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. Here, we have proposed withaferin A as a system pharmacophore employing molecular docking strategy using AutoDock Vina and utilising different bioinformatics tools like PharmMapper, STRING database and PANTHER Pathway enrichment analysis. Docking results show that withaferin A exhibits a significant binding affinity with P2Y12 receptor, vitamin D-binding protein and annexin A5, hence implying that it could play a role in anti-thrombosis. Protein-protein interaction network showed its importance in innate immune system. Results also show that this molecule may have significant potential to modulate T cell activation too. Text mining results showed association of STAT3 with withaferin A. Our studies propose that withaferin A might also conquer the cytokine storm via STAT3. This study concludes that two strong targets of withaferin A, i.e. vitamin D-binding protein and STAT3, have been identified and that withaferin A can be used as a system pharmacophore for drug development in order to combat COVID-associated complicacies.

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. Deciphering the 3D structure of HIV-1 ASP would throw light on its potential role in HIV lifecycle and host-virus interaction. Hence, using extensive molecular modeling and dynamics simulation for 200 ns, we predicted the plausible 3D-structures of ASP from two reference strains of HIV-1 namely, Indie-C1 (subtype-C) and NL4-3 (subtype-B) so as to derive its functional implication through structural domain analysis. In spite of sequence and structural differences in subtype B and C ASP, both structures appear to share common domains like the Von Willebrand Factor Domain-A (VWFA), Integrin subunit alpha-X (ITGSX), and ETV6-Transcriptional repressor, thereby reiterating the potential role of HIV-1 ASP in transcriptional repression and autophagy, as reported in earlier studies. Gromos-based cluster analysis of the centroid structures also reassured the accuracy of the prediction. This is the first study to elucidate a highly plausible structure for HIV-1 ASP which could serve as a feeder for further experimental validation studies.

Target prioritization of novel substituted 5-aryl-2-oxo-/thioxo-2,3-dihydro-1H-benzo[6,7]chromeno[2,3-d]pyrimidine-4,6,11(5H)-triones as anticancer agents using in-silico 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. In present study, synthesis of 40 novel substituted 5-aryl-2-oxo-/thioxo-2,3-dihydro-1H-benzo[6,7]chromeno[2,3-d]pyrimidine-4,6,11(5H)-triones has been accomplished followed by molecular target identification using different in silico approaches. The target prioritization methodology involved identification and selection of targets, molecular docking followed by molecular dynamic simulation and determination of binding free energy using MM-GBSA technique. Systematic and stepwise virtual screening of biological targets lead to identification of B-cell lymphoma 6 protein (BCL6), lysine-specific histone demethylase 1 A (LSD1), nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB P65) and poly (ADP-ribose) polymerase 1 (PARP1) as suitable anticancer targets for the set of synthesized compounds.Communicated by Ramaswamy H. Sarma.

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. CORINA was used to model the small molecules and HBAT to compute the hydrogen bonding. Among the six targets, ß1- adrenergic receptors, HMG-CoA and Angiotensinogen-converting enzyme showed significant interaction with Withaferin A. Pharmacophore modeling was done using PharmaGist to understand the pharmacophoric potential of Withaferin A. Clustering of Withaferin A with different existing drug molecules for cardiovascular disease was performed with ChemMine based on structural similarity and physicochemical properties. The ability of natural active component, Withaferin A to interact with different receptors associated with cardiovascular disease was elucidated with various modeling techniques. These studies conclusively revealed Withaferin A as a potent lead compound against multiple targets associated with cardiovascular disease.

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

The draft genome sequence of a nitrate- and phosphate-removing, Gram-positive Bacillus 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.

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 Bacillus sp., WBUNB009, isolated from a raw sewage canal in nitrate broth (Himedia M439) with a G+C content of 34.9% is reported. It removes 60.23% nitrate and 96% phosphate within 16 h at 37°C.

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. Response amplitude in the majority of the neurones tested further (19/28) was significantly reduced, though not always completely abolished, during reversible inactivation of visuotopically corresponding regions of the ipsilateral primary visual cortex (striate cortex, area V1). Thus, the present data indicate that signals originating in S-cones reach area MT, either via V1 or via a pathway that does not go through area V1. We did not find a significant difference between the mean latencies of spike responses of MT neurones to signals that bypass V1 and those that do not; the considerable overlap we observed precludes the use of spike-response latency as a criterion to define the routes through which the signals reach MT.

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. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta-Notch complex have been proposed based on interaction energy parameter and planarity studies.

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. Crystal structure of mammalian Notch extracellular ligand binding domain contains 11 and 12 EGF-like repeats. Here a portion of the Delta protein of Drosophila, known to interact with Notch extracellular domain (ECD) has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein docking method using GRAMM. MD simulations of the modeled structures were performed. The structure for Delta-Notch complex has been proposed based on interaction energy parameter and planarity studies.

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

Transforming growth factor-beta superfamily growth factors (TGF-ß) regulate a diverse range of cellular functions, including proliferation, differentiation, extracellular matrix secretion and cell adhesion. TGF-ß 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. Analysis of the OPN promoter sequence reveals both Hoxc8 and Hoxa9 (mouse homeotic gene) recognize and utilize the same consensus TAAT motif in the binding sequence to mediate the repression. Hoxa9 functions as a strong transcriptional repressor, similar to Hoxc-8 (X. Shi, X. Yang, D. Chen, Z. Chang, and X. Cao, J Biol Chem 274, 13711-13717, 1999). The DNA-binding protein Hoxa9 interacts with Smad4 (X. Shi, S. Bai, L. Li and X, and Cao X, J Biol Chem 276, 850-855, 2001), but not with Smad3 (which binds to OPN promoter), and the interaction between Smad4 and Hoxa9 results in the transcriptional activation of OPN in response to TGF- stimulation. In this paper we have proposed two possible model structures of Hoxa9 and Smad4 complex. These have been modeled based on homology modeling and a new method has been used to model the flexible loop part. Manual docking has been used to achieve the final model involving the Hoxa9 -Smad4 complex which tallies with the experimental results. We have mutated some selective important residues and looked at their effect in terms of interaction energy in complex formation in both the models.

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. The detail dynamical structural characteristics of the complex, water mediating interactions in the complex and also the detail study of the free DNA and protein has not done. In the present paper we have reported the results of 20ns MD simulation of this complex with the presence of explicit water and also the 20ns MD simulation of the protein and the DNA separately in explicit water. The results show that the complex remains stable during the last 8ns of the simulation. The part of the protein which is interacting with the DNA has fewer fluctuations than other part of the protein. The pattern of water distribution around the interacting center has a typical pattern for this complex and it is quite different from the free protein and the free DNA. Water molecules penetrate into the interacting center during the simulation. Several water bridges have been identified which is responsible for recognition but not observed in the crystal structure. The recognized DNA sequence (14 mer) has been characterized by helical and step parameters. The correlated motions of the DNA and the protein in the complexed form and the free form has been analyzed.

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. Cells were classified using cone-isolating stimuli to identify their cone inputs. Our results indicate that the majority of cells carrying signals from S-cones are located either in the koniocellular layers or in the 'koniocellular bridges' that fully or partially span the parvocellular layers. By contrast, the R/G-opponent cells are located in the parvocellular layers. We conclude that anatomical segregation of B/Y- and R/G-opponent afferent signals for color vision is common to the LGNs of New World and Old World diurnal monkeys.

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. Alternatively, isocoumarins, bearing hydroxyl or bromine functionalities, have been prepared by ZnCl(2)- and Pd(PPh(3))(4)-mediated cyclization of the corresponding o-iodobenzoic acid and appropriate terminal alkynes. The resulting isocoumarins were further diversified by derivatization of the hydroxyl or bromine groups. A small set of isoquinolinones were also prepared from the corresponding 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. Moreover, we observe that error-minimizing property has significant influence in differentiating the synonymous codon usage between thermophilic and mesophilic prokaryotes. Biological implications of these results are discussed.

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.

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. Considering the above aspects, it is of interest to see if Cu(II) complexes of these drugs can exert their effects directly at the DNA level. In this study, we have used UV-Vis spectroscopy to characterize the complexation between Cu(II) and two NSAIDs belonging to the oxicam group viz. piroxicam and meloxicam, both of which exhibit anticancer properties. For the first time, this study shows that, Cu(II)-NSAID complexes can directly bind with the DNA backbone, and the binding constants and the stoichiometry or the binding site sizes have been determined. Thermodynamic parameters from van't Hoff plots showed that the interaction of these Cu(II)-NSAID complexes with ctDNA is an entropically driven phenomenon. Circular dichroism (CD) spectroscopy showed that the binding of these Cu(II)-NSAIDs with ctDNA result in DNA backbone distortions which is similar for both Cu(II)-piroxicam and Cu(II)-meloxicam complexes. Competitive binding with a standard intercalator like ethidium bromide (EtBr) followed by CD as well as fluorescence measurements indicate that the Cu(II)-NSAID complexes could intercalate in the DNA.

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. We assumed direct correlations of these patterns to the expectation values that a given compound may behave like a drug. On the basis of this assumption, we have defined a simple druglike index or score (DLS) combining the contributions coming from the descriptors considered. This index scales the druglikeness of a compound in the range 0.0-1.0, 1.0 being the highest druglikeness. The index applied for a drug data set, a mixed data set, and three different bioactive databases produced expected features and indicated that even the marketed drugs have druglike scores varying over a considerable range. A total of 73.3% of the drugs considered showed DLS > 0.5, while it is only 44.7% for the HIC-Up compounds (unbiased ligand database). For the ChemBank, Asinex-Gold collection, and NCI databases 61.2%, 76.0%, and 79.1% of the compounds have DLS > 0.5.

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. Mutation was obtained by changing the relevant base pairs into the DNA of the model of the corresponding wild type complex developed by homology modeling and MD simulation in water for 2.0 ns. Comparison of the structure, dynamics and interactions between the hypothetical mutant model with those of the similarly refined wild type model shows that the loss of affinity of the mutant DNA to Hoxc8 has two different origins: (i) loss of several strong H-bonds as the direct consequences of mutation and (ii) reduced H-bonds in the common parts due to a net loss or inferior H-bonding geometry induced by the mutation as indirect effects. The net change in the interaction energy between the DNA and the protein in the best possible configuration indicated the experimentally observed destabilization effects. No significant change in the groove width was observed and no correlation was found between the water-bridges and the loss of affinity.

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. Different membrane parameters are expected to guide the first level of interaction of these drugs before they are presented to their targets. Our earlier studies have demonstrated the crucial role of surface charges of membrane mimetic systems like micelles and mixed micelles on the interaction of oxicam NSAIDs. In order to see whether net surface charges of membranes are essential for the interaction of oxicam NSAIDs, we have studied the incorporation of two oxicam NSAIDs, viz., piroxicam and meloxicam in DMPC vesicles using the intrinsic fluorescence properties of the drugs. To see whether different prototropic forms of the drugs can interact with DMPC vesicles, studies were carried out under different pH conditions. Transmission electron microscopy (TEM) was used to characterize the SUVs those were formed at different pH values. Steady state fluorescence anisotropy measurements show that both forms of the two drugs, viz., global neutral and anion can be incorporated into the DMPC vesicles. Partition coefficient (KP) between DMPC and the aqueous buffer used has been calculated in all cases from fluorescent intensity measurements. The KP values for the neutral and anionic forms of piroxicam are 219.0 and 25.8, respectively, and that for meloxicam are 896.7 and 110.2, respectively. From the KP values it is evident that irrespective of the nature of the prototropic forms, meloxicam has a higher KP value than piroxicam. This correlates with the previously calculated log KP values between n-octanol and aqueous phase, which demonstrates that in absence of net surface charges of DMPC vesicles the hydrophobic interaction is the principal driving force for incorporation. Our results imply that for bio-membranes having no net surface charges hydrophobic effect plays a principal role to guide these NSAIDs to their targets.