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MY RESEARCH PUBLICATIONS

1.    P. Srinivasan, A. Sudha, A. Shahul Hameed, S. Prasanth Kumar and M. Karthikeyan, 2011. Screening of medicinal plant compounds against NS5B polymerase of hepatitis C virus (HCV) using molecular docking studies. Journal of Pharmacy Research 4(1): pp.136-140.

2.      S. Prasanth Kumar, P. Srinivasan, Saumya K. Patel, Ravi Kapopara and Yogesh T. Jasrai, 2011. In silico development of inhibitors against pantothenate synthetase of Mycobacterium tuberculosis. Journal of Advanced Bioinformatics and Research 2(2): pp. 142-148.

3.    Saumya K. Patel, S. Prasanth Kumar, Himanshu A. Pandya, Yogesh T. Jasrai and Mehul I. Patni, 2011. 2D-QSAR analysis of dihydrofolate reductase (DHFR) inhibitors with activity in Toxoplasma gondii and Lactobacillus casei. Journal of Advanced Bioinformatics and Research 2(2): pp.161-166.

4.  S. K. Patel, S. Prasanth Kumar, Y. T. Jasrai, H. A. Pandya and R. M. Rawal, 2011. Computational analysis of naturally occurring marine compounds (NOMC) targeting gap junctions and cell adhesive molecules for the identification of anticancer drug targets. The Journal of Computational Intelligence in Bioinformatics 4(2): pp. 161-171.

5.   S. Prasanth Kumar, 2011. Organic Virtual Library (ORVIL) – A combinatorial library construction based on organic constituents and without scaffold hopping. International Journal of Applied Research on Information Technology and Computing 2(2): pp.57-62.

6.   S. Prasanth Kumar and Muthusamy Meenatchi, 2011. Virtual quantification of protein stability using applied kinetic and thermodynamic parameters. IIOAB Letters 1: pp.21-28.

7.    Ravi Kapopara, S. Prasanth Kumar, Saumya K. Patel, Dhananjay K. Sadhu, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal, 2011. Virtual screening of natural bioactives in combating cancer through epigenetic modulation. South Asian Journal of Experimental Biology 1(5-S1): pp.12-16.

8.      Pappu Srinivasan, Sivakumar Prasanth Kumar, Muthusamy Karthikeyan, Jeyaram Jeyakanthan, Yogesh T. Jasrai, Himanshu A. Pandya, Rakesh M. Rawal and Saumya K. Patel, 2011. Epitope-based immunoinformatics and molecular docking studies of nucleocapsid protein and ovarian tumor domain of Crimean-Congo hemorrhagic fever virus. Frontiers in Bioinformatics and Computational Biology 2(72): 1-9. doi: 10.3389/fgene.2011.00072. PMID: 22303367; PMC3268625.

                                                                                            

9.   S. Prasanth Kumar, Ravi G. Kapopara, Saumya K. Patel, Mehul I. Patni, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal, 2011. Molecular descriptor enhancement of a common structure towards the development of α-glucosidase and α-amylase inhibitors for post-prandial hyperglycemia (PPHG). Asian Journal of Biomedical and Pharmaceutical Sciences 1(3): pp.01-12.

10. S. Prasanth Kumar, Ravi G. Kapopara, Yogesh. T. Jasrai and Rakesh M. Rawal, 2012. Computational studies on the interaction of core histone tail domains with CpG island.  International Journal of Pharma and Biosciences 3(1): pp. B581-590.

11.  S. Prasanth Kumar, Ravi G. Kapopara, Saumya K. Patel, Himanshu A. Pandya and Yogesh T. Jasrai, 2012. Conformational Ensemble of Digoxin and Digitoxin and its Interamolecular Energy in Torsional Space. International Journal of Pharmacy and Biological Sciences 2(2): pp. 57-66.  

12.  S. Prasanth Kumar, Ravi G. Kapopara, Mehul I. Patni, Himanshu A. Pandya, Yogesh T. Jasrai and Saumya K. Patel. Exploring the Polymerase Activity of Chikungunya Viral non structural Protein 4 (nsP4) using Molecular Modeling, e-Pharmacophore and Docking Studies. International Journal of Pharmacy and Life Sciences 3(6): pp. 1752-1765.

13.  Saumya Patel, S. Prasanth Kumar and Mehul Patni, 2012. Statistical and Biocomputational Studies on Spondyloarthritis. Tatiana Melnic (Ed), LAP LAMBERT Academic Publishing GmbH & Co. KG, Saarbrűcken, Germany, ISBN: 978-3-659-14306-9.

14.  S. Prasanth Kumar, Saumya K. Patel and Himanshu A. Pandya, 2012. Normal and binding mode analysis of breast cancer resistance protein. Alina Covali (Ed), LAP LAMBERT Academic Publishing GmbH & Co. KG, Saarbrűcken, Germany, ISBN: 978-3-659-15312-9.

15.  Saumya Patel, Prasanth Kumar and Yogesh T. Jasrai, 2012. Molecular Optimization of Calcineurin Inhibitors for Prion Disease: A Pharmacophore Study. Tatiana Melnic (Ed), LAP LAMBERT Academic Publishing GmbH & Co. KG, Saarbrűcken, Germany, ISBN: 978-3-659-15895-7.

16.  S. Prasanth Kumar. CpGP dynamics- The dynamics of CpG island and promoter to validate nucleosomal gene expression. International Journal of Bio-Science and Bio-Technology 4(2): pp. 11-26. Program is accessible at http://cpgpdynamics.webs.com.

17.  S. Prasanth Kumar. Docking and in silico bioavailability analysis of CDK6 flavonol inhibitors and its analogues for acute lymphoblastic leukemia. The Journal of Computational Intelligence in Bioinformatics, Accepted.

18.  S. Prasanth Kumar, Saumya K. Patel, Yogesh T. Jasrai,  Himanshu A. Pandya and P. Srinivasan, 2012. Biocomputational analysis of citrullinated fillagrin sequence repeats for rheumatoid arthritis. Electronic Journal of Biology, 8(2):29-33.

ABSTRACTS PUBLICATION AND POSTERS PRESENTATION:

1. Poster Presented and Recognized as Best Research Work in the 4th Seminar on Modern Laboratory Techniques in Molecular Biology on the topic “in silico Epitope-based Immunoinformatics and Molecular Docking Studies of Nucleocapsid Protein (NP) and Ovarian Tumor (OTU) Domain of Crimean-Congo Haemorrhagic Fever Virus (CCHFV)” held at Gujarat Cancer and Research Institute (GCRI), Ahmedabad on Feb 28, 2011.

2. Presented a work on “Initiation of Eukaryotic Genome Replication: Interaction of RFC and Brd4 proteins” in Tamil National Scientific Conference, held at Alagappa University between Sept 11-13, 2009 and published ISBN-93-80043-33-3

3. S. Prasanth Kumar, Ravi G. Kapopara, Saumya K. Patel, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal. Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease:  Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 158).

4. Ravi G. Kapopara, S. Prasanth Kumar, Yogesh T. Jasrai, Himanshu A. Pandya and Rakesh M. Rawal. Management of Diabetes by Developing New Alpha Glucosidase Inhibitors (AGIs). (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 162).

5. Saumya K. Patel, S. Prasanth Kumar, Ravi G. Kapopara, Yogesh T. Jasrai and Himanshu A. Pandya. Plant Bioactive Driven Fragment-based Drug Designing and Epitope-baesd Immunoinformatics Study of EspC protein of Mycobacterium tuberculosis. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 166).

6. Mehul I. Patni, S. Prasanth Kumar, Saumya K. Patel, Yogesh T. Jasrai and Himanshu A. Pandya. 2D-QSAR Analysis of ACE Inhibitors with Activity in Oryctolagus cuniculus and Rattus norvegicus. (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Bioinformatics and Use of Newer Technologies, pp. 167).

7. Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya. Bioinformatic analysis on Maize sugary1 gene (Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, Theme: Budding Researchers, pp. 173).

ABSTRACTS PUBLISHED IN THE NATIONAL SYMPOSIUM

ABSTRACTS PUBLISHED IN THE Proceedings of the National Symposium on Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources, held at Department of Botany, Gujarat University, Ahmedabad- 380 009 between Oct 13-15, 2011.

Download these abstracts in PDF format here: http://www.slideshare.net/prasanthperceptron/soft-copy-of-abstracts

Code: IO- 2 Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease:  Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein

(Young Scientist Awarded Presentation)


DOWNLOAD THE PRESENTATION HERE:
http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation

S. Prasanth Kumar¹, Ravi G. Kapopara^1, Saumya K. Patel¹, Yogesh T. Jasrai*, Himanshu A. Pandya¹ and Rakesh M. Rawal²

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences,Gujarat University, Ahmedabad- 380 009. ²Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer  Biology, The Gujarat Cancer & Research Institute (GCRI), Ahmedabad- 380 016.

ABSTRACT

Tomato leaf curl disease (TLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface and stunted plant growth caused by tomato yellow leaf curl virus (TYLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]). We found that the amino acids in coat protein required for systemic infection, viral particle formation and insect transmission to host cells were sufficiently diverged. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the plant DNA required for host cell arrest and propagation of viral particle was studied. We further emphasized the role of loops in coat protein structure as molecular recognition interface.

Keywords: Tomato leaf curl disease, Tomato yellow leaf curl virus, Geminate viral particle, Evolution, Modeling.

__________________________________________________________

Code: IO-6 Management of Diabetes by Developing New Alpha Glucosidase Inhibitors (AGIs)

Ravi G. Kapopara*¹ S. Prasanth Kumar¹, Yogesh T. Jasrai¹, Himanshu A. Pandya¹ and Rakesh M. Rawal²

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009. ²Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer  Biology, The Gujarat Cancer & Research Institute (GCRI), Ahmedabad- 380 016.

ABSTRACT

The most challenging goal in the management of diabetic patient is to achieve normal blood glucose levels caused by post-prandial hyperglycemia (PPHG) or hyperinsulinemia, the individual risk factor contributes to the development of macrovascular complications. Synthetic hypoglycemic agents are available which has its own limitations and serious side-effects. The present study deals about the development of a common small molecular structure by enhancing the molecular descriptors required for binding with α-glucosidase and α-amylase enzymes, the two major targets of PPHG and to develop a monosaccharide-type inhibitor with many insights derived from pharmacophore studies, molecular alignment and molecular docking studies of known inhibitors. A hypothesis was designed which suggest the essential and/or minimal requirement of molecular descriptors to be an efficient binder of these two hydrolytic enzymes and subsequently, molecules with naturally occurring flavonoid structural architecture obeying the hypothesis was developed and evaluated in silico.

Keywords: Post-prandial hyperglycemia, Molecular descriptors, α-glucosidase, α-amylase, Pharmacophore features, Molecular docking, Hypothesis design.
__________________________________________________________

Code: IP-3 Plant Bioactive Driven Fragment-based Drug Designing and Epitope-based Immunoinformatics Study of  EspC protein of Mycobacterium tuberculosis

Saumya K. Patel¹, S. Prasanth Kumar¹, Ravi G. Kapopara¹, Yogesh T. Jasrai¹ and Himanshu A. Pandya¹

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009

ABSTRACT

Multi-drug resistant Mycobacterium tuberculosis is one of the major obstacles for the treatment of tuberculosis. ESX-1 secretion system establishes infection in host cells by secreting virulence factors. Genes belonging to this system are attenuated in currently used BCG vaccine strain and are no longer proven efficacy in treating tuberculosis. In the present study, vasicine, a plant bioactive from Vasaka herb having known antitubercular properties is used to develop inhibitors against a chief component of the ESX-1 secretory pathway, called EspC through fragment-based drug designing approach. Epitope-based immunoinformatics study of EspC protein is also carried out which showed regions of interest for developing vaccines with due consideration across all the genetically heterogeneous inheritance. It is found that designing T-cell epitopes against the C-terminal region of EspC protein will have greater benefits as compared to other regions as it acts as a recognition element for its cognate AAA ATPases and protein interaction.  Hence, designing inhibitors based on plant bioactive with known activity will direct to the generation of potential antitubercular lead molecules. In the other hand, the in vitro expression studies of EspC in individuals with heterogeneous genetic inheritance will helpful in choosing a better region for developing vaccine without any harm to the human.

Key-words: ESX-1 secretion system, Vasaka herb, fragment-based drug designing, immunoinformatics
__________________________________________________________

Code: IP-4 2D-QSAR Analysis of ACE Inhibitors with Activity in   Oryctolagus cuniculus and Rattus norvegicus 


Mehul I. Patni¹, S. Prasanth Kumar¹, Saumya K. Patel¹,  Yogesh T. Jasrai*¹ and Himanshu A. Pandya¹

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009

ABSTRACT

Quinapril, an inhibitor of angiotensin-converting enzyme (ACE), is a known drug prescribed in the treatment of hypertension and congestive heart failure. Due to its side effect such as angioedema, the patient has to discontinue the chemotherapy. In the present study, ACE inhibitors which are structurally similar to Quinapril and had reported biological activity in model organisms such as Oryctolagus Cuniculus and Rattus norvegicus was considered. A 2D-QSAR was modeled based on certain topological and constitutional descriptors along with its biological activity and found best inhibitory molecules. in vitro validation of these inhibitors will be an alternative for effective drug development against  hypertension.

Keywords: Quinapril, ACE inhibitors, hypertension, 2D-QSAR, Descriptors
__________________________________________________________

Code: JP-5 Bioinformatics analysis on Maize sugary 1 gene


DOWNLOAD THE POSTER IN PPT FORMAT HERE:
http://www.slideshare.net/prasanthperceptron/maize-poster

Vishal H. Desai, Chirag N. Patel, Vijay P. Mehta, S. Prasanth Kumar, Yogesh T. Jasrai and Himanshu A. Pandya

Bioinformatics Laboratory, Department of Botany, Gujarat University,  Ahmedabad-380 009.

ABSTRACT

Maize (Zea mays Linn.) holds a unique position in the global agricultural ground due to its high carbohydrate content. Maize sugary 1 (su1) gene encodes an essential starch debranching enzyme (SBEIIb) which hydrolysis α-(1→6) glycosidic bonds involved in starch biosynthesis. Genetic mutations in this gene contributes for the shrunken and immature kernel phenotypically and accumulation of simple sugars genotypically. In the present study, su1 gene was analyzed using Bioinformatics approaches. We made attempts to search for homologs in other sugar-rich plants. The maize su1 gene was predicted to be the characteristic feature promoting starch content and no evolutionary trace was identified. Further, maize cultivars distributed throughout the world showed a conserved pattern. We also noticed that the contents of GC bases are found to be relatively higher showing signs of highly de-regularized gene structure (CpG island). Conceptual translation of gene sequence provided an insight of ordered structure with a single stretch of disorderness at its N-terminal. Thus, we emphasize that the de-regularized gene structure of su1 makes its own way to diverge from other plant genera and the protein (enzyme) secondary structure level information showed that it is dense with high helix- rich content and a member of isoamylase enzyme family.

Keywords: Sugary 1 gene, Starch debranching enzyme, Bioinformatics, GC content, Disorderness.

Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease: Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein

S. Prasanth Kumar¹, Yogesh T. Jasrai*¹, Himanshu A. Pandya¹ and Rakesh M. Rawal²

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad- 380 009.

²Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer  Biology, The Gujarat Cancer & Research Institute (GCRI), Ahmedabad- 380 016                                                                                                                         

Recipient of Young Scientist Award for Research Article Presentation on “Emergence of Indian Tomato Yellow Leaf Curl Viral (TYLCV) Disease:  Insights from Evolutionary Divergence and Molecular Prospects of Coat Protein” on an National Symposium on “Evolving Paradigm to Improve Productivity from Dynamic Management and Value Addition for Plant Genetic Resources” held at Department of Botany, Gujarat University, Ahmedabad- 380 009 between Oct 13-15, 2011.


DOWNLOAD THE PRESENTATION HERE:
http://www.slideshare.net/prasanthperceptron/s-prasanth-kumar-young-scientist-awarded-presentation

ABSTRACT

Tomato leaf curl disease (TLCD) is manifested by yellowing of leaf lamina with upward leaf curl, leaf distortion, shrinking of the leaf surface and stunted plant growth caused by tomato yellow leaf curl virus (TYLCV). In the present study, we explored the evolutionary and molecular prospects of viral coat protein derived from an isolate of Vadodara district, Gujarat (ToLCGV-[Vad]).  We found that the amino acids in coat protein required for systemic infection, viral particle formation and insect transmission to host cells were sufficiently diverged. Modeling of coat protein revealed a topology similar to characteristic Geminate viral particle consisting of antiparallel β-barrel motif with N-terminus α-helix. The molecular interaction of coat protein with the plant DNA required for host cell arrest and propagation of viral particle was studied. We further emphasized the role of loops in coat protein structure as molecular recognition interface.

Keywords: Tomato leaf curl disease, Tomato yellow leaf curl virus, Geminate viral particle, Evolution, Modeling.

Need of Softwares/Author's Manuscript

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If you are in a need of any software/programs developed by me as well as the manuscripts (full text), I will be privileged to send the author manuscript/software as per your request.

Thank you.

MOLECULAR DESCRIPTORS ENHANCEMENT OF A COMMON STRUCTURE TOWARDS THE DEVELOPMENT OF α-GLUCOSIDASE AND α-AMYLASE INHIBITORS FOR POST-PRANDIAL HYPERGLYCEMIA (PPHG)

S. Prasanth Kumar*¹, Ravi G. Kapopara*¹, Saumya K. Patel¹,Yogesh T. Jasrai¹, Himanshu A. Pandya¹ and Rakesh M. Rawal²

¹Bioinformatics Laboratory, Department of Botany, University School of Sciences, Gujarat University, Ahmedabad-380 009.

²Division of Cancer Biology, Department of Medicinal Chemistry and Pharmacogenomics, Gujarat Cancer and Research Institute (GCRI), Ahmedabad- 380016.

Please navigate to this page for full text article: http://jbiopharm.com/index.php/ajpsbr/article/view/39



ABSTRACT:

The most challenging goal in the management of diabetic patient is to achieve normal blood glucose levels caused by post-prandial hyperglycemia (PPHG) or hyperinsulinemia, the individual risk factor contributes to the development of macrovascular complications. Synthetic hypoglycemic agents are available which has its own limitations and serious side-effects. The present study deals about the development of a common small molecular structure by enhancing the molecular descriptors required for binding with α-glucosidase and α-amylase enzymes, the two major targets of PPHG and to develop a monosaccharide-type inhibitor with many insights derived from pharmacophore studies, molecular alignment and molecular docking studies of known inhibitors. An hypothesis was designed which suggest the essential and/or minimal requirement of molecular descriptors in order to be an efficient binder of these two hydrolytic enzymes and subsequently, molecules with naturally occurring flavonoid structural architecture obeying the hypothesis was developed and evaluated in silico.

Prasanth Virtual Bioinfo Lab

READERS/FOLLOWERS- ATTENTION PLEASE

Dear Readers/Followers,

I would like to bring to your kind notice that programs hosted in this blog are  distributed under creative commons rights, which means no restriction in distribution, usage and exhibition with proper citation and acknowledgment. All the programs hosted here are developed by me. But, it is very disheartening that one of the readers/followers is removing all the cross-links which has been primarily used for uploading software and manuals. As a contributor in Science, no matter how little is it? please make room for others to reside and develop knowledge and don't be an obstacle for me and for others who are in real thrust for knowledge and developing something very important. I really apologize to those kind heart peoples who are always appreciating and praising my work for making such comments general which is very much important.

Thank you,

“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.

Download the Author's Proof here:
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

MY RESEARCH PROFILE

Dear Followers/Readers/Bloggers,

Wanna know more about me. Here is my CV




http://www.slideshare.net/prasanthperceptron/prasanth-kumar-cv-11397561

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


Kindly download this article here
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

COPYRIGHTED PROJECTS

Dear Readers/Followers,

I am pleased to inform you that the following projects submitted in the Bioinformatics Laboratory, Applied Botany Center, Gujarat University, Ahmedadbad is a part of the progressive projects developed in this Center with our research group. If you found any contents or disclosure of such titles for endorsement in public domain, it should be considered as 'Copyright Infringement' and no part can be reproduced in any means without the consent from the department and from me. Modifying the titles is also not allowed.
Any guide/co-guide are not involved in this projects.

KINDLY UNDERSTAND THAT THE PROJECTS MENTIONED BELOW ARE NOT DISTRIBUTED UNDER CREATIVE COMMON RIGHTS. Thank You.

1. Plant Bioactive Driven Fragment-based Drug Designing and Epitope-based Immunoinformatics Study of EspC protein of Mycobacterium tuberculosis  (Techniques : Fragment-based Drug Designing, Immunoinformatics)

2.2D-QSAR Analysis of Dihydrofolate reductase (DHFR) inhibitors with activity in Toxoplasma gondii and Lactobacillus casei  (Techniques : 2D-QSAR)

3. Pharmacophore-assisted Molecular Optimization of Calcineurin Inhibitors for Human Prion      Disease (Techniques : Molecular Docking, Pharmacophore Mapping, Manual Interpretation [Copyrighted protocol])

4. Biocomputational Analysis of Citrullinated Filaggrin Repeats for Rheumatoid Arthritis  (Techniques : Electrostatic Potential, Antigencity)

Concepts in Bioinformatics- All together in PPTS

Here, I am making it very easy to navigate and understand the key concepts of the hot spots topics.

Bioinformatics Practicals- A Complete Illustrated Guide to Beginners	http://www.slideshare.net/prasanthperceptron/bioinfo-practicals-prasanth-kumar
Epitope Prediction and its Algorithms	http://www.slideshare.net/prasanthperceptron/epitope-prediction-and-its-algorithms-7368259
Gene Order/Synteny	http://www.slideshare.net/prasanthperceptron/gene-order-7368257
Virtual Library Screening (VLS)	http://www.slideshare.net/prasanthperceptron/vls-7368188
The Mechanism of Protein Folding	http://www.slideshare.net/prasanthperceptron/the-mechanism-of-protein-folding
Sequence Alignment and its Algorithms	http://www.slideshare.net/prasanthperceptron/sequence-alignments-complete-coverage
SAGE technology	http://www.slideshare.net/prasanthperceptron/sage-technology
Proteome Databases	http://www.slideshare.net/prasanthperceptron/proteome-databases
Protein-Protein Interactions	http://www.slideshare.net/prasanthperceptron/protein-protein-interactions
Protein-DNA Interactions	http://www.slideshare.net/prasanthperceptron/protein-dna-interaction
Protein-DNA Interactions –An Illustrated Example	http://www.slideshare.net/prasanthperceptron/protein-dna-interaction-practical
Primary Databases-NCBI	http://www.slideshare.net/prasanthperceptron/primary-databases-ncbi
Pharmacophore Identification	http://www.slideshare.net/prasanthperceptron/pharmacophore-identification
Bibliographical Databases- MEDLINE	http://www.slideshare.net/prasanthperceptron/medline-7368165
In silico drug design an intro	http://www.slideshare.net/prasanthperceptron/in-silico-drug-design-an-intro
Identification of disease genes	http://www.slideshare.net/prasanthperceptron/identification-of-disease-genes
Genomics Application using GRAMENE	http://www.slideshare.net/prasanthperceptron/genomics-application-using-gramene
Gene Expression Profiling – Part I	http://www.slideshare.net/prasanthperceptron/gene-expression-profiling-i
Gene Expression Profiling – Part II	http://www.slideshare.net/prasanthperceptron/gene-expression-profiling-ii
Fragment Based Drug Designing (FBDD)	http://www.slideshare.net/prasanthperceptron/fbdd
De novo Drug Design	http://www.slideshare.net/prasanthperceptron/de-novo-drug-design
Biological Databases	http://www.slideshare.net/prasanthperceptron/biological-databases
Secondary Structural Elements with special attention to Ramachandran Plot	http://www.slideshare.net/prasanthperceptron/secondary-structural-elements-ramachandran-plot
Potential Energy Surface (PES) and Molecular Graphics	http://www.slideshare.net/prasanthperceptron/potential-energy-surface-molecular-graphics
Diagnosis of Genetic Diseases and Infectious Diseases	http://www.slideshare.net/prasanthperceptron/diagnosis-of-genetic-disorders-infectious-diseases-2188671
Softwares for Phylogenetic Analysis- What we expect?	http://www.slideshare.net/prasanthperceptron/softwares-for-phylogentic-analysis