Browsing by Author "Neelabh"

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2-Mercaptoquinoline Analogues: A Potent Antileishmanial Agent
(Wiley-Blackwell, 2018) Suvajit Koley; Neeraj Tiwari; Neelabh; Rakesh Kumar Singh; Maya Shankar Singh
Leishmaniases are endemic in various countries and parasite is developing resistance against available drugs. Thus, development of new drugs against Leishmania is an open area of investigation for synthetic organic chemist. In order to meet this challenge, a series of 2-mercaptoquinoline derivatives have been synthesized and docked into the active site of Trypanothione reductase (TryR) enzyme required for redox balance of parasite. These were screened on promastigote and intracellular amastigote stages of L. donovani and found to show high levels of antileishmanial activity together with no cytotoxicity. Some of the synthesized compounds tested here, exhibited very steady and promising leishmanicidal activity against both promastigotes & intracellular amastigotes form, and the observations have been superbly supported by the docking results. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
A Comprehensive Review on Mustard-Induced Allergy and Implications for Human Health
(Humana Press Inc., 2019) Akanksha Sharma; Alok K. Verma; Rinkesh Kumar Gupta; Neelabh; Premendra D. Dwivedi
Mustard is widely used in a variety of foods/food products to enhance the flavor and nutritional value that subsequently raise the risk of hypersensitivity reactions. Mustard allergy has been reported for many years and is increasing gradually especially in the areas where its consumption is comparatively higher, and it may be considered among the most important food allergies. A number of relevant clinical studies focused on mustard-induced allergic manifestations are summarized in the current review. In addition, the knowledge regarding the immunological as well as biochemical characteristics of mustard allergens that have been known till date and their cross-reactivity with other food allergens have also been discussed here. Notably, mustard may also be present as a hidden allergen in foods; therefore, it is important to recognize food products that may contain mustard as it may pose potential risk for the allergic individuals. Additionally, the better understanding of the underlying mechanism in mustard allergy is a prerequisite for the development of specific therapeutic procedures. Conclusively, mustard sensitivity should be routinely tested in patients with idiopathic anaphylaxis for the safety of the allergic patients. © 2017, Springer Science+Business Media, LLC.
A computational study of B-cell epitopes of wheat allergens and identification of its IgE binding residues
(Springer Science and Business Media B.V., 2021) Amogh Johri; Neelabh; Meenakshi Srivastava
In the contemporary research, biological computational tools have emerged to play a pivotal role in facilitating both cost and time efficient research in several domains of biology. One such domain is addressing the prevailing food allergy issues, where these computational tools have been proven of vital importance. Different tools use different mathematical modelling methods and computational algorithms to predict the result. Due to use of different methodologies in prediction of result the results received by various servers needs to be evaluated for similarity. In the present study, we discuss the identification of IgE binding allergy causing B-Cell epitopes of wheat (Triticum aestivum) allergens, namely ‘Tri a 14’, ‘Tri a 18’, ‘Tri a 19’, ‘Tri a 25’, ‘Tri a 26’, ‘Tri a 36’ and ‘Tri a 37’. Using total seven web servers (ABCPred, ElliPro, BepiPred 1.0b, BcePred, BCPred, CBTOPE and Disco Tope 2.0) 59 linear epitopes and 8 conformational epitopes were predicted in present study. Numbers of linear and conformational epitopes predicted by majority of employed web servers are shown in result. The predicted epitopes are analysed in terms of residues having hydrophilicity, polar nature and having exposed surface. In case of unavailability of suitable structure, in-silico homology modelling has been employed. Cross reactivity of T. aestivum with other food items has also been studied. © 2021, Bharati Vidyapeeth's Institute of Computer Applications and Management.
A gain-of-function mutation in CITED2 is associated with congenital heart disease
(Elsevier B.V., 2021) Manohar Lal Yadav; Dharmendra Jain; Neelabh; Damyanti Agrawal; Ashok Kumar; Bhagyalaxmi Mohapatra
CITED2 is a transcription co-activator that interacts with TFAP2 and CBP/ P300 transcription factors to regulate the proliferation and differentiation of the cardiac progenitor cells. It acts upstream to NODAL-PITX2 pathways and regulates the left-right asymmetry. Both human genetic and model organism studies have shown that altered expression of CITED2 causes various forms of congenital heart disease. Therefore, we sought to screen the coding region of CITED2 to identify rare genetic variants and assess their impact on the structure and function of the protein. Here, we have screened 271 non-syndromic, sporadic CHD cases by Sanger's sequencing method and detected a non-synonymous variant (c.301C>T, p.P101S) and two synonymous variants (c.21C>A, p.A7A; c.627C>G, p.P209P). The non-synonymous variant c.301C>T (rs201639244) is a rare variant with a minor allele frequency of 0.00011 in the gnomAD browser and 0.0018 in the present study. in vitro analysis has demonstrated that p.P101S mutation upregulates the expression of downstream target genes Gata4, Mef2c, Nfatc1&2, Nodal, Pitx2, and Tbx5 in P19 cells. Luciferase reporter assay also demonstrates enhanced activation of downstream target promoters. Further, in silico analyses implicate that increased activity of mutant CITED2 is possibly due to phosphorylation of Serine residue by proline-directed kinases. Homology modeling and alignment analysis have also depicted differences in hydrogen bonding and tertiary structures of wild-type versus mutant protein. The impact of synonymous variations on the mRNA structure of CITED2has been analyzed by Mfold and relative codon bias calculations. Mfold results have revealed that both the synonymous variants can alter the mRNA structure and stability. Relative codon usage analysis has suggested that the rate of translation is attenuated due to these variations. Altogether, our results from genetic screening as well as in vitro and in silico studies support a possible role of nonsynonymous and synonymous mutations in CITED2contributing to pathogenesis of CHD. © 2021
A Novel model for fast and robust retrieval of3d bio-images using intelligent vision algorithm
(Serials Publications, 2016) Meenakshi Srivastava; S.K. Singh; S.Q. Abbas; Neelabh
Vast growth of multimedia information like images, audio and video on web has induced the scientific community for storage and retrieval of multimedia information more intuitively. Since one image can be interpreted in numerous ways, keyword based searching systems can retrieve the information to a limited extent. Moreover in few domains for example, as in the case of Bio Images, the content information is not even of textual nature. This limitation has led to the requirement for development of Content Based Image Retrieval Systems. Image Retrieval systems which can recognize the objects like the human eyes have been most popular. To construct a good intelligent vision system, high dimension feature vectors of images are required for pattern recognition. Though high dimension feature vectors provides good recall rate, they retard the search process speed. Search time duration increases further with increase in number of images in database. In the present manuscript authors have proposed a model which adequately addresses these constraints and provides a robust and fast retrieval mechanism of Bio Images. © International Science Press.
AMIPRO: A content-based search engine for fast and efficient retrieval of 3D protein structures
(Springer Science and Business Media Deutschland GmbH, 2018) Meenakshi Srivastava; S.K. Singh; S.Q. Abbas; Neelabh
Proteins are macromolecules which are virtually involved in all of the life processes. The study of protein structures is of utmost importance in the field of bioinformatics. With the advancement in the field of computational biology, there has been tremendous upsurge in the sequential and the structural data deposition. The structure of a protein depends upon the sequence of the amino acids present in it, although similarity in sequence does not guarantee a similarity in structure. Despite the fact that the three-dimensional structure of protein molecule is very important to predict its functionality, yet the backbone of the searching has been majorly dependent upon the sequences rather than the structures. The leading platforms for searching structural similarity in proteins make use of sequence-based searching or text-based searching but do not provide the desired results. In the current manuscript, a model has been proposed to perform “content-based searching” on protein images. Content-based searching takes into account the visual/structure-based similarity and the information contained in the data sets rather than the traditional sequence-based searching. Intelligent Vision Algorithm has been applied to extract the visual features from the protein images for determining the similarity between two proteins. The proposed search engine model will result in an efficient and fast retrieval of similar protein structures. © 2018, Springer Nature Singapore Pte Ltd.
EVALUATION OF ANTI-CRYPTOCOCCAL ACTIVITY OF BACITRACIN
(Slovak University of Agriculture, 2020) Neelabh; Karuna Singh
Cryptococcosis is amongst potentially deadly diseases whose impact has aggrandized with the advent of AIDS and antifungal resistance. Antifungals used presently are short of broad spectrum activity and furthermore are involved in several side effects. Henceforth, the present manuscript focuses on the evaluation of antifungal activity of bacitracin against Cryptococcus neoformans var. grubii, the causative agent of the disease. Minimum inhibitory concentration, flow cytometric analysis and confocal microscopy were used to determine the in-vitro fungal susceptibilities. Light microscopy was used to determine the changes in the micromorphology of the fungal organism. Swiss mice were used for testing the efficacy of bacitracin in-vivo.Bacitracin showed cidal activity against C. n. grubii at 5.5 mg/ml which is on the higher side but on testing under in-vivo conditions it was observed that doses as high as 15 mg/kg bw/day did not show any adverse effect in the body. Better survival rate of the bacitracin treated mice, lowering of the fungal load and changes showing improvement in the tissue morphology depicts the mild anticryptococcal activity of bacitracin. Although, bacitracin has proved to be a potent antifungal yet there are several limitations like low bioavailability and its peptide nature. However, these problems can be limited by developing suitable analogs of the compound. © 2020. All Rights Reserved.
Evaluation of antifungal activity of cinnamaldehyde against Cryptococcus neoformans var. grubii
(Springer Science and Business Media B.V., 2020) Neelabh; Karuna Singh
Cryptococcosis is a potentially fatal fungal disease which has aggrandized with the emergence of AIDS and antifungal resistance. The currently used antifungals lack the broad-spectrum activity and result in several toxicities during long treatment regimens. Thus, the present study aims to evaluate the antifungal activity of cinnamaldehyde against Cryptococcus neoformans var. grubii, the etiological agent of the disease. Quantitative and qualitative in vitro fungal susceptibilities were carried out by minimum inhibitory concentration assay, flow cytometric analysis, and confocal microscopy. Micromorphological alterations were studied through scanning electron and light microscopies. “In vivo” antifungal efficacy of cinnamaldehyde was assessed. Cinnamaldehyde showed antifungal activity against C. neoformans in a dose-dependent manner. A concentration of 1.37 mg/mL of cinnamaldehyde was found to be inhibitory and fungicidal while the low concentration (0.68 mg/mL) was found to induce micromorphological changes and formation of giant/titan-like cells in this pathogen. The reparative activity of cinnamaldehyde and its ability to prolong the life even after the advent of cryptococcal meningitis in mice was also noticed. This study suggests potent anti-cryptococcal activity of cinnamaldehyde. Though, it has a couple of limitations like allergy and low bioavailability. However, these problems can be circumvented by developing suitable analogs of the compound. It, therefore, could be used as a therapeutic option against cryptococcosis and cryptococcal meningitis. Moreover, the evaluation of its pharmacokinetic and pharmacodynamic properties is desirable. © 2020, Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.
Glycation of clinically relevant chickpea allergen attenuates its allergic immune response in Balb/c mice
(Elsevier Ltd, 2017) Rinkesh Kumar Gupta; Alok Raghav; Akanksha Sharma; Kriti Gupta; Neelabh; Payal Mandal; Anurag Tripathi; Irfan Ahmad Ansari; Mukul Das; Premendra D. Dwivedi
Glycation of food allergens may alter their immunological behaviour. We sought to investigate the impact of glycation on the allergenicity of a food protein. Herein, a chickpea protein (≈26 kDa) was purified and characterized as lectin. Further, glycation of this purified protein was carried out. Thereafter, allergic behaviour of this glycated protein was compared with its native form, using various allergic parameters in Balb/c mice. The reduced allergenicity of glycated protein was observed as lesser allergic phenotypes, reduced serum immunoglobulins and allergic mediators, lower mast cells and eosinophil counts, lower protein expressions of Th2 cytokines and associated transcription factors. In addition, more Th1 and less Th2 cytokine production in exposed splenocyte, were evident in the glycated protein treated mice as compared to its native protein treatment. Thus, glycation of the chickpea allergen attenuated the sensitizing potential and allergic responses in Balb/c mice significantly and could also be clinically beneficial. © 2017 Elsevier Ltd
In silico studies on the effect of griseofulvin on tubulin protein of Cryptococcus neoformans and its in vitro validation
(Slovak University of Agriculture, 2017) Neelabh; Karuna Singh
Griseofulvin is a well known drug against dermatophytes. It is particularly prescribed for an infection called scrap ringworm or tinea capitis. In general, griseofulvin inhibits the tubulin protein that is responsible for the cell division. Not much is known about the effect of griseofulvin on Cryptococcus neoformans. Therefore, the authors made an effort to check the activity of griseofulvin against it. The webservers (T-Coffee, Bluues simulation and CASTp) and software (Autodock 4.0) have been used in order to determine the activity of griseofulvin against the beta subunit of tubulin protein of C. neoformans. The results obtained from the in silico studies show a high affinity of griseofulvin towards the beta chain of tubulin protein. The negative value of binding energy (-9.02 kcal/mol) also shows that the complex is thermodynamically favourable and stable. These in silico results were further validated by MIC assay showing 74.1% inhibition of C. neoformans (isolate no. 5) against griseofulvin. The present study reports that apart from dermatophytes, the drug has significant effect on C. neoformans and it may be used in the combinatorial therapy against the same.
In-silico and in-vitro studies on fungal chitinase as a target enzyme for antifungal activity of closantel
(Slovak University of Agriculture, 2018) Neelabh; Neha Nidhi Tirkey; Karuna Singh
Drug development is a dynamic field which undergoes changes continuously. The past decade or so has witnessed huge strides in the field of screening of the drugs as well as target and ligand identifications but unfortunately this has not led to useful drugs. Many diseases still remain untreatable because we do not have proper drugs against them. In case of fungi the situation is graver due to the limited drug targets peculiar to fungi. Thus, in order to combat the fungal diseases the need of the hour is to develop new antifungals that have fewer side effects and broad spectrum activity. The current work deals with closantel, a veterinary drug targeting chitinase, which is utilized as a therapeutic option against helminths. The fact that chitin is an important constituent of the cell wall of the fungi also and it undergoes regular degradation and remodelling through an enzyme called fungal chitinase motivated the authors to test the efficacy of closantel against fungal chitinase. In the present study Cryptococcus neoformans has been used as a model organism against which the antifungal activity of closantel has been tested. In-silico studies carried out using PatchDock and FireDock predicted the global energy (binding energy)involved in docking closantel on chitinase as -47.58 Kcal/mol. Further, the results obtained through the in-silico studies were validated by the minimum inhibitory concentration assay (MIC). It was observed that 736 (±7.024) μg/ml of closantel can inhibit the cryptococcal growth by 80% (MIC80). © 2018, Slovak University of Agriculture.
In-silico prediction of T and B cell epitopes in the evolutionary conserved pathway of glycolysis for human pathogens: Coccidiodes immitis, Histoplasma capsulatum and Pneumocystis carnii
(Association of Biotechnology and Pharmacy, 2017) Neelabh; Karuna Singh
Fungal diseases are amongst the emerging diseases to which humans are most susceptible pertaining to the present day life style. New drugs are being made but at a slow pace, not matching the resistance developing capacity of the fungal pathogens. Therefore, it is important to choose new drug targets peculiar to fungi but absent in humans.A common practice till date has been to use the virulence proteins in order to devise medicines against micro-organisms. However, we have used in-silico techniques to analyze enzymes involved in the evolutionary conserved pathway of glycolysis which is the most primitive pathway for ATP production in aerobic as well as anaerobic organisms. Therefore, on successfully targeting these enzymes microorganism can be killed. We have chosen 3 fungal pathogens viz.Coccidiodes immitis, Histoplasma capsulatum and Pneumocystis carnii that cause serious diseases in human beings and their effect on the morbidity and mortality of humans has been substantial. MEME-Motif discovery tool was used to devise a single motif sequence per glycolytic enzyme from the three fungi. Further, online servers such as ABCpred, Bcepred, BepiPred and Tools from Immunomedicine group have been used in order to predict the linear epitopes from the motif sequences of the different glycolytic enzymes. Analysis of these epitopes was performed through PepCalc and NetSurfP in terms of parameters such as hydrophilicity, coil forming residues and exposed residues. Analysis of ten proteins of glycolysis from each fungus reveals the regions that can elicit an immunological response. This study most importantly projects aldolase to be an enzyme of importance which in future can be used as a potential vaccine target for these three fungi. © 2017, Association of Biotechnology and Pharmacy. All rights reserved.
In-silico studies of some natural, synthetic and semi-synthetic antifungal drugs for their multi-targeting nature
(Slovak University of Agriculture, 2018) Neelabh; Karuna Singh
Research has shown that drugs or therapeutic agents which are directed at a particular target often undergo a reduction in efficacy, undesired safety profiles, compensatory and neutralizing effects, anti-target and counter target activities and also resistance against the drug. Proper utilization of multiple targets can lead to a perfect blend between the efficacy and safety when compared against single-targeted drug design. The authors have utilized this concept in case of the antifungal drugs which generally act against one of the targets amongst chitinase, chitin synthase, 1, 3 beta glucan synthase and lanosterol 14 a-demethylase. Henceforth, the present study is an attempt to screen the known drugs for their multi-targeting nature, and to compare natural product based drugs with semi-synthetic and synthetic drugs in-silico. In the present study, eleven (7 synthetic and 4 natural) drugs namely Allosamidine, Methylxanthine, Acetozolamide, Nikkomycin Z, Polyoxin L, Caspofungin, Fluconazole, Argifin, Obovatol, Papulacandin and Ro-091470 have been chosen to study their effect against different targets. This exciting and unique in-silico study provides insight that some drugs can function equally good against all targets, while some have a better efficiency against a different target than the known one. All four studied natural product based drugs are found to be good at multi-targeting. All the drugs that were shown to have a good multi-targeting efficiency bind at the same region where the known drugs against that target bind. Furthermore, lanosterol 14 a-demethylase is found to be the best target amongst all the aforesaid fungal targets. © 2018 Journal of Microbiology, Biotechnology and Food Sciences.
Sequential and Structural Aspects of Antifungal Peptides from Animals, Bacteria and Fungi Based on Bioinformatics Tools
(Springer New York LLC, 2016) Neelabh; Karuna Singh; Jyoti Rani
Emerging drug resistance varieties and hyper-virulent strains of microorganisms have compelled the scientific fraternity to develop more potent and less harmful therapeutics. Antimicrobial peptides could be one of such therapeutics. This review is an attempt to explore antifungal peptides naturally produced by prokaryotes as well as eukaryotes. They are components of innate immune system providing first line of defence against microbial attacks, especially in eukaryotes. The present article concentrates on types, structures, sources and mode of action of gene-encoded antifungal peptides such as mammalian defensins, protegrins, tritrpticins, histatins, lactoferricins, antifungal peptides derived from birds, amphibians, insects, fungi, bacteria and their synthetic analogues such as pexiganan, omiganan, echinocandins and Novexatin. Insilico drug designing, a major revolution in the area of therapeutics, facilitates drug development by exploiting different bioinformatics tools. With this view, bioinformatics tools were used to visualize the structural details of antifungal peptides and to predict their level of similarity. Current practices and recent developments in this area have also been discussed briefly. © 2016, Springer Science+Business Media New York.
SNPs in ERCC1, ERCC2, and XRCC1 genes of the DNA repair pathway and risk of male infertility in the Asian populations: association study, meta-analysis, and trial sequential analysis
(Springer New York LLC, 2019) Vertika Singh; Sandeep Kumar Bansal; D.V.S. Sudhakar; Neelabh; Arijit Chakraborty; Sameer Trivedi; Gopal Gupta; Kumarasamy Thangaraj; Singh Rajender; Kiran Singh
Purpose: We investigated if substitutions in the ERCC1, ERCC2, and XRCC1 genes of the DNA repair pathway correlate with non-obstructive azoospermia and male infertility. Methods: A total of 548 azoospermic infertile males and 410 fertile controls were genotyped for XRCC1 399A > G, 280G > A, and ERCC1 C > A 3′ UTR and 541 azoospermic infertile males and 416 fertile controls were genotyped for ERCC2 751A > C using iPLEX Gold Assay. Meta-analyses were performed on XRCC1 399A > G (1022 cases and 1004 controls), ERCC1 C > A 3′ UTR (879 cases and 1059 controls), and ERCC2 751A > C (914 cases and 850 controls) polymorphisms to quantitatively estimate the significance of the association between these polymorphisms and the risk of infertility. Results: Statistically significant association between ERCC2 751A > C SNP and male infertility was found using the codominant model (p = 0.03). Results of meta-analysis suggested a lack of correlation with male infertility risk, which could be due to pooling of studies from different ethnic populations. Due to limited the number of studies, a stratified analysis for different ethnic groups could not be performed. Conclusion (s): In conclusion, AA genotype of 751A > C SNP in ERCC2 correlated with a higher risk of male infertility and may contribute to an increased risk of azoospermia and male infertility in Indian men. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.
Synthesis, Structure Elucidation, Homology Modeling and Antifilarial Activity of 7-Benzamidocoumarin Derivatives
(Wiley-Blackwell, 2019) Priyanka; Neelabh; Neha Tiwari; Rajesh K. Sharma; Poonam Gupta; Sweta Misra; Shailja Misra-Bhattacharya; Ray J. Butcher; Karuna Singh; Diksha Katiyar
A series of 7-benzamidocoumarin derivatives 10–25 starting from 7-amino coumarins 7 and 8 has been synthesized, characterized and evaluated in vitro for antifilarial activity against the human lymphatic filarial parasite, Brugia malayi. Compounds 13 and 20–23 showed permanent paralysis of the worm with 90–95% inhibition of motility of adult worms at 10 μM. All the synthesized compounds were docked on the modeled receptor of Onchocerca volvulus chitinase OvCHT1. Compound 13 with binding energy of −7.95 Kcal/mol showing three hydrogen bonds with the active site of the enzyme emerged as the best inhibitor. © 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
The Southeastern Asian house mouse (Mus musculus castaneus Linn.) as a new passenger host for Cryptococcus neoformans var. grubii molecular type VNI
(Oxford University Press, 2017) Karuna Singh; Jyoti Rani; Neelabh; Govind Kumar Rai; Major Singh
We describe Mus musculus castaneus as a new mammalian host for Cryptococcus neoformans var. grubii (VNI). Eighteen apparently healthy adults and pups of the rodent were collected from human dwellings in Varanasi, a city of India. Both clinical and behavioral examinations of the rodents did not reveal any sign of the disease. Among visceral organs, histological examination of only liver exhibited the presence of single celled, encapsulated, Southgate's mucicarmine positive fungal structures consistent with C. neoformans. Nevertheless, culture of tissue homogenates of brain, lungs, liver, and kidneys yielded white colonies on Sabouraud's dextrose agar and brown mucoid colonies of C. neoformans on Staib's and Tobacco agar media. The pathogen was isolated from habitat soil as well as fresh faeces of the animals. All isolates were urease positive, nitrate and canavanine-glycine bromothymol blue negative, exhibited phenoloxidase activity and grew at 37°C. The isolates were identified as C. neoformans var. grubii with ITS primers and unique marker (GACA)4. The pathogen when inoculated in immunosuppressed mice showed low pathogenicity. To our knowledge, we for the first time report case cluster of Mus musculus castaneus as new passenger host for C. neoformans var. grubii (VNI). © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved.