Experimental and computational insights of Albizia amara phytoconstituents targeting anthranilate phosphoribosyltransferase from Malassezia globosa.

The fungus Malassezia globosa is often responsible for superficial mycoses posing significant treatment challenges because of the unfavourable side effects of available antifungal drugs. To reduce potential hazards to the host and overcome these hurdles, new therapeutic medicines must be developed that selectively target enzymes unique to the pathogen. This study focuses on the enzyme anthranilate phosphoribosyltransferase (AnPRT), which is vital to M. globosa's tryptophan production pathway. To learn more about the function of the AnPRT enzyme, we modeled, validated, and simulated its structure. Moreover, many bioactive components were found in different extracts from the plant Albizia amara after phytochemical screening. Interestingly, at doses ranging from 500 to 2000 µg/ml, the chloroform extract showed significant antifungal activity, with inhibition zones measured between 11.0 ± 0.0 and 25.6 ± 0.6 mm. According to molecular docking analyses, the compounds from the active extract, particularly 2-tert-Butyl-4-isopropyl-5-methylphenol, interacted with the AnPRT enzyme's critical residues, ARG 205 and PHE 214, with an effective binding energy of -4.9 kcal/mol. The extract's revealed component satisfies the requirements for drug-likeness and shows promise as a strong antifungal agent against infections caused by M. globosa. These findings imply that using plant-derived chemicals to target the AnPRT enzyme is a viable path for the creation of innovative antifungal treatments.

Algerian Prickly Pear Seed By-Products: Fatty Acids Composition, Antioxidant, Enzyme Inhibitory Activities towards Tyrosinase, Urease, α-Amylase, and Cholinesterase, along with the Ability to Protect from Thermal Protein Denaturation.

Prickly pear seed is a source of the most expensive oil in the world, which is rich in vitamins and polyunsaturated fatty acids. Its extraction generates a large quantity of press cake. These two by-products need to be valued. The current study aimed to assess the fatty acid composition of oil and the phytochemical composition of press cake. In addition, the antioxidant and the inhibition of thermal protein denaturation effects of both Algerian seed by-products were evaluated with their inhibitory action against the activities of urease, tyrosinase, α-amylase, and cholinesterase enzymes. The GC MS analysis result revealed the richness of our oil in linoleic (74%) and palmitic (13%) acids methyl esters, respectively. The chemical composition of press cake was characterized by a high value of dry matter (94.94 ± 0.05%), especially the carbohydrates (85.13 ± 0.94%). The results of antioxidant activity presented by IC50 and A0.5 ranged from 7.51 ± 0.03 to 88.10 ± 0.92 µg/mL. Furthermore, the IC50 values were 40.19 ± 1.21 and 61.18 ± 0.03 µg/mL in thermal protein denaturation assay, and ranging from 22.97 ± 0.72 to 385.99 ± 0.27 µg/mL for the inhibition of enzymatic activities. These results indicate that the studied oil can be one of the strongest oils for its impressive effects and also encourage us to reuse its press cake in feed livestock.

Identifying the molecular mechanisms of action of wound healing properties of Mathan tailam and Mahamegarajanga tailam in Wistar albino rats: Evidence through IL-10/VEGF/TNF-α signalling pathways.

The Siddha system of medicine (SSM) is the oldest medical science practised in the ancient period of the southern part of India and Sri Lanka. Many formulations were described for wound healing in the SSM, with specific diagnostic differentiation in the Siddha literature. Most preparations for wound healing were available in the form of oil-based formulations, especially for external usage. Mathan tailam (MT) and Mahamegarajanga tailam (MMRT) have been used by Siddha physicians and traditional practitioners to treat wounds. Mathan tailam is a popular regimen for skin lacerations, burns, skin infections, diabetic wounds, and dermatitis. Mahamegarajanga tailam has long been used by traditional vaidyars to treat cuts and burns. Both MT and MMRT are clinically well-appreciated drugs for wound healing and need to be studied for their mechanisms of action for scientific documentation. In an in vivo study on albino rats -excisional wound model, the histopathological changes, histo-immune response, biomarker analysis, and mRNA expression were studied and analysed. Wounds treated with MT and MMRT healed faster (p < 0.05) than the untreated group (CNT). Histological investigation showed rapid re-epithelialization, dense collagen deposition, increased enzymatic antioxidant activities and decreased lipid peroxidation in the MT and MMRT groups. mRNA expression reveals MT and MMRT-treated tissues able to induce convergent cell motility in wound space. Our study for the first time provides strong in vivo experimental evidence that Mathan tailam and Mahamegarajanga tailam play a crucial role in promoting skin tissue wound healing through IL-6/VEGF/TNF-α mediated mechanisms. Traditional practices continue to teach us valuable lessons, as seen by their continuous use in their locality for years.

Comprehensive phytochemical analysis of Salvia hispanica L. callus extracts using LC-MS/MS.

In this research, the study utilized the root, leaf, and petiole parts of in vitro grown Salvia hispanica plants as explants. Following UV-C treatment applied to developing callus, methanol extracts were obtained and analyzed using liquid chromatography-mass spectrometry (LC/MS) to investigate their anticancer properties. First, the seeds of S. hispanica were soaked in commercial bleach for 6 min to ensure surface sterilization. The most effective antimicrobial activity on Gram-negative bacteria, with a zone diameter (11 ± 0.82 mm), was noticed in callus extracts obtained from the petiole explant in the second protocol against Klebsiella pneumoniae EMCS bacteria. Anticancer activities on SH-SY5Y human neuroblastoma cells were investigated by using 1000, 500, 250, 125, 62.5, 31.25, 15.62, and 78.12 µg/mL doses of the extracts, and the most effective cytotoxic activity was determined at the 1000 µg/mL dose of the extracts obtained from both protocols. The extracts were determined to inhibit hCAI, hCAII, AChE, and BChE enzymes. The content of 53 different phytochemical components of the extracts was analyzed by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Rosmarinic acid, quinic acid, and caffeic acid were found in the highest concentration. The comprehensive LC-MS/MS analysis of S. hispanica extracts revealed a diverse array of phytochemical compounds, highlighting its potential for therapeutic applications.

Investigating lactic acid bacteria genus Lactococcus lactis properties: Antioxidant activity, antibiotic resistance, and antibacterial activity against multidrug-resistant bacteria Staphylococcus aureus.

Background: Lactic acid bacteria (LAB) are utilized as a starter culture in the manufacturing of fermented dairy items, as a preservative for various food products, and as a probiotic. In our country, some research has been carried out, even if LAB plays a principal role in food preservation and improves the texture and taste of fermented foods, that is why we tried to evaluate their probiotic effect. The objective of this research was to determine the antibacterial activity of Lactococcus lactis (L. lactis) against Staphylococcus aureus (S. aureus) ATCC 29213, investigate their antioxidant activity, and characterize their sensitivity against 18 antibiotics. Methods: A total of 23 LAB (L. lactis subsp. cremoris, L. lactis subsp. Lactis diacetylactis, L. lactis subsp. lactis) were isolated from cow's raw milk. The antibacterial activity was performed using two techniques, competition for nutrients and a technique utilizing components nature, using the disk diffusion method. The sensitivity of the studied LAB to different antibiotics was tested on Man rogosa sharp (MRS) agar using commercial antibiotic disks. All strains of LAB were examined for their antioxidant activity. The antioxidant activity of L. lactis was tested by 2,2-diphenyl-1 picrylhydrazyl (DPPH). Results: The results showed that the MRS medium was more adapted than Muller Hinton Agar (MHA) to investigate the antibacterial activity of L. lactis against S. aureus ATCC 29213. Also, L. lactis exhibited a notable degree of antibacterial activity against S. aureus ATCC 29213. L. Lactis subsp. Lactis displayed higher antibacterial activities, followed by L. lactis ssp. lactis biovar. diacetylactis, and lastly, L. lactis ssp. cremoris against S. aureus ATCC 29213. Lc 26 among all strains of L. lactis showed a high potential antibacterial activity reaching 40 ± 3 mm against S. aureus ATCC 29213. All strains of L. lactis showed a slightly moderate antioxidant activity (10.56 ± 1.28%-26.29 ± 0.05 %). The results of the antibiotic resistance test indicate that all strains of L. lactis were resistant to cefotaxime, sulfamethoxazole-trimethoprim, and streptomycin and were sensitive to Ampicillin, Amoxicillin, Penicillin G, Teicoplanin, Vancomycin, Gentamicin 500, Tetracycline, and Chloramphenicol. These test results indicate that this strain falls within the criteria of not posing any harmful effects on human health. The important antibacterial properties recorded for all L. Lactis strains were derived from the production of antibacterial active metabolites, such as protein, diacetyl, hydrogen peroxide, and lactic acid, together with the fight for nutrients. Conclusion: This study suggests that the strains of L. lactis could be added as an antibacterial agent against S. aureus ATCC 29213 and can provide an important nutritional property for their antioxidant potential.

Unlocking the Therapeutic Potential of Stevia rebaudiana Bertoni: A Natural Antiglycating Agent and Non-Toxic Support for HDF Cell Health.

Sugar carbonyl groups interact with protein amino groups, forming toxic components referred to as advanced glycation end products (AGEs). The glycation system (BSA, a model protein, and fructose) was incubated for five weeks at 37 °C in the presence and absence of Stevia leaf extract. The results indicated that the leaf extract (0.5 mg/mL) decreased the incidence of browning (70.84 ± 0.08%), fructosamine (67.27 ± 0.08%), and carbonyl content (64.04 ± 0.09%). Moreover, we observed an 81 ± 8.49% reduction in total AGEs. The inhibition of individual AGE (argpyrimidine, vesper lysine, and pentosidine) was ~80%. The decrease in the protein aggregation was observed with Congo red (46.88 ± 0.078%) and the Thioflavin T (31.25 ± 1.18%) methods in the presence of Stevia leaf extract. The repercussion of Stevia leaf extract on DNA glycation was examined using agarose gel electrophoresis, wherein the DNA damage was reversed in the presence of 1 mg/mL of leaf extract. When the HDF cell line was treated with 0.5 mg/mL of extract, the viability of cells decreased by only ~20% along with the same cytokine IL-10 production, and glucose uptake decreased by 28 ± 1.90% compared to the control. In conclusion, Stevia extract emerges as a promising natural agent for mitigating glycation-associated challenges, holding potential for novel therapeutic interventions and enhanced management of its related conditions.

Indexing hematological and serum biochemical reference intervals of Himalayan snow trout, Schizothorax esocinus to instrument in health assessment.

Schizothorax esocinus, commonly known as snow trout, is one of the main contributors of food and livelihood in the colder zone of Himalayan region. The comprehensive information on its hematological and serum biochemical reference intervals is not reported yet. In the present study an attempt has been made to elucidate the hematological and serum biochemical reference intervals of S. esocinus from River Jhelum using protocols of the American Society of Veterinary Clinical Pathology (ASVCP). Wild fish were sampled over a period of 2 years from the pollution free sites of river Jhelum. Fish blood was harvested through caudal venipuncture and hemato-biochemical analysis performed thereof. Data values from a total of healthy 432 adult fish specimens (216 male, 216 female) were systematically recorded. The reference intervals for hematological and serum biochemical parameters of S. esocinus were established using Reference Value Advisor software v 2.1. RIs for hematological and serum analytes ranged as: hemoglobin (Hb) 78.38-116.35 (g/L); white blood cells (WBC) 10-20 (×109/L); red blood cells (RBC) 1.30-2.15 (×1012/L); packed cell volume 27.00-39.45 (%); total protein 39.21-61.62 (g/L); albumin 8.20-22.02 (g/L); globulin 27.58-49.55 (g/L); glucose 3.25-7.18 (mmol/L); urea 0.96-2.38 (mmol/L); cholesterol 3.80-6.90 (mmol/L). The study also depicted that certain blood measurands were influenced with respect to sex. Significantly (p < 0.05) higher values of Hb, red blood cells count and serum glucose were noted in male as compared to female which, on the other hand, registered higher white blood cells count and serum cholesterol level (Mann Whitney U test, p < 0.05). The work, therefore, provides baseline information on hematological and serum biochemical analytes of this species which holds high commercial importance. RIs reported here can help monitor the health status of fish by improving the use of non-lethal diagnostic methods in piscine medicine.

Identification of Plant Peptides as Novel Inhibitors of Orthohepevirus A (HEV) Capsid Protein by Virtual Screening.

Hepatitis E virus (HEV) is the notable causative agent of acute and chronic hepatic, renal, pancreatic, neurological, and hematopoietic blood cell infections with high risk in immunocompromised patients. Hepatic failure is mostly documented among adults, pregnant women, and patients with preexisting liver disease. HEV is a positive sense RNA virus of 7.2 kb genome size with typically three open reading frames (ORFs) which play essential roles in viral replication, genome assembly, and transcription. The mutational substitution in the viral RNA genome makes more it difficult to understand the actual relationship in the host-virus association. ORFs of HEV encode different structural and non-structural proteins and one of them is the capsid protein which is coded by ORF2. The capsid protein mediates the encapsulation of the viral genome as well as being involved in virion assembly. In the current study, the ligand-based docking approach was employed to inhibit the active amino acids of the viral capsid protein. Depending upon S-score, ADMET profiling, and drug scanning, the top ten tetrapeptides were selected as potential drug candidates with no toxicity counter to HEV receptor protein. The S-score or docking score is a mathematical function which predicts the binding affinities of docked complexes. The binding affinity of the predicted drug-target complexes helps in the selectivity of the desired compound as a potential drug. The best two selected peptides (i.e., TDGH with S-score of -8.5 and EGDE with S-score of -8.0) interacted with the active site amino acids of the capsid protein (i.e., Arg399, Gln420, and Asp444). The molecular dynamics simulations of RMSD trajectories of TDGH-capsid protein and EDGE-capsid protein have revealed that both docked complexes were structurally stable. The study revealed that these tetrapeptides would serve as strong potential inhibitors and a starting point for the development of new drug molecules against the HEV capsid protein. In future, in vivo studies are needed to explore selected peptides as potential drug candidates.

Bioremediation of Cadmium Toxicity in Wheat (Triticum aestivum L.) Plants Primed with L-Proline, Bacillus subtilis and Aspergillus niger.

Cadmium toxicity is one of the deleterious abiotic factors that reduce wheat production. Two different cultivars (Akbar and Dilkash) were compared for their cadmium (0, 40 and 80 mg/kg) tolerance and responses towards Bacillus subtilis NA2, Aspergillus niger PMI-118 and L-proline. Both microbes were tested for heavy metal tolerance and production of various plant hormones and biological active enzyme characteristics under normal and cadmium stress. A completely randomized design (two cultivars × four treatments × three cadmium levels × three replicates) was adopted using distilled water as a control. The growth promotion potential of these strains under cadmium stress was determined by N-fixation, IAA synthesis, P-solubilization, amylase and proteases production. A pot experiment under controlled conditions was conducted to evaluate the effect of bacteria, fungi, and L-proline under cadmium stress. It was indicated from the result that plant biomass (46.43%), shoot length (22.40%), root length (25.06%), chlorophyll (17.17%), total sugars (27.07%), total proteins (86.01%) and ascorbic acid (83.27%) were improved with inoculation under control and cadmium stress. The accumulation of total flavonoids (48.64%), total phenolics (24.88%), hydrogen peroxide (53.96%) and activities of antioxidant enzymes CAT (26.37%) and APX (43.71%) were reduced in the plants treated with bacteria, fungi and L-proline than those under control. With parallel aids, Bacillus subtilis NA2 showed a higher cadmium tolerance and plant growth stability as compared to Aspergillus niger PMI-118 and L-proline and may be adopted in the future.

Potassium bromate-induced oxidative stress, genotoxicity and cytotoxicity in the blood and liver cells of mice.

Potassium bromate (KBrO3) is an oxidising agent that is extensively used as a food additive, it is also a product of cosmetic and pharmaceutical relevance. The objective of this study was to evaluate the oxidative stress, genotoxicity, and apoptosis induced by KBrO3 in an experimental animal model. To study the toxic effects and oxidative stress, different doses of KBrO3 below LD50 (The half maximal lethal dose, 50, 100 and 150 mg/kg body weight) were given intraperitoneally to the mice for multiple time periods (24, 48, and 72 h). The results showed that KBrO3 significantly induces oxidative damage by increasing the levels of reactive oxygen species (ROS) and lipid peroxidase and depleted the levels of catalase (CAT), superoxide dismutase (SOD) and glutathione (GSH) enzymes in the serum and liver. Moreover, a significant increase of chromosomal aberrations in bone marrow cells and an elevated incidence of micronuclei in the peripheral blood of mice were observed. KBrO3 induces 3 ´ -OH end double-strand DNA breaks, which was evident in liver sections of the treated mice, and increases the percentage of apoptotic cells, as observed in TUNEL assays and flow cytometry analysis. The present findings indicate that KBrO3 induces oxidative stress, genotoxicity, and cytotoxicity in a dose- and time-dependent manner in mice.

Transcriptome characterization of Larrea tridentata and identification of genes associated with phenylpropanoid metabolic pathways.

Larrea tridentata (Sesse and Moc. ex DC.) Coville (family: Zygophyllaceae) is an aromatic evergreen shrub with resin-covered leaves, known to use in traditional medicine for diverse ailments. It also has immense pharmacological significance due to presence of powerful phenylpropanoids antioxidant, nordihydroguaiaretic acid (NDGA). The RNA sequence/transcriptome analyses connect the genomic information into the discovery of gene function. Hence, the acquaint analysis of L. tridentata is in lieu to characterize the transcriptome, and to identify the candidate genes involved in the phenylpropanoid biosynthetic pathway. To gain molecular insight, the bioinformatics analysis of transcriptome was performed. The total bases covered 48,630 contigs of length greater than 200 bp and above came out to 21,590,549 with an average GC content of 45% and an abundance of mononucleotide, SSR, including C3H, FAR1, and MADS transcription gene families. The best enzyme commission (EC) classification obtained from the assembled sequences represented major abundant enzyme classes e.g., RING-type E3 ubiquitin transferase and non-specific serine/threonine protein kinase. The KEGG pathway analysis mapped into 377 KEGG different metabolic pathways. The enrichment of phenylpropanoid biosynthesis pathways (22 genes i.e., phenylalanine ammonia-lyase, trans-cinnamate 4-monooxygenase, 4-coumarate-CoA ligase, cinnamoyl-CoA reductase, beta-glucosidase, shikimate O-hydroxycinnamoyl transferase, 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase, cinnamyl-alcohol dehydrogenase, peroxidase, coniferyl-alcohol glucosyltransferase, caffeoyl shikimate esterase, caffeoyl-CoA O-methyltransferase, caffeate O-methyltransferase, coniferyl-aldehyde dehydrogenase, feruloyl-CoA 6-hydroxylase, and ferulate-5-hydroxylase), and expression profile indicated antioxidant, anti-arthritic, and anticancer properties of L. tridentata. The present results could provide an important resource for squeezing biotechnological applications of L. tridentata.

Reactive Oxygen Species-Mediated Cytotoxicity in Liver Carcinoma Cells Induced by Silver Nanoparticles Biosynthesized Using Schinus molle Extract.

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is ranked as the third most common cause of cancer-related mortality worldwide. Schinus molle (S. mole) L. is an important medicinal plant that contains many bioactive compounds with pharmacological properties. The role of S. molle leaf extract in the biosynthesis of silver nanoparticles (AgNPs) was determined. The biosynthesized AgNPs were thoroughly characterized by UV-vis spectrophotometry, transmission electron microscopy (TEM), X-ray diffraction (XRD), and dynamic light scattering (DLS) techniques. Furthermore, the cytotoxic effect of the biosynthesized AgNPs using S. molle (SMAgNPs) against HepG2 liver cancer cells was investigated. Reactive oxygen species generation, apoptosis induction, DNA damage, and autophagy activity were analyzed. The results clearly showed that the biosynthesized silver nanoparticles inhibited the proliferation of HepG2 by significantly (p < 0.05) inducing oxidative stress, cytotoxicity, DNA damage, apoptosis, and autophagy in a dose- and time-dependent manner. These findings may encourage integrating the potential of natural products and the efficiency of silver nanoparticles for the fabrication of safe, environmentally friendly, and effective anticancer agents.

Artesunate induces substantial topological alterations in the SARS-CoV-2 Nsp1 protein structure.

The need for novel antiviral treatments for coronavirus disease 2019 (COVID-19) continues with the widespread infections and fatalities throughout the world. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the deadly disease, relies on the non-structural protein Nsp1 for multiplication within the host cells and disarms the host immune defences by various mechanisms. Herein, we investigated the potential of artemisinin and its derivatives as possible inhibitors of SARS-CoV-2 Nsp1 through various computational approaches. Molecular docking results show that artemisinin (CID68827) binds to Nsp1 with a binding energy of -6.53 kcal/mol and an inhibition constant of 16.43 µM. The top 3 derivatives Artesunate (CID6917864), Artemiside (CID53323323) and Artemisone (CID11531457) show binding energies of -7.92 kcal/mol, -7.46 kcal/mol and -7.36 kcal/mol respectively. Hydrophobic interactions and hydrogen bonding with Val10, Arg11, and Gln50 helped to stabilize the protein-ligand complexes. The pharmacokinetic properties of these molecules show acceptable properties. The geometric parameters derived from large-scale MD simulation studies provided insights into the changes in the structural topology of Nsp1 upon binding of Artesunate. Thus, the findings of our research highlight the importance of artemisinin and its derivatives in the development of drugs to inhibit SARS-CoV-2 Nsp1 protein.

Identification of Novel Drug Candidates for the Inhibition of Catalytic Cleavage Activity of Coronavirus 3CL-like Protease Enzyme.

BACKGROUND: There has been tremendous pressure on healthcare facilities globally due to the recent emergence of novel coronavirus infection known as COVID-19 and its rapid spread across the continents. The lack of effective therapeutics for the management of the pandemic calls for the discovery of new drugs and vaccines. OBJECTIVE: In the present study, a chemical library was screened for molecules against three coronavirus 3CL-like protease enzymes (SARS-CoV-2 3CLpro, SARS-CoV 3CLpro and MERS-CoV 3CLpro), which are a key player in the viral replication cycle. METHODS: Extensive computational methods such as virtual screening and molecular docking were employed in this study. RESULTS: Two lead molecules, ZINC08825480 (4-bromo-N'-{(E)-[1-phenyl-3-(pyridin-3-yl)-1H-pyrazol- 4-yl]methylidene}benzene-1-sulfonohydrazide) and ZINC72009942 (N-[[2-[[(3S)-3-methyl-1-piperidyl] methyl]phenyl]methyl]-6-oxo-1-(p-tolyl)-4,5-dihydro-1,2,4-triazine-3-carboxamide), were identified with better affinity with the three target enzymes as compared to the approved antiviral drugs. Both the lead molecules possessed favorable drug-like properties, fit well into the active site pocket close to His- Cys dyad and showed a good number of hydrogen bonds with the backbone as well as side chains of key amino acid residues. CONCLUSION: Thus, the present study offers two novel chemical entities against coronavirus infections which can be validated through various biological assays.

Molecular modelling studies unveil potential binding sites on human serum albumin for selected experimental and in silico COVID-19 drug candidate molecules.

Human serum albumin (HSA) is the most prevalent protein in the blood plasma which binds an array of exogenous compounds. Drug binding to HSA is an important consideration when developing new therapeutic molecules, and it also aids in understanding the underlying mechanisms that govern their pharmacological effects. This study aims to investigate the molecular binding of coronavirus disease 2019 (COVID-19) therapeutic candidate molecules to HSA and to identify their putative binding sites. Binding energies and interacting residues were used to evaluate the molecular interaction. Four drug candidate molecules (ß-D-N4-hydroxycytidine, Chloroquine, Disulfiram, and Carmofur) demonstrate weak binding to HSA, with binding energies ranging from -5 to -6.7 kcal/mol. Ivermectin, Hydroxychloroquine, Remdesivir, Arbidol, and other twenty drug molecules with binding energies ranging from -6.9 to -9.5 kcal/mol demonstrated moderate binding to HSA. The strong HSA binding drug candidates consist of fourteen molecules (Saquinavir, Ritonavir, Dihydroergotamine, Daclatasvir, Paritaprevir etc.) with binding energies ranging from -9.7 to -12.1 kcal/mol. All these molecules bind to different HSA subdomains (IA, IB, IIA, IIB, IIIA, and IIIB) through molecular forces such as hydrogen bonds and hydrophobic interactions. Various pharmacokinetic properties (gastrointestinal absorption, blood-brain barrier permeation, P-glycoprotein substrate, and cytochrome P450 inhibitor) of each molecule were determined using SwissADME program. Further, the stability of the HSA-ligand complexes was analyzed through 100 ns molecular dynamics simulations considering various geometric properties. The binding free energy between free HSA and compounds were calculated using Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) approach. The findings of this study might be useful in understanding the mechanism of COVID-19 drug candidates binding to serum albumin protein, as well as their pharmacodynamics and pharmacokinetics.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India).

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor.

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread around the world jeopardizing the global economy and health. The rapid proliferation and infectivity of the virus can be attributed to many accumulating mutations in the spike protein leading to continuous generation of variants. The spike protein is a glycoprotein that recognizes and binds to cell surface receptor known as angiotensin-converting enzyme 2 (ACE2) leading to the fusion of the viral and host cell membranes and entry into the host cells. These circulating variants in the population have greatly impacted the virulence, transmissibility, and immunological evasion of the host. The present study is aimed at understanding the impact of the major mutations (L452R, T478K and N501Y) in the receptor-binding domain (RBD) of spike protein and their consequences on the binding affinity to human ACE2 through protein-protein docking and molecular dynamics simulation approaches. Protein-protein docking and Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) binding free energy analysis reveal that the spike mutants-L452R, T478K and N501Y have a higher binding affinity to human ACE2 as compared to the native spike protein. The increase in the number of interface residues, interface area and intermolecular forces such as hydrogen bonds, salt bridges and non-bonded contacts corroborated with the increase in the binding affinity of the spike mutants to ACE2. Further, 75 ns all-atom molecular dynamics simulation investigations show variations in the geometric properties such as root mean square deviation (RMSD), radius of gyration (Rg), total solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs) in the mutant spike:ACE2 complexes with respect to the native spike:ACE2 complex. Therefore, the findings of this study unravel plausible molecular mechanisms of increase in binding affinity of spike mutants (L452R, T478K and N501Y) to human ACE2 leading to higher virulence and infectivity of emerging SARS-CoV-2 variants. The study will further aid in designing novel therapeutics targeting the interface residues between spike protein and ACE2 receptor.

An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19.

The recent outbreak of the deadly coronavirus disease 19 (COVID-19) pandemic poses serious health concerns around the world. The lack of approved drugs or vaccines continues to be a challenge and further necessitates the discovery of new therapeutic molecules. Computer-aided drug design has helped to expedite the drug discovery and development process by minimizing the cost and time. In this review article, we highlight two important categories of computer-aided drug design (CADD), viz., the ligand-based as well as structured-based drug discovery. Various molecular modeling techniques involved in structure-based drug design are molecular docking and molecular dynamic simulation, whereas ligand-based drug design includes pharmacophore modeling, quantitative structure-activity relationship (QSARs), and artificial intelligence (AI). We have briefly discussed the significance of computer-aided drug design in the context of COVID-19 and how the researchers continue to rely on these computational techniques in the rapid identification of promising drug candidate molecules against various drug targets implicated in the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The structural elucidation of pharmacological drug targets and the discovery of preclinical drug candidate molecules have accelerated both structure-based as well as ligand-based drug design. This review article will help the clinicians and researchers to exploit the immense potential of computer-aided drug design in designing and identification of drug molecules and thereby helping in the management of fatal disease.

Molecular docking and dynamics simulation study of bioactive compounds from Ficus carica L. with important anticancer drug targets.

Ficus carica L., commonly known as fig, has been used in traditional medicine for metabolic disorders, cardiovascular diseases, respiratory diseases and cancer. Various bioactive compounds have been previously isolated from the leaves, fruit, and bark, which have different pharmacological properties, but the anticancer mechanisms of this plant are not known. In the current study we focused on understanding the probable mechanisms underlying the anticancer activity of F. carica plant extracts by molecular docking and dynamic simulation approaches. We evaluated the drug-likeness of the active constituents of the plant and explored its binding affinity with selected anticancer drug target receptors such as cyclin-dependent kinase 2 (CDK-2), cyclin-dependent kinase 6 (CDK-6), topoisomerase-I (Topo I), topoisomerase-II (Topo II), B-cell lymphoma 2 (Bcl-2), and vascular endothelial growth factor receptor 2 (VEGFR-2). In silico toxicity studies revealed that thirteen molecules out of sixty-eight major active compounds in the plant extract have acceptable drug-like properties. Compound 37 (ß-bourbonene) has a good binding affinity with the majority of drug targets, as revealed by molecular docking studies. The complexes of the lead molecules with the drug receptors were stable in terms of molecular dynamics simulation derived parameters such as root mean square deviation and radius of gyration. The top ten residues contributing significantly to the binding free energies were deciphered through analysis of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA). Thus, the results of our studies unravel the potential of F. carica bioactive compounds as anticancer candidate molecules against selected macromolecular receptors.

Identification of potential SARS-CoV-2 entry inhibitors by targeting the interface region between the spike RBD and human ACE2.

Coronavirus disease 2019 (COVID-19) is a fatal infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The virus infection is initiated upon recognition and binding of the spike (S) protein receptor-binding domain (RBD) to the host cell surface receptor, angiotensin-converting enzyme 2 (ACE2). Blocking the interaction between S protein and ACE2 receptor is a novel approach to prevent the viral entry into the host cell. The present study is aimed at the identification of small molecules which can disrupt the interaction between SARS-CoV-2 S protein and human ACE2 receptor by binding to the interface region. A chemical library consisting of 1,36,191 molecules were screened for drug-like compounds based on Lipinski's rule of five, Verber's rule and in silico toxicity parameters. The filtered drug-like molecules were next subjected to molecular docking in the interface region of RBD. The best three hits viz; ZINC64023823, ZINC33039472 and ZINC00991597 were further taken for molecular dynamics (MD) simulation studies and binding free energy evaluations using Molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and Molecular mechanics-Generalized Born surface area (MM-GBSA). The protein-ligand complexes showed stable trajectories throughout the simulation time. ZINC33039472 exhibited binding free energy value lower as compared to the control (emodin) with a higher contribution by gas-phase energy and van der Waals energy to the total binding free energy. Thus, ZINC33039472 is identified to be a promising interfacial binding molecule which can inhibit the interaction between the viral S protein and human ACE2 receptor which would consequently help in the management of the disease.