous silica NPs, as evidenced by single-cell-based analysis of peripheral blood mononuclear cells using cytometry by time-of-flight (CyToF), while silane modification of the NPs mitigated their toxicity. Using human THP-1 cells as a model, we observed cellular internalization of silica NPs by nanoscale secondary ion mass spectrometry (nanoSIMS) and this was confirmed by transmission electron microscopy. Lipid droplet accumulation was also noted in the exposed cells. Furthermore, time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealed specific changes in plasma membrane lipids, including phosphatidylcholine (PC) in silica NP-exposed cells, and subsequent studies suggested that lysophosphatidylcholine (LPC) acts as a cell autonomous signal for inflammasome activation in the absence of priming with a microbial ligand. Moreover, we found that silica NPs elicited NLRP3 inflammasome activation in monocytes, whereas cell death transpired through a non-apoptotic, lipid peroxidation-dependent mechanism. Together, these data further our understanding of the mechanism of sterile inflammation.

Withania somnifera-derived carbon dots protect human epidermal cells against UVB-induced cell death and support growth factor-mediated wound healing.

Solar radiation comprising UVA and UVB regions is considered a skin-damaging factor inducing inflammation, oxidative stress, hyperpigmentation, and photo-aging. Photoluminescent carbon dots (CDs) were synthesized from the root extract of a Withania somnifera (L.) Dunal plant and urea, using a one-step microwave method. These Withania somnifera CDs (wsCDs) were 14.4 ± 0.18 d nm in diameter and presented photoluminescence. UV absorbance showed the presence of π-π* (C[double bond, length as m-dash]C) and n-π* (C[double bond, length as m-dash]O) transition regions in wsCDs. FTIR analysis indicated the presence of nitrogen and carboxylic functional groups on the surface of wsCDs. HPLC analysis of wsCDs showed the presence of withanoside IV, withanoside V, and withanolide A. The wsCDs were found to be biocompatible in human skin epidermal (A431) cells and hindered UVB irradiation-induced loss of metabolic activity and oxidative stress. The wsCDs supported rapid dermal wound healing through augmented TGF-ß1 and EGF gene expression levels in A431 cells. Finally, wsCDs were found to be biodegradable through a myeloperoxidase-catalyzed peroxidation reaction. The study concluded that under in vitro conditions, Withania somnifera root extract-derived biocompatible carbon dots provided photo-protection against UVB-stimulated epidermal cell damage and supported rapid wound healing.

Knowledge mining of unstructured information: application to cyber domain.

Information on cyber-related crimes, incidents, and conflicts is abundantly available in numerous open online sources. However, processing large volumes and streams of data is a challenging task for the analysts and experts, and entails the need for newer methods and techniques. In this article we present and implement a novel knowledge graph and knowledge mining framework for extracting the relevant information from free-form text about incidents in the cyber domain. The computational framework includes a machine learning-based pipeline for generating graphs of organizations, countries, industries, products and attackers with a non-technical cyber-ontology. The extracted knowledge graph is utilized to estimate the incidence of cyberattacks within a given graph configuration. We use publicly available collections of real cyber-incident reports to test the efficacy of our methods. The knowledge extraction is found to be sufficiently accurate, and the graph-based threat estimation demonstrates a level of correlation with the actual records of attacks. In practical use, an analyst utilizing the presented framework can infer additional information from the current cyber-landscape in terms of the risk to various entities and its propagation between industries and countries.

Investigating the Role of Classical Ayurveda-Based Incineration Process on the Synthesis of Zinc Oxide Based Jasada Bhasma Nanoparticles and Zn2+ Bioavailability.

Jasada bhasma (JB) is a zinc oxide-based Indian traditional Ayurveda-based herbo-metallic nanoparticle used for the treatment of zinc (Zn) deficiency and autoimmune and inflammatory disorders. JB is made by following the Ayurveda-based guidelines using zinc oxide (ZnO) as a raw material and going through 17 cycles of the high-temperature incineration and trituration process known as "Ma̅rana" in the presence of herbal decoctions prepared from the leaves ofAzadirachta indica andAloe vera gel. These cycles improve the purity of the parent material and transform its physicochemical properties, converting it into nanoparticles. However, there still exists a knowledge gap regarding the role of incineration in the physicochemical transformation of the Zn raw material into JB nanoparticles and the biological interaction of the final product. In the present study, the JB samples obtained during different Ma̅rana cycles were carefully studied for their physicochemical transformation using analytical methods such as powdered X-ray diffraction (XRD), small-angle X-ray scattering (SAXS), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy, Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, and dynamic light scattering (DLS). According to the XRD results, the Zn and oxygen molecules in hexagonal ZnO wurtzite crystals gradually realigned as a result of repeated heat treatments that caused lattice tension and crystal size reduction from 53.14 to 42.40 nm. A morphological transition from 1.5 µm rod shape to 31 nm in the JB particles can be seen using FESEM and SAXS analyses. The existence of 10 nm-sized nanoparticles in the finished product was confirmed by HRTEM. The presence of ZnO was confirmed in all samples by FTIR and Raman spectroscopies. Cell viability analysis showed an inhibitory concentration 50% of >1000 µg/mL for JB nanoparticles, revealing no adverse effects in human colon Caco-2 cells. A dose-dependent uptake and intracellular accumulation of JB nanoparticles were observed in Caco-2 cells using inductively coupled plasma-based mass spectroscopy (ICP-MS). Bioavailability of Zn2+ ions (6% w/w) through JB dissolution in acidic pH 4.0 was observed, representing the stomach and intracellular lysosomal physiological conditions. Therefore, the study showed that the repeated incineration cycles produced biocompatible JB nanoparticles through the physicochemical transformation at molecular levels capable of delivering bioavailable Zn2+ ions under physiological conditions. In conclusion, the medicinal properties of JB nanoparticles described in Ayurveda were found to originate from their small size and dissolution properties, formed through the classical incineration-based synthesis process.

Multi-Epitope Vaccine Design against Monkeypox Virus via Reverse Vaccinology Method Exploiting Immunoinformatic and Bioinformatic Approaches.

(1) Background: The monkeypox virus is a zoonotic orthopox DNA virus that is closely linked to the virus. In light of the growing concern about this virus, the current research set out to use bioinformatics and immunoinformatics to develop a potential vaccine against the virus. (2) Methods: A multiepitope vaccine was constructed from the B-cell and T-cell epitopes of the MPXVgp181 strain using adjuvant and different linkers. The constructed vaccine was predicted for antigenicity, allergenicity, toxicity, and population coverage. In silico immune simulation studies were also carried out. Expression analysis and cloning of the constructed vaccine was carried out in the pET-28a(+) vector using snapgene. (3) Results: The constructed vaccine was predicted to be antigenic, non-allergenic, and non-toxic. It was predicted to have excellent global population coverage and produced satisfactory immune response. The in silico expression and cloning studies were successful in E. coli, which makes the vaccine construct suitable for mass production in the pharmaceutical industry. (4) Conclusion: The constructed vaccine is based on the B-cell and T-cell epitopes obtained from the MPXVgp181 strain. This research can be useful in developing a vaccine to combat the monkeypox virus globally after performing in-depth in vitro and in vivo studies.