Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition.

Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6'-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski's rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go-go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.

Sakuranetin and its therapeutic potentials - a comprehensive review.

Sakuranetin (SKN), a naturally derived 7-O-methylated flavonoid, was first identified in the bark of the cherry tree (Prunus spp.) as an aglycone of sakuranin and then purified from the bark of Prunus puddum. It was later reported in many other plants including Artemisia campestris, Boesenbergia pandurata, Baccharis spp., Betula spp., Juglans spp., and Rhus spp. In plants, it functions as a phytoalexin synthesized from its precursor naringenin and is the only known phenolic phytoalexin in rice, which is released in response to different abiotic and biotic stresses such as UV-irradiation, jasmonic acid, cupric chloride, L-methionine, and the phytotoxin coronatine. Till date, SKN has been widely reported for its diverse pharmacological benefits including antioxidant, anti-inflammatory, antimycobacterial, antiviral, antifungal, antileishmanial, antitrypanosomal, glucose uptake stimulation, neuroprotective, antimelanogenic, and antitumor properties. Its pharmacokinetics and toxicological properties have been poorly understood, thus warranting further evaluation together with exploring other pharmacological properties such as antidiabetic, neuroprotective, and antinociceptive effects. Besides, in vivo studies or clinical investigations can be done for proving its effects as antioxidant and anti-inflammatory, antimelanogenic, and antitumor agent. This review summarizes all the reported investigations with SKN for its health-beneficial roles and can be used as a guideline for future studies.

Synergistic Role of Thymoquinone on Anticancer Activity of 5-Fluorouracil in Triple Negative Breast Cancer Cells.

BACKGROUND: Triple Negative Breast Cancer (TNBC) is considered as the most deadly subtype of breast cancer, because of heterogeneity, less treatment options and resistance to chemotherapy. OBJECTIVE: To find out an efficient chemotherapeutic options, in this study we have investigated the combined therapy of 5-Fluorouracil (5-FU) and thymoquinone (TQ) against TNBC cell lines BT-549 and MDA-MB-231. METHODS: We have tested 5-FU and TQ alone and in combination (5-FU + TQ) to observe the cellular growth, cell cycle and apoptosis status of BT-549 and MDA-MB-231 cells. Also we have measured the mRNA level expression of genes related to cell cycle and apoptosis. RESULTS: Experimental results suggest that both of 5-FU and TQ are effective in controlling cell growth, cell cycle and inducing apoptosis, but their combination is much more effective. 5-FU was found to be more effective in controlling cell growth, while TQ was found to be more effective in inducing apoptosis, but in both cases, their combination was most effective. TQ was found more effective in increasing and BAX/BCL-2 ratio, while 5-FU was more effective in inhibiting thymidylate synthase. They showed significant increasing effects on caspases and P53 and decreasing effect on CDK-2, where their combination was found most effective. CONCLUSION: Thus, TQ and 5-FU probably showed synergistic effect on both of cell cycle and apoptosis of tested TNBC cell lines. Our study reveals that TQ can synergise 5-FU action, and increase its anticancer efficiency against TNBC cells, which might be good choice in drug development for TNBC treatment.

Nature-Derived Hit, Lead, and Drug-Like Small Molecules: Current Status and Future Aspects Against Key Target Proteins of Coronaviruses.

BACKGROUND: COVID-19 pandemic, the most unprecedented event of the year 2020, has brought millions of scientists worldwide in a single platform to fight against it. Though several drugs are now in the clinical trial, few vaccines are available on the market already, but the lack of an effect of those is making the situation worse. AIM OF THE STUDY: In this review, we demonstrated comprehensive data of natural antiviral products showing activities against different proteins of Human Coronaviruses (HCoV) that are responsible for its pathogenesis. Furthermore, we categorized the compounds into the hit, lead, and drug based on the IC50/EC50 value, drug-likeness, and lead-likeness test to portray their potentiality to be a drug. We also demonstrated the present status of our screened antiviral compounds with respect to clinical trials and reported the lead compounds that can be promoted to clinical trial against COVID-19. METHODS: A systematic search strategy was employed focusing on Natural Products (NPs) with proven activity (in vitro, in vivo, or in silico) against human coronaviruses, in general, and data were gathered from databases like PubMed, Web of Science, Google Scholar, SciVerse, and Scopus. Information regarding clinical trials retrieved from the Clinical Trial Database. RESULTS: Total "245" natural compounds were identified initially from the literature study. Among them, Glycyrrhizin, Caffeic acid, Curcumin is in phase 3, and Tetrandrine, Cyclosporine, Tacrolimus, Everolimus are in phase 4 clinical trial. Except for Glycyrrhizin, all compounds showed activity against COVID-19. CONCLUSION: In summary, our demonstrated specific small molecules with lead and drug-like capabilities clarified their position in the drug discovery pipeline and proposed future research against COVID-19.

Ziziphus oenoplia Mill.: A Systematic Review on Ethnopharmacology, Phytochemistry and Pharmacology of an Important Traditional Medicinal Plant.

BACKGROUND: Ziziphus oenoplia Mill. (Family- Rhamnaceae) an important shrub, often found throughout the hot regions of tropical Asia and northern Australia, is commonly well known as Jackal jujube in English. It is a folk herbal medicine used as an abdominal pain killer and antidiarrhoeal agent. OBJECTIVE: The review aims to provide up-to-date information on the vernacular information, botanical characterization, distribution, ethnopharmacological uses, pharmacological activities, and chemical constituents of Z. oenoplia for possible exploitation of treatment for various diseases and to suggest future investigations. METHODS: This review was performed by studying online resources relating to Z. oenoplia and diverse resources, including scientific journals, books, and worldwide accepted databases from which information was assembled to accumulate significant information and relevant data in one place. RESULTS: Investigations on Z. oenoplia have been focused on its pharmacological activities, including its antimicrobial, antidiabetic, antihepatotoxic, antiulcer, antiplasmodial, anticancer, wound healing, anthelmintic, antioxidant, analgesic and antinociceptive, hypolipidemic activity, anti-inflammatory, immunomodulatory and antidiarrheal activities. Phytochemical studies resulted in the isolation of fatty acids, flavonoids, phenols, pentacyclic triterpenes, hydroxycarboxylic acids, aliphatic hydroxy ether, and cyclopeptide alkaloids. CONCLUSION: Most of the ethnopharmacological relevance of Z. oenoplia is justified, but more studies are needed. Further investigations are necessary to fully understand the mode of action of the active constituents and to exploit its preventive and therapeutic potentials.

GreenMolBD: Nature Derived Bioactive Molecules' Database.

BACKGROUND: One of the essential resources for developing new drugs are naturally derived biologically active lead compounds. Biomedical researchers and pharmaceutical companies are highly interested in these plant-derived molecules to develop the new drug. In this process, collective information of the plants and their phytoconstituents with different properties and descriptors would greatly benefit the researchers to identify the hit, lead or drug-like compound. AIM AND OBJECTIVE: Therefore, the work intended to develop a unique and dynamic database Green- MolBD to provide collective information regarding medicinal plants, such as their profile, chemical constituents, and pharmacological evidence. We also aimed to present information of phytoconstituents, such as in silico description, quantum, drugability and biological target information. METHODS: For data mining, we covered all accessible literature and books, and for in silico analysis, we employed a variety of well-known software and servers. The database is integrated by MySQL, HTML, PHP and JavaScript. RESULTS: GreenMolBD is a freely accessible database and searchable by keywords, plant name, synonym, common name, family name, family synonym, compound name, IUPAC name, InChI Key, target name, and disease name. We have provided a complete profile of individual plants and each compound's physical, quantum, drug likeliness, and toxicity properties (48 type's descriptor) using in silico tools. A total of 1846 associated targets related to 6,864 compounds already explored in different studies are also incorporated and synchronized. CONCLUSION: This is the first evidence-based database of bioactive molecules from medicinal plants specially grown in Bangladesh, which may help explore and foster nature-inspired rational drug discovery.

Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.

Biological Role of AKT and Regulation of AKT Signaling Pathway by Thymoquinone: Perspectives in Cancer Therapeutics.

BACKGROUND: AKT/PKB is an important enzyme with numerous biological functions, and its overexpression is related to carcinogenesis. AKT stimulates different signaling pathways that are downstream of activated tyrosine kinases and phosphatidylinositol 3-kinase, hence functions as an important target for anti-cancer drugs. OBJECTIVE: In this review article, we have interpreted the role of AKT signaling pathway in cancer and the natural inhibitory effect of Thymoquinone (TQ) in AKT and its possible mechanisms. METHOD: We have collected the updated information and data on AKT, its role in cancer and the inhibitory effect of TQ in AKT signaling pathway from Google Scholar, PubMed, Web of Science, Elsevier, Scopus, and many more. RESULTS: Many drugs are already developed, which can target AKT, but very few among them have passed clinical trials. TQ is a natural compound, mainly found in black cumin, which has been found to have potential anti-cancer activities. TQ targets numerous signaling pathways, including AKT, in different cancers. In fact, many studies revealed that AKT is one of the major targets of TQ. The preclinical success of TQ suggests its clinical studies on cancer. CONCLUSION: This review article summarizes the role of AKT in carcinogenesis, its potent inhibitors in clinical trials, and how TQ acts as an inhibitor of AKT and TQ's future as a cancer therapeutic drug.

Adhatoda vasica (Nees.): A Review on its Botany, Traditional uses, Phytochemistry, Pharmacological Activities and Toxicity.

BACKGROUND: Adhatoda vasica (Nees.) of the family Acanthaceae has been used in the Southeast tropical zone as it is efficacious against headache, colds, cough, whooping cough, fever, asthma, dyspnea, phthisis, jaundice, chronic bronchitis, and diarrhea. It exhibits commendable pharmacological activities. OBJECTIVE: The aim of the review is to provide a systematic overview of pharmacological activities with toxicity and clinical assessment, phytochemistry of A. vasica along with its characterization, geographical observation, phenology, traditional uses, as well as an organized representation of the findings. METHOD: The overall information of A. vasica was collected from various resources, including books, review papers, research papers, and reports which were obtained from an online search of globallyaccepted scientific databases. ChemDraw software was used to draw the compound's structure. RESULTS: Phytochemical review on A. vasica has led to the collection of 233 compounds of different types such as alkaloids, flavonoids, essential oils, terpenoids, fatty acids, phenols, etc. It is a promising source of potential phytopharmaceutical agent that exhibits diverse pharmacological activities, including antibacterial, antifungal, hepatoprotective, anti-ulcer, abortifacient, antiviral, antiinflammatory, thrombolytic, hypoglycemic, anti-tubercular, antioxidant, and antitussive activities. CONCLUSIONS: Sufficient number of studies on ethnopharmacology, traditional uses, and pharmacological activities of A. vasica are conducted. Furthermore, it is necessary to study the activity of chemical constituents for new drug design and discovery from natural products.

A Comprehensive Review on Linum usitatissimum Medicinal Plant: Its Phytochemistry, Pharmacology, and Ethnomedicinal Uses.

BACKGROUND: Linum usitatissimum or flax has been broadly utilized in numerous milieus worldwide as a primeval medicinal plant because of its health benefits in diverse types of diseases. OBJECTIVE: The objective of this review is to assemble the latest information on the botanical description, distribution, conventional uses, and biochemical constituents, along with the pharmacological activities and toxicity of flax. METHODS: For this purpose, data on Linum was accumulated from scientific journals, books, and worldwide acknowledged scientific databases via a library and electronic search. RESULTS: Phytochemical analysis showed that the major chemical constituents of L. usitatissimum are ω-3 fatty acid, phytoestrogenic-lignans (secoisolariciresinol diglucoside-SDG), phenols, flavonoids, sterols, proteins, antioxidants as well as various soluble and insoluble fibres. Among them, secoisolariciresinol diglucosides (SDG) are the major bioactive compounds of L. usitatissimum with prospective pharmacological accomplishments. Pure compounds and crude extracts isolated from L. usitatissimum exhibited significant anti-cancer, antioxidant, anti-microbial, anti-inflammatory, anti-obesity, antidiabetic, anti-diarrheal, anti-malarial, hepato-protective, reno-protective, immunosuppressive, antiarrhythmic, and cognitive effects. Studies indicated that the toxicological effect from the consumption of flaxseed is because of its cyanogenic glycosides, linatine, and cadmium, but the level does not seem to be adequately concentrated to contribute to any physiological impact. CONCLUSIONS: Further studies are expected to comprehend the detailed mode of action of its dynamic constituents as potent therapeutics and to completely reveal its preventive and healing potentials.

Brassica oleracea var. capitata f. alba: A Review on its Botany, Traditional uses, Phytochemistry and Pharmacological Activities.

BACKGROUND: Brassica oleracea var. capitata f. alba (white cabbage) is a cruciferous vegetable used as a vegetable and traditional medicine all over the world. Different preparation from several parts of the plant- roots, shoots, leaves, and the whole plant are used to treat a wide range of diseases, including diabetes, cancer, gastric, inflammation, hypertension, hypercholesterolemia, bacterial, oxidation, and obesity. OBJECTIVE: The aim of the current review is to evaluate the botany, distribution, traditional uses, phytochemistry, and pharmacological activities of B. oleracea var. capitata. Moreover, this review will guide to fill the existing gaps in information and highlight additional research prospects in the field of phytochemistry and pharmacology. METHOD: Various resources, including research papers, review papers, books, and reports, were collected to obtain overall information on Brassica oleracea var. capitata, which were obtained by an online search of worldwide-accepted scientific databases. Phytochemical constituents' structures were drawn by ChemDraw software. RESULTS: About 72 isolated phytochemical compounds of B. oleracea var. capitata have been collected from different articles, which included different types of compounds such as alkaloids, flavonoids, organic acids, glucosinolates, steroids, hydrocarbons, etc. Crude extracts and phytoconstituents of B. oleracea var. capitata have various pharmacological effects, including antidiabetic, anticancer, antihypertensive, anticholesterolemic, antioxidant, anti-inflammatory, antibacterial, anti-obesity, anticoagulant, and hepatoprotective. We have enlisted all these pharmacological data along with all the phytochemical constituents of Brassica oleracea var. capitata. CONCLUSION: The study was focused on the traditional uses, pharmacological activities, and phytochemistry of Brassica oleracea var. capitata, and the findings indicated that B. oleracea var. capitata is an important medicinal plant that shows several pharmacological effects. We hope our review of this plant will provide more basic and useful information and fill some research gaps for further investigation and drug design. Although we found some important traditional uses and pharmacological activities of Brassica oleracea var. capitata, there is insufficient work in the field of phytochemical activities.

Phytochemistry, Traditional Uses and Pharmacological Properties of Enhydra fluctuans Lour: a Comprehensive Review.

BACKGROUND: Enhydra fluctuans Lour, a tropical herb, commonly known as helencha or harkuch, belongs to the family Asteraceae. It is an edible semi-aquatic herbaceous vegetable plant with serrate leaves and grows commonly in different parts of the world. Enhydra fluctuans possesses potential pharmacological role against inflammation, cancer, diarrhea, microbial infection, diabetes, etc. Aim: This review aims to provide the most current information on the botanical characterization, distribution, traditional uses, chemical constituents, as well as the pharmacological activities of Enhydra fluctuans Lour. MATERIALS AND METHODS: The recently updated information on Enhydra fluctuans was gathered from scientific journals, books, and worldwide accepted scientific databases via a library and electronic search PubMed, Elsevier, Google Scholar, Springer, Scopus, Web of Science, Wiley online library. All of the full-text articles and abstracts related to Enhydra were screened. The most important and relevant articles were carefully chosen for study in this review. RESULTS: Crude extracts and isolated compounds of Enhydra fluctuans Lour have been reported to be pharmacologically active against cytoprotective, analgesic and anti-inflammatory, antimicrobial, anticancer, antidiarrheal, antihelmintic, CNS depressant, hepatoprotective, thrombolytic, antidiabetic, antioxidant, phagocytic and cytotoxic, and neuroprotective potential activities. DISCUSSION: Phytochemical analysis from different studies has reported Germacranolide, Sesquiterpene lactone, Flavonoid, Essential oil, Steroid, Diterpenoid, Melampolide, Sesquiterpene lactone, and Isoflavone glycoside as major compounds of Enhydra fluctuans Lour. CONCLUSION: However, more research is needed to explore the mode of action of bioactive components of the plant and its therapeutic capabilities.

Targeting kinases with thymoquinone: a molecular approach to cancer therapeutics.

Kinases are enzymes that are important for cellular functions, but their overexpression has strong connections with carcinogenesis, rendering them important targets for anticancer drugs. Thymoquinone (TQ) is a natural compound with proven anticancer activities, at least in preclinical studies. TQ can target several kinases, including phosphoinositide 3-kinase (PI3K), mitogen-activated protein kinase (MAPK), Janus kinase/signal transducers and activators of transcription (JAK/STAT), polo-like kinase 1 (PLK1), and tyrosine kinase in different cancer cells and animal models. Inhibiting the activity of kinases or suppressing their expression might be among the mechanisms of TQ anticancer activity. In this review, we discuss the role of TQ in kinase regulation in different cancer models.

A Review of Saurauia roxburghii Wall. (Actinidiacaea) as a Traditional Medicinal Plant, Its Phytochemical Study and Therapeutic Potential.

Saurauia roxburghii Wall. is an interesting plant, found growing chiefly along the eastern and south-eastern countries of Asia. The various ethnic groups of these regions use the plant as a medication for relieving a wide spectrum of diseases and conditions, including indigestion, boils, fever, gout, piles, eczema, asthma, ulcers, bronchitis, epilepsy, and hepatitis B. This review aims to appraise the vernacular information, botanical characterization, geographical distribution, traditional uses, phytochemistry, and pharmacological activities of S. roxburghii as well as to conduct a critical analysis on the findings. To understand the therapeutic potential and provide an overall idea about the ethnomedicinal practices, phytochemistry, and pharmacological activities of S. roxburghii, relevant information was collected via a library and electronic search of online journals, books, and reputed databases. Phytochemical examination revealed the presence of alkaloids, glycosides, O-glycosides, flavonoids, carbohydrates, saponins, steroids, reducing sugars, tannins, phlobatannins, and triterpenoids. The sterols were identified as Stigmasterol and beta-Sitosterol. The triterpenes were found to be Ursolic acid, Corosolic acid, Maslinic acid, 24-Hydroxy corosolic acid, 3b,7b,24-trihydroxy-urs-12-en-28-oic acid, Oleanolic acid, beta-Amyrin, cis-3-O-p-Hydroxycinnamoyl ursolic acid, trans-3-O-p- Hydroxycinnamoyl ursolic acid, and 7,24-dihydroxyursolic acid. Several in-vivo and in-vitro tests revealed anti-bacterial, anti-cancer, anti-diabetic, anti-oxidant, and anti-viral activities of the plant leaves. Detailed analysis of the information collected on S. roxburghii suggested some promising leads for future drug development. However, many scientific gaps were found in the study of this and further extensive investigation is needed to fully understand the mechanism of action of the active constituents and exploit its therapeutic promises.

Current Landscape of Natural Products against Coronaviruses: Perspectives in COVID-19 Treatment and Anti-viral Mechanism.

BACKGROUND: SARS-CoV-2 is a coronavirus, and the infection by SARS-CoV-2, termed as COVID-19, was first reported in Wuhan, China, at the end of 2019, and this outbreak became a pandemic in February of 2020. Till now, there is no effective drug or vaccine against this virus that can make a complete cure; however, a number of drugs are in trials. OBJECTIVES: In this review, we have focused on an alternative therapeutic approach using natural products utilizing the host anti-viral responses for resolving COVID-19 pathogenesis. METHODS: We have searched databases like PubMed, Scopus, Web of Science, and Google Scholar for articles related to natural products and viral diseases, with a specific focus on coronaviruses, as well as other RNA viruses and recent updates on the COVID-19 pandemic, and collected articles and reviewed them comprehensively. RESULTS: Scientific studies clarified the viral pathogenesis that involved viral entrance into host cells and anti-viral response inside the cells, which can be effectively targeted by numerous natural compounds from different sources. Many of these compounds can potentially target viral genomic material or protein machinery. Natural products that were found effective against other coronaviruses, especially SARS-CoV or MERS-CoV (which emerged in 2002 and 2012, respectively), might be effective against SARS-CoV-2 due to their structural similarities. CONCLUSION: COVID-19 pandemic is a global emergency thus, urgent drug development is necessary. Natural products can be the biggest source of drugs, as they have been found to be effective in other coronaviruses previously; however, time is required to establish the clinical success of these drugs for clinical applications.

Design of novel viral attachment inhibitors of the spike glycoprotein (S) of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) through virtual screening and dynamics.

To date, the global COVID-19 pandemic has been associated with 11.8 million cases and over 545481 deaths. In this study, we have employed virtual screening approaches and selected 415 lead-like compounds from 103 million chemical substances, based on the existing drugs, from PubChem databases as potential candidates for the S protein-mediated viral attachment inhibition. Thereafter, based on drug-likeness and Lipinski's rules, 44 lead-like compounds were docked within the active side pocket of the viral-host attachment site of the S protein. Corresponding ligand properties and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profile were measured. Furthermore, four novel inhibitors were designed and assessed computationally for efficacy. Comparative analysis showed the screened compounds in this study maintain better results than the proposed mother compounds, VE607 and SSAA09E2. The four designed novel lead compounds possessed more fascinating output without deviating from any of Lipinski's rules. They also showed higher bioavailability and the drug-likeness score was 0.56 and 1.81 compared with VE607 and SSAA09E2, respectively. All the screened compounds and novel compounds showed promising ADMET properties. Among them, the compound AMTM-02 was the best candidate, with a docking score of -7.5 kcal/mol. Furthermore, the binding study was verified by molecular dynamics simulation over 100 ns by assessing the stability of the complex. The proposed screened compounds and the novel compounds may give some breakthroughs for the development of a therapeutic drug to treat SARS-CoV-2 proficiently in vitro and in vivo.

Metal based donepezil analogues designed to inhibit human acetylcholinesterase for Alzheimer's disease.

Among neurodegenerative disorders, Alzheimer's disease (AD) is one of the most common disorders showing slow progressive cognitive decline. Targeting acetylcholinesterase (AChE) is one of the major strategies for AD therapeutics, as cholinergic pathways in the cerebral cortex and basal forebrain are compromised. Herein, we report the design of some copper and other metal based donepezil derivatives, employing density functional theory (DFT). All designed compounds are optimized at the B3LYP/SDD level of theory. Dipole moments, electronic energie, enthalpies, Gibbs free energies, and HOMO-LUMO gaps of these modified compounds are also investigated in the subsequent analysis. The molecules were then subjected to molecular docking analysis with AChE to study the molecular interactions broadly. Ensemble based docking and molecular dynamics (MD) simulations of the best candidates were also performed. Docking and MD simulation reveal that modified drugs are more potent than unmodified donepezil, where Trp86, Tyr337, Phe330 residues play some important roles in drug-receptor interactions. According to ensemble based docking, D9 shows greater binding affinity compared to the parent in most conformations obtained from protein data bank and MD simulation. In addition, it is observed that the π- π stacking with the residues of Trp86, Tyr337, Tyr341, Tyr124 and Trp286 may be required for strong ligand binding. Moreover, ADME/T analysis suggests that modified derivatives are less toxic and have improved pharmacokinetic properties than those of the parent drug. These results further confirm the ability of metal-directed drugs to bind simultaneously to the active sites of AChE and support them as potential candidates for the future treatment of Alzheimer's disease.

Identification and structural characterization of deleterious non-synonymous single nucleotide polymorphisms in the human SKP2 gene.

In SCF (Skp, Cullin, F-box) ubiquitin-protein ligase complexes, S-phase kinase 2 (SKP2) is one of the major players of F-box family, that is responsible for the degradation of several important cell regulators and tumor suppressor proteins. Despite of having significant evidence for the role of SKP2 on tumorgenesis, there is a lack of available data regarding the effect of non-synonymous polymorphisms. In this communication, the structural and functional consequences of non-synonymous single nucleotide polymorphisms (nsSNPs) of SKP2 have been reported by employing various computational approaches and molecular dynamics simulation. Initially, several computational tools like SIFT, PolyPhen-2, PredictSNP, I-Mutant 2.0 and ConSurf have been implicated in this study to explore the damaging SNPs. In total of 172 nsSNPs, 5 nsSNPs were identified as deleterious and 3 of them were predicted to be decreased the stability of protein. Guided from ConSurf analysis, P101L (rs761253702) and Y346C (rs755010517) were categorized as the highly conserved and functional disrupting mutations. Therefore, these mutations were subjected to three dimensional model building and molecular dynamics simulation study for the detailed structural consequences upon the mutations. The study revealed that P101L and Y346C mutations increased the flexibility and changed the structural dynamics. As both these mutations are located in the most functional regions of SKP2 protein, these computational insights might be helpful to consider these nsSNPs for wet-lab confirmatory analysis as well as in rationalizing future population based studies and structure based drug design against SKP2.

Structure-based identification of potent VEGFR-2 inhibitors from in vivo metabolites of a herbal ingredient.

Vascular endothelial growth factor receptor-2 (VEGFR-2) is one of the regulatory elements of angiogenesis that is expressed highly in various diseases and is also essential for solid tumor growth. The present study was aimed at identifying potent inhibitors of VEGFR-2 by considering herbal secondary metabolites; as natural molecules are less toxic than synthetic derivatives. A structure-based virtual screening protocol consisting of molecular docking, MM-GBSA and ADME/T analysis was initially used to screen a library of in vivo metabolites of the herbal ingredient. Using a fixed cutoff value, four potent virtual hits were identified from molecular docking, ADME/T and binding affinity calculations, which were considered further for molecular dynamics (MD) simulation to broadly describe the binding mechanisms to VEGFR-2. The results suggested that these molecules have high affinity for the catalytic region of VEGFR-2, and form strong hydrophobic and polar interactions with the amino acids involved in the binding site of ATP and linker regions of the catalytic site. Subsequently, the stability of the docked complexes and binding mechanisms were evaluated by MD simulations, and the energy of binding was calculated through MM-PBSA analysis. The results uncovered two virtual hits, designated ZINC14762520 and ZINC36470466, as VEGFR-2 inhibitors, and suggested that they bind to kinase domain in an ATP-competitive manner. These virtual hits will offer a suitable starting point for the further design of their various analogs, allowing a rational search for more effective inhibitors in the future. Graphical abstract.

Prospecting and Structural Insight into the Binding of Novel Plant-Derived Molecules of Leea indica as Inhibitors of BACE1.

BACKGROUND: Alzheimer disease (AD) can be considered as the most common age related neurodegenerative disorder and also an important cause of death in elderly patients. A number of studies showed the correlation of this disease pathology with BACE1 inhibitor and it is also evident that BACE1 inhibitor can function as a very potent strategy in treating AD. METHODS: In this present study, we aimed to prospect for novel plant-derived BACE1 inhibitors from Leea indica and to realise structural basis of their interactions and mechanisms using combined molecular docking and molecular dynamics based approaches. An extensive library of Leea indica plant derived molecule was compiled and computationally screened for inhibitory action against BACE1 by using virtual screening approaches. Furthermore, induced fit docking and classical molecular dynamics along with steered molecular dynamics simulations were employed to get insight of the binding mechanisms. RESULTS: Two triterpenoids, ursolic acid and lupeol were identified through virtual screening; wherein, lupeol showed better binding free energy in MM/GBSA, MM/PBSA and MM/GBVI approaches. Furthermore classical and steered dynamics revealed the favourable hydrophobic interactions between the lupeol and the residues of flap or catalytic dyadof BACE1; however, ursolic acid showed disfavorable interactions with the BACE1. CONCLUSION: This study therefore unveiled the potent BACE1 inhibitor from a manually curated dataset of Leea indica molecules, which may provide a novel dimension of designing novel BACE1 inhibitors for AD therapy.