“One has to go through all the experiences in Life because it makes you understand your own frailties and also helps you develop respect for God.”

N.R. Narayana Murthy

Virtual Epitope Excision: Strategies Developed from Mass Spectrometry Proteolytic Footprinting.

We will be bringing you shortly Virtual Epitope Excision: Strategies Developed from Mass Spectrometry Proteolytic Footprinting. An online server which will guide the choice of proteinases and the free fragments generation to scrutinize the entire mass spectrometry analysis. Another role of this server is to make you decide the prediction accuracy of other epitope prediction programs.

Combating Cancer through Epigenetic Modulation by Virtual Screening of Natural Bioactives

Ravi Kapopara*¹, S. Prasanth Kumar², Saumya K. Patel¹, Dhananjay K. Sadhu¹,  

Yogesh T. Jasrai¹, Himanshu A. Pandya¹ and Rakesh M. Rawal³

¹Bioinformatics Laboratory, Department of Botany, Gujarat University, Gujarat, India.

²Department of Bioinformatics, Alagappa University, Tamil Nadu, India

³Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology,

The Gujarat Cancer and Research Institute (GCRI), Gujarat, India.

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http://www.slideshare.net/prasanthperceptron/ravi-kapopara-s-prasanth-kumar-sajeb-9804422

Abstract

Epigenetic events are due to altered gene expression without any changes in the genetic material and characteristic of heritability via cell division. The impact of epigenetic control over cancer is one among the thrust area of research in cancer biology. The present study deals about the virtual screening of plant derived natural bioactives directed against the key molecular regulators of the epigenetic events viz. DNA methyltransferases (DNMT1, DNMT2 and DNMT3B), Histone acetyltransferase (HAT), Histone deacetylase 8 (HDAC8), Histone H3 lysine 27 methyl transferase (H3K27MT) and Histone H3 specific lysine 4 demethylase (H3K4DM). This computational screening identified the most efficient binders with respect to individual targets in terms of ligand binding energy. We hope that structure optimization of the best scored docked conformations will reveal new insights and development of natural bioactives to combat cancer.  

Keywords: Epigenetics, Virtual screening, Natural bioactives, Ligand binding energy

Computational Analysis of Naturally Occurring Marine Compounds (NOMC) Targeting Gap Junctions and Cell Adhesive Molecules for the Identification of Anticancer Drug Targets

S.K. Patel*, S. Prasanth Kumar1, Y.T. Jasrai1,H.A. Pandya1, and R.M. Rawal2
1Department of Botany, University School of Sciences,
Gujarat University, Ahmedabad-382415, Gujarat, India
2Division of Medicinal Chemistry & Pharmacogenomics,
Department of Cancer Biology, The Gujarat Cancer & Research Institute,
Asarwa, Ahmedabad-380 016, India.

The Journal of Computational Intelligence in Bioinformatics 2011: 4(2), pp. 161-171

Abstract

Compounds and metabolites from marine organisms established a new arena

for marine pharmacy primarily due to their diverse biological activities. In the

long run of anticancer drug development pipeline, some of the naturally

occurring marine compounds (NOMCs) appear to be potential candidates and

few are commercialized. In the present study, investigation of NOMCs from

Marine Algae, Sponges, Corals, Bacteria, Cnardians, and Marine Fish was

carried out targeted against Gap junctions (Connexin 26, Connexin 43) and

Cell Adhesive molecules (Cadherins, Integrins) via molecular docking studies.

The in silico effectiveness of NOMCs was studied based upon the interaction

with the protein’s active site residues with less binding energy. The interacting

NOMCs were further filtered to predict the bioavailability and drug likeness

properties. Manoalide from Marine Sponges was shown to be a better

interacting ligand with low binding energy (-121.693 kcal/mol) and passed all

the physicochemical parameters for drug likeness. This work encourages the

development of NOMCs with some chemical modifications to augment more

efficacy and better activity.

Keywords: Naturally occurring marine compounds (NOMCs), Gap junctions,

Cell adhesive molecules, Molecular docking, Anticancer activity

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in silico DEVELOPMENT OF INHIBITORS AGAINST PANTOTHENATE SYNTHETASE OF Mycobacterium tuberculosis

S. Prasanth Kumar¹, P. Srinivasan², Saumya K. Patel¹, Ravi Kapopara¹ and Yogesh T. Jasrai¹

¹Bioinformatics Laboratory, Applied Botany Center, Gujarat University, Ahmedabad -380009, Gujarat, India.

²Department of Bioinformatics, Alagappa University, Karaikudi – 630003, Tamil Nadu, India.

ABSTRACT:

Multi-drug resistant Mycobacterium tuberculosis is one of the major obstacles for the treatment of tuberculosis. There is an urgent need for identification of novel drug targets which are known to establish infection in the host cells. In the present study, pantothenate synthetase (PS), an essential metabolic enzyme in the pantothenate biosynthetic pathway is used as target. Fourteen inhibitory molecules were computationally analyzed using Glide module and found that sulfamoyl adenylate inhibitors possessed better binding affinities against the PS enzyme. Further, structure optimization and in vitro validation of these inhibitors will prove its efficacy as a better candidate in the drug designing pipeline. 

Keywords: Multi-drug resistant, Pantothenate synthetase, Glide module, Sulfamoyl adenylate inhibitors


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http://bipublication.com/files/JABARv2i2201102.pdf

2D-QSAR ANALYSIS OF DIHYDROFOLATE REDUCTASE (DHFR) INHIBITORS WITH ACTIVITY IN Toxoplasma gondii and Lactobacillus casei

Saumya K. Patel, S. Prasanth Kumar, Himanshu A. Pandya, Yogesh T. Jasrai and Mehul I. Patni

Bioinformatics Laboratory Applied Botany Center, Gujarat University, Ahmedabad -380009, Gujarat, India.

ABSTRACT:

Methotrexate (MTX), an inhibitor of Dihydrofolate reductase (DHFR), is a well known drug given in the treatment of rheumatoid arthritis (RA). Due to its potential neurotoxicity, the patient has to discontinue the chemotherapy. In the present study, DHFR inhibitors which were structurally similar to MTX and had reported biological activity in model organisms such as Toxoplasma gondii and Lactobacillus casei was considered. A 2D-QSAR was modeled based on certain topological and constitutional descriptors along with its biological activity and found best 5 inhibitory molecules. in vitro validation of this inhibitors will be an alternative for effective drug development against RA.


Keywords: Methotrexate, Dihydrofolate reductase, Rheumatoid arthritis, 2D-QSAR, Descriptors.

Kindly download this article linked here:
http://bipublication.com/files/JABARv2i2201107.pdf