Withaferin A for COVID-19: a Network Pharmacology Approach.

COVID-19 has become a global challenge as there are very few treatment options available. This has proved to impact several physiological implications like immunological injury, myocardial infarction, micro-thrombus formation, neurological complications and multi-organ dysfunction. A combination therapy or a systems pharmacology approach can be adopted to fight against COVID-19.

Structural analysis and molecular dynamics simulation studies of HIV-1 antisense protein predict its potential role in HIV replication and pathogenesis.

The functional significance of the HIV-1 Antisense Protein (ASP) has been a paradox since its discovery. The expression of this protein in HIV-1-infected cells and its involvement in autophagy, transcriptional regulation, and viral latency have sporadically been reported in various studies. Yet, the definite role of this protein in HIV-1 infection remains unclear.

Target prioritization of novel substituted 5-aryl-2-oxo-/thioxo-2,3-dihydro-1-benzo[6,7]chromeno[2,3-]pyrimidine-4,6,11(5)-triones as anticancer agents using approach.

Cancer is a multi-origin collection of diseases attributed by abnormal and uncontrolled cell growth spread from origin to other parts of body eventually leading to death. After decades of research, anticancer drug therapy is still very much limited to inhibiting growth and controlling the spread of tumour cells. Finding novel molecular targets and drug candidates using assimilation of experimental and computational approaches is among the recent strategies adopted by researchers to speed up the anticancer drug discovery process.

Interaction Studies of Withania Somnifera's Key Metabolite Withaferin A with Different Receptors Assoociated with Cardiovascular Disease.

Withania somnifera commonly known as Ashwagandha in India is used in many herbal formulations to treat various cardiovascular diseases. The key metabolite of this plant, Withaferin A was analyzed for its molecular mechanism through docking studies on different targets of cardiovascular disease. Six receptor proteins associated with cardiovascular disease were selected and interaction studies were performed with Withaferin A using AutoDock Vina.

Draft Genome Sequence of a Nitrate- and Phosphate-Removing Bacillus sp., WBUNB009.

The draft genome sequence (5,868,741 bp) of a nitrate- and phosphate-removing sp., WBUNB009, isolated from a raw sewage canal in nitrate broth (Himedia M439) with a G+C content of 34.9% is reported.

Draft Genome Sequence of a Phosphate-Accumulating Bacillus sp., WBUNB004.

The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive sp. with optimum growth at 37°C and pH 7 in nitrate broth (HiMedia M439) isolated from rhizosphere of a water lily, with a genome size of 5,465,157 bp and a G+C content of 35.0%, is reported here.

Multiple pathways carry signals from short-wavelength-sensitive ('blue') cones to the middle temporal area of the macaque.

We recorded spike activity of single neurones in the middle temporal visual cortical area (MT or V5) of anaesthetised macaque monkeys. We used flashing, stationary spatially circumscribed, cone-isolating and luminance-modulated stimuli of uniform fields to assess the effects of signals originating from the long-, medium- or short- (S) wavelength-sensitive cone classes. Nearly half (41/86) of the tested MT neurones responded reliably to S-cone-isolating stimuli.

Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies.

Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta.

Molecular modeling and molecular dynamics simulation studies of Delta-Notch complex.

Notch is a single-pass transmembrane receptor protein which is composed of a short extracellular region, a single-pass transmembrane domain and a small intracellular region. Notch ligand like Delta, member of the DSL protein family, is also single-pass transmembrane protein. It has been demonstrated that of the 36 EGF repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta.

Two models of Smad4 and Hoxa9 complex are proposed: structural and interactional perspective.

Transforming growth factor-beta superfamily growth factors (TGF-β) regulate a diverse range of cellular functions, including proliferation, differentiation, extracellular matrix secretion and cell adhesion. TGF-β is also one of the most abundant of the known growth factors. Osteopontin (OPN), the major non-collagenous bone matrix protein is a secreted, arginine-glycine-aspertate containing phosphorylated glycoprotein.

20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: water interaction and DNA structure analysis.

Homeodomains are one of the important families of eukaryotic DNA-binding motifs and provide an important model system for studying protein-DNA interactions. The crystal structure and NMR structure of the antennapedia homeodomain-DNA complex and comparison between them is available. Although earlier works have shown that the direct contacts and water mediated contacts are important for the binding and specificity.

Segregation of short-wavelength-sensitive (S) cone signals in the macaque dorsal lateral geniculate nucleus.

An important problem in the study of the mammalian visual system is whether functionally different retinal ganglion cell types are anatomically segregated further up along the central visual pathway. It was previously demonstrated that, in a New World diurnal monkey (marmoset), the neurones carrying signals from the short-wavelength-sensitive (S) cones [blue-yellow (B/Y)-opponent cells] are predominantly located in the koniocellular layers of the dorsal lateral geniculate nucleus (LGN), whereas the red-green (R/G)-opponent cells carrying signals from the medium- and long-wavelength-sensitive cones are segregated in the parvocellular layers. Here, we used extracellular single-unit recordings followed by histological reconstruction to investigate the distribution of color-selective cells in the LGN of the macaque, an Old World diurnal monkey.

Solution-phase synthesis of a diverse isocoumarin library.

The solution-phase synthesis of a 167-member library of isocoumarins is described. The key intermediates for library generation, 4-iodoisocoumarins, are easily prepared by iodocyclization of the corresponding 2-(1-alkynyl)arenecarboxylate esters. The 4-iodoisocoumarins undergo palladium-catalyzed Sonogashira, Suzuki-Miyura, and Heck reactions to yield a diverse set of isocoumarins.

Palladium- and copper-catalyzed solution phase synthesis of a diverse library of isoquinolines.

The solution-phase synthesis of a 111 member isoquinoline library is described. The isoquinoline scaffold has been accessed through the palladium- and copper-catalyzed cyclization of iminoalkynes and the palladium-catalyzed iminoannulation of internal alkynes, followed by diversification of hydroxyl functionality where it is present.

On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes.

Synonymous codon usage analysis between thermophilic and mesophilic prokaryotes has gained wide attention in recent years. Although it is known that thermophilic and mesophilic prokaryotes use different subset of synonymous codons, no reason for this difference is known so far. In the present communication, by analyzing a large number of thermophilic and mesophilic prokaryotes, we provide evidence that bias in the selection of synonymous codons between thermophilic and mesophilic prokaryotes is related to differential folding pattern of mRNA secondary structures.

A practical method for the synthesis of indolylaryl- and bisindolylmaleimides.

[reaction: see text] Indolylaryl and indolylheteroarylmaleimides, including bisindolylmaleimides, are easily prepared by the reaction of N-methylindole-3-glyoxylamide with methyl aryl acetates in the presence of potassium tert-butoxide in THF.

A simple approach for indexing the oral druglikeness of a compound: discriminating druglike compounds from nondruglike ones.

A knowledge-based simple score has been developed for indexing the oral druglikeness of compounds based on the concept that oral druglikeness should be independent of the drug targets and, thus, are closely related to the global absorption, distribution, metabolism, and excretion related properties. We have considered several simple molecular descriptors as the key determinants of druglikeness. The patterns of the distributions of these molecular descriptors for a set of drug molecules have been extracted using a nonlinear neural network method.

Direct binding of Cu(II)-complexes of oxicam NSAIDs with DNA backbone.

Drugs belonging to the non-steroidal anti-inflammatory drug group (NSAID) are not only used as anti-inflammatory and analgesic agents, but also exhibit chemopreventive and chemosuppressive effects on various cancer cell lines. They exert their anticancer effects by inhibiting both at the protein level and/or at the transcription level. Cu(II) complexes of these NSAIDs show better anti-cancer effects than the bare drugs.

Exploring the potential of complex formation between a mutant DNA and the wild type protein counterpart: a MM and MD simulation approach.

We have demonstrated that the methods of molecular modeling and molecular dynamics simulation might be used to assess whether a specific mutation in the DNA would destabilize a known DNA-protein complex. The approach is based on probing the changes in the interaction that would be induced into the complex if within the already formed wild type complex the mutation could be introduced. We have used Hoxc8-DNA complex as a test system where it is known that the Hoxc8 binding affinity of the DNA is completely lost upon mutation of the DNA by replacing TAAT stretch to GCCG.

Interaction of oxicam NSAIDs with DMPC vesicles: differential partitioning of drugs.

Small unilamellar vesicles (SUVs) formed by the dimyristoylphosphatidylcholine (DMPC), a phospholipid; serve as a membrane mimetic system that can be used to study the effect of absence of net surface charges on drug-membrane interaction. The targets of non-steroidal anti-inflammatory drugs (NSAIDs) are cyclooxygenases, which are membrane active enzymes. Hence, to approach their targets NSAIDs have to pass different bio-membranes.

Homology modeling based solution structure of Hoxc8-DNA complex: role of context bases outside TAAT stretch.

The 3D structure of neither Hoxc8 nor Hoxc8-DNA complex is known. The repressor protein Hoxc8 binds to the TAAT stretch of the promoter of the osteopontin gene and modulates its expression. Over expression of the osteopontin gene is related to diseases like osteoporosis, multiple sclerosis, cancer et cetera.

Revision and confirmation of the regiochemistry of isoxazoles derived from methyl oleanonate and lanost-8-en-3-one. Synthesis of a new lanostane triterpenoid with a cyano-enone functionality in ring A.

It was previously reported that methyl oleanonate (5) and lanost-8-en-3-one (10) give predominantly [3,2-c]isoxazoles. On the contrary, we have confirmed that both compounds 5 and 10 do not give [3,2-c]isoxazoles but rather afford regioselectively [2,3-d]isoxazoles in good yields. Consequently, a new lanostane triterpenoid with a cyano-enone functionality in ring A was synthesized in two steps from the corresponding [2,3-d]isoxazole, which is interesting from the perspective of biological activity because lanosterol is the biogenetic precursor of steroids.

Stabilization and improvement of catalytic activity of a low molar mass cellobiase by cellobiase-sucrase aggregation in the culture filtrate of Termitomyces clypeatus.

The extracellular cellobiase (EC 3.2.1.