Ashoke Sharon

Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India

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Publications (84)144.93 Total impact

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    ABSTRACT: Calsequestrin (CASQ) exists as two distinct isoforms CASQ1 and CASQ2 in all vertebrates. Although the isoforms exhibit unique functional characteristic, the structural basis for the same is yet to be fully defined. Interestingly, the C-terminal region of the two isoforms exhibit significant differences both in length and amino acid composition; forming Dn-motif and DEXn-motif in CASQ1 and CASQ2 respectively. Here, we investigated if the unique C-terminal motifs possess Ca(2+) -sensitivity and affect protein function. Sequence analysis shows that both the Dn- and DEXn-motifs are intrinsically disordered regions (IDRs) of the protein, a feature that is conserved from fish to man. Using purified synthetic peptides, we show that these motifs undergo distinctive Ca(2+) -mediated folding suggesting that these disordered motifs are Ca(2+) -sensitivity. We generated chimeric proteins by swapping the C-terminal portions between CASQ1 and CASQ2. Our studies show that the C-terminal portions do not play significant role in protein folding. An interesting finding of the current study is that the switching of the C-terminal portion completely reverses the polymerization kinetics. Collectively, these data suggest that these Ca(2+) -sensitivity IDRs located at the back-to-back dimer interface influence isoform-specific Ca(2+) -dependent polymerization properties of CASQ.
    Biopolymers 08/2014; · 2.88 Impact Factor
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    ABSTRACT: High genetic variability in hepatitis C virus (HCV), emergence of drug resistant viruses and side effects demand the requirement for development of new scaffolds to show an alternate mechanism. Herein, we report discovery of new scaffold I based on 4-hydroxyamino α-pyranone carboxamide as promising anti-HCV agents. A comprehensive structure-activity relationship (SAR) was explored with several newly synthesized compounds. In all promising compounds (17-19, 21-22, 24-25, and 49) with EC50 ranging 0.15 to 0.40 μM, the aryl group at C-6 position of α-pyranone were unsubstituted. In particular, 25 demonstrated potential anti-HCV activity with EC50 of 0.18 μM in cell based HCV replicon system with lower cytotoxicity (CC50 > 20 μM) and provided a new scaffold for anti-HCV drug development. Further investigations, including biochemical characterization, are yet to be performed to elucidate its possible mode of action.
    ACS Medicinal Chemistry Letters 03/2014; 5(3):259-263. · 3.31 Impact Factor
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    ABSTRACT: The clinical management of herpes virus diseases is limited due to ineffective clearance of virus particles and frequent emergence of drug-resistant viruses, particularly in immunocompromised patients, pregnant women and neonates. In our continued quest for new antiviral lead, α-pyrone carboxamide propanol derivatives were synthesized and evaluated in HSV infected Vero cells. The compound 3d showed potent antiviral activity against HSV-IF (EC50 = 9.8 µg/ml and EC99 = 18.0 µg/ml) and HSV-2G (EC50 = 12.4 µg/ml and EC99 = 24.0 µg/ml) at 4-6 h post-infection. Further mode of action studies demonstrated that 3d did not interfere in viral attachment or penetration, however, reduced the expression of ICP4 and ICP27 (immediate-early gene products) as well as the HSV DNA polymerase.
    RSC Advances 01/2014; · 3.71 Impact Factor
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    ABSTRACT: In our continued quest for identifying novel molecules from ethnomedicinal source we have isolated an alkaloid 7-methoxy-1-methyl-4,9-dihydro-3H-pyrido[3,4-b]indole, also known as Harmaline (HM), from an ethnomedicinal herb Ophiorrhiza nicobarica. The compound exhibited a potent anti-HSV-1 activity against both wild type and clinical isolates of HSV-1. Further we demonstrated that HM did not interfere in viral entry but the recruitment of lysine-specific demethylase-1 (LSD1) and the binding of immediate-early (IE) complex on ICP0 promoter. This leads to the suppression of viral IE gene synthesis and thereby the reduced expression of ICP4 and ICP27. Moreover, HM at its virucidal concentration is nontoxic and reduced virus yields in cutaneously infected Balb/C mice. Thus, the interference in the binding of IE complex, a decisive factor for HSV lytic cycle or latency by HM reveals an interesting target for developing non-nucleotide antiherpetic agent with different mode of action than Acyclovir.
    Antiviral research 01/2014; · 3.61 Impact Factor
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    ABSTRACT: The pharmacophoric hybridization and computational design approach were applied to generate a novel series of α-pyrone analogs as plausible anti-malarial lead candidate. A putative active site in flexible loop close to wing-helix domain of PfRIO2 kinase was explored computationally to understand the molecular basis of ligand binding. All the synthesized molecules (3a-g) exhibited in vitro antimalarial activity. Oxidative stress induced by 3a-d were calculated and found to be significantly higher in case of 3b. Therefore, 3b, which shown most significant result was identified as promising lead for further SAR study to develop potent anti-malarials.
    European Journal of Medicinal Chemistry 10/2013; 70C:607-612. · 3.43 Impact Factor
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    ABSTRACT: Computer-aided approaches coupled with medicinal chemistry were used to explore novel carbocyclic nucleosides as potential anti-hepatitis C virus (HCV) agents. Conformational analyses were carried out on 6-amino-1H-pyrazolo[3,4-d]pyrimidine (6-APP)-based carbocyclic nucleoside analogues, which were considered as nucleoside mimetics to act as HCV RNA-dependent RNA polymerase (RdRp) inhibitors. Structural insight gained from the modeling studies revealed the molecular basis behind these nucleoside mimetics. The rationally chosen 6-APP analogues were prepared and evaluated for anti-HCV activity. RdRp SiteMap analysis revealed the presence of a hydrophobic cavity near C7 of the nucleosides; introduction of bulkier substituents at this position enhanced their activity. Herein we report the identification of an iodinated compound with an EC50 value of 6.6 μM as a preliminary anti-HCV lead.
    ChemMedChem 08/2013; · 2.84 Impact Factor
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    Current Diabetes Reviews 06/2013; 9(4):275-285.
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    ABSTRACT: Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70-80 Ca(2+) ions. However, the nature of Ca(2+)-binding sites has not yet been fully characterized. In this study, we employed in silico approaches to identify the Ca(2+) binding sites and to understand the molecular basis of CASQ1-Ca(2+) recognition. We built the protein model by extracting the atomic coordinates for the back-to-back dimeric unit from the recently solved hexameric CASQ1 structure (PDB id: ) and adding the missing C-terminal residues (aa350-364). Using this model we performed extensive 30 ns molecular dynamics simulations over a wide range of Ca(2+) concentrations ([Ca(2+)]). Our results show that the Ca(2+)-binding sites on CASQ1 differ both in affinity and geometry. The high affinity Ca(2+)-binding sites share a similar geometry and interestingly, the majority of them were found to be induced by increased [Ca(2+)]. We also found that the system shows maximal Ca(2+)-binding to the CAS (consecutive aspartate stretch at the C-terminus) before the rest of the CASQ1 surface becomes saturated. Simulated data show that the CASQ1 back-to-back stacking is progressively stabilized by the emergence of an increasing number of hydrophobic interactions with increasing [Ca(2+)]. Further, this study shows that the CAS domain assumes a compact structure with an increase in Ca(2+) binding, which suggests that the CAS domain might function as a Ca(2+)-sensor that may be a novel structural motif to sense metal. We propose the term "Dn-motif" for the CAS domain.
    Molecular BioSystems 04/2013; · 3.35 Impact Factor
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    ABSTRACT: Malaria is most prevalent in tropical climate and causes 1–3 million deaths annually. RIO-2 kinase, an atypical kinase regulates ribosome biogenesis and is necessary for cell cycle progression. Structural characterization of PFD0975w (PfRIO-2 kinase) indicates N-terminal DNA binding winged helix domain (1–84), a linker region (85–147), and C-terminal kinase domain (148–275). Heterocyclic compounds present in different databases represent an enormous reservoir to screen and develop the suitable inhibitor. An extensive screening of heterocyclic compounds present in zinc database, PubChem and ChemBank database was done to identify potent PfRIO-2 kinase specific inhibitors. Initial screening gave 41 compounds with high affinity toward PfRIO-2 kinase than natural substrate ATP. A substrate competition experiment and analysis of binding mode conformation within the ATP binding pocket identifies five compounds; Zc-49775260, Pc-44415375, Pc-44215930, Cb-2082655, and Cb-832054 as potential PfRIO-2 kinase inhibitors. Further analysis of top hits in ADMET parameters, Caco-2 cell permeability profile, human oral absorption, and drug-like properties indicates Pc-44215930 as the best suitable compound among the top hits. Searching top hits candidate heterocyclic compounds in the drug database picked up clindamycin, nelfinavir, methacycline, and other drugs in circulation. Most of these drugs are targeting ribosome maturation and highlights the possibility of PfRIO-2 kinase as a drug target. Hence, screening and substrate competition studies along with ADME analysis of top hit compounds allowed us to identify potential PfRIO-2 kinase inhibitors. We are hopeful that the current study will help to develop effective chemotherapy against malaria utilizing PfRIO-2 kinase as a target.
    Medicinal Chemistry Research 01/2013; · 1.61 Impact Factor
  • Biophysical Journal 01/2013; 104(2):173a. · 3.67 Impact Factor
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    ABSTRACT: Biophysical studies have shown that each molecule of calsequestrin 1 (CASQ1) can bind about 70-80 Ca2+ ions. However, the nature of Ca2+-binding sites has not yet been fully characterized. In this study, we employed in-silico approaches to identify the Ca2+ binding sites and to understand the molecular basis of CASQ1-Ca2+ recognition. We built the protein model by extracting the atomic coordinates for the back-to-back dimeric unit from the recently solved hexameric CASQ1 structure (PDB id: 3UOM) and adding the missing C-terminal residues (aa350-364). Using this model we performed extensive 30 ns molecular dynamics simulations exposed to wide range of Ca2+ concentrations ([Ca2+]). Our results show that the Ca2+-binding sites on CASQ1 differ both in affinity and geometry. The high affinity Ca2+-binding sites share a similar geometry and interestingly, majority of them were found to be induced by increased [Ca2+]. We also found that the system undergoes maximal Ca2+-binding to the CAS (consecutive asparta
    Molecular BioSystems 01/2013; · 3.35 Impact Factor
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    ABSTRACT: Herpes genitalis, caused by HSV-2, is an incurable genital ulcerative disease transmitted by sexual intercourse. The virus establishes life-long latency in sacral root ganglia and reported to have synergistic relationship with HIV-1 transmission. Till date no effective vaccine is available, while the existing therapy frequently yielded drug resistance, toxicity and treatment failure. Thus, there is a pressing need for non-nucleotide antiviral agent from traditional source. Based on ethnomedicinal use we have isolated a compound 7-methoxy-1-methyl-4,9-dihydro-3H-pyrido[3,4-b]indole (HM) from the traditional herb Ophiorrhiza nicobarica Balkr, and evaluated its efficacy on isolates of HSV-2 in vitro and in vivo. The cytotoxicity (CC50), effective concentrations (EC50) and the mode of action of HM was determined by MTT, plaque reduction, time-of-addition, immunofluorescence (IFA), Western blot, qRT-PCR, EMSA, supershift and co-immunoprecipitation assays; while the in vivo toxicity and efficacy was evaluated in BALB/c mice. The results revealed that HM possesses significant anti-HSV-2 activity with EC50 of 1.1-2.8 µg/ml, and selectivity index of >20. The time kinetics and IFA demonstrated that HM dose dependently inhibited 50-99% of HSV-2 infection at 1.5-5.0 µg/ml at 2-4 h post-infection. Further, HM was unable to inhibit viral attachment or penetration and had no synergistic interaction with acyclovir. Moreover, Western blot and qRT-PCR assays demonstrated that HM suppressed viral IE gene expression, while the EMSA and co-immunoprecipitation studies showed that HM interfered with the recruitment of LSD-1 by HCF-1. The in vivo studies revealed that HM at its virucidal concentration was nontoxic and reduced virus yield in the brain of HSV-2 infected mice in a concentration dependent manner, compared to vaginal tissues. Thus, our results suggest that HM can serve as a prototype to develop non-nucleotide antiviral lead targeting the viral IE transcription for the management of HSV-2 infections.
    PLoS ONE 01/2013; 8(10):e77937. · 3.53 Impact Factor
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    ABSTRACT: The structure-based approaches were implemented to design and rationally select the molecules for synthesis and anti-HCV activity evaluation. The systematic structure-activity relationships of previously discovered molecules (types I, II, III) were analyzed to design new molecules (type IV) by bioisosteric replacement of the amino group. The ligand conformation, binding mode studies and drug like properties were major determinant for selection of molecules for final synthesis. The replacement of amino group with methyl restored the interactions with RNA-template (Tem 799) through bifurcated weak H-bond (C-H…O). This is an interesting finding observed from molecular modeling studies. It was found that 6c-e has anti-HCV activity (EC(50) in 37-46μM) while 6a, 6b and 6g were inactive. The compound 6f (EC(50) 28μM) was the most active among the series however it also showed some cytotoxicity (CC(50) 52.8μM). Except 6f, none of the compounds were found to be cytotoxic (CC(50)>100μM). The present study discloses structure-based approach for novel anti-HCV lead discovery and opens a future scope of lead optimization.
    Bioorganic & medicinal chemistry letters 10/2012; · 2.65 Impact Factor
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    ABSTRACT: Among approximately 65 kinases of the malarial genome, RIO2 (right open reading frame) kinase belonging to the atypical class of kinase is unique because along with a kinase domain, it has a highly conserved N-terminal winged helix (wHTH) domain. The wHTH domain resembles the wing like domain found in DNA binding proteins and is situated near to the kinase domain. Ligand binding to this domain may reposition the kinase domain leading to inhibition of enzyme function and could be utilized as a novel allosteric site to design inhibitor. In the present study, we have generated a model of RIO2 kinase from Plasmodium falciparum utilizing multiple modeling, simulation approach. A novel putative DNA-binding site is identified for the first time in PfRIO2 kinase to understand the DNA binding events involving wHTH domain and flexible loop. Induced fit DNA docking followed by minimization, molecular dynamics simulation, energetic scoring and binding mode studies are used to reveal the structural basis of PfRIO2-ATP-DNA complex. Ser105 as a potential site of phosphorylation is revealed through the structural studies of ATP binding in PfRIO2. Overall the present study discloses the structural facets of unknown PfRIO2 complex and opens an avenue toward exploration of novel drug target.
    Journal of Molecular Modeling 09/2012; · 1.98 Impact Factor
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    ABSTRACT: Several options for treating Herpes Simplex Virus type 1 and type 2 are available. However, non-specific inhibition and drug resistance warrants the discovery of new anti-herpetic compounds with better therapeutic profile or different mode of action. The non-nucleoside inhibitors of HSV DNA polymerase target the site that is less important for the binding of a natural nucleoside or nucleoside inhibitors. In the present study, we have explored the possibility to find a new lead molecule based on α-pyrone analogs as non-nucleoside inhibitors using structure based modeling approach. The designed molecules were synthesized and evaluated for anti-HSV activity using MTT assay. The compound 5h with EC(50) 7.4μg/ml and CC(50) 52.5μg/ml was moderately active against HSV when compared to acyclovir. A plaque reduction assay was also carried out and results reveal that 5h is more effective against HSV-1 with better selective index of 12.8 than against HSV-2 (SI=3.6). The synthesized compounds were also evaluated for anti-HIV activity, but none were active.
    Bioorganic & medicinal chemistry letters 08/2012; 22(19):6261-6. · 2.65 Impact Factor
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    ABSTRACT: This paper is an attempt to evaluate the anti-inflammatory and analgesic activities and the possible mechanism of action of tender leaf extracts of Shorea robusta, traditionally used in ailments related to inflammation. The acetic-acid-induced writhing and tail flick tests were carried out for analgesic activity, while the anti-inflammatory activity was evaluated in carrageenan-and dextraninduced paw edema and cotton-pellet-induced granuloma model. The acetic-acid-induced vascular permeability, erythrocyte membrane stabilization, release of proinflammatory mediators (nitric oxide and prostaglandin E2), and cytokines (tumor necrosis factor-α, and interleukins-1β and -6) from lipopolysaccharide-stimulated human monocytic cell lines were assessed to understand the mechanism of action. The results revealed that both aqueous and methanol extract (400 mg/kg) caused significant reduction of writhing and tail flick, paw edema, granuloma tissue formation (P < 0.01), vascular permeability, and membrane stabilization. Interestingly, the aqueous extract at 40 μg/mL significantly inhibited the production of NO and release of PGE2, TNF-α, IL-1β, and IL-6. Chemically the extract contains flavonoids and triterpenes and toxicity study showed that the extract is safe. Thus, our study validated the scientific rationale of ethnomedicinal use of S. robusta and unveils its mechanism of action. However, chronic toxicological studies with active constituents are needed before its use.
    Evidence-based Complementary and Alternative Medicine 01/2012; Article ID: 254849(Volume 2012, Article ID: 254849, DOI: 10.1155/2012/254849-2012):14 pages. · 1.72 Impact Factor

Publication Stats

176 Citations
144.93 Total Impact Points

Institutions

  • 2011–2014
    • Birla Institute of Technology, Mesra
      • Department of Applied Chemistry
      Ranchi, Jharkhand, India
  • 2010–2011
    • The Ohio State University
      • Department of Physiology and Cell Biology
      Columbus, OH, United States
  • 2006–2011
    • University of Georgia
      • Department of Pharmaceutical and Biomedical Sciences
      Athens, GA, United States
  • 2001–2010
    • Central Drug Research Institute
      • • Medicinal and Process Chemistry Division (CDRI)
      • • Molecular and Structural Biology Division (CDRI)
      Lakhnau, Uttar Pradesh, India
  • 2009
    • Athens State University
      Athens, Alabama, United States