Bioinformatics Centre
      (a Sub-DIC established at MGIMS in 1999 with funding from DBT, Ministry of Science & Technology, Govt of India)
   Biochemistry | JB Tropical Disease Research Centre | Mahatma Gandhi Institute of Medical Sciences, Sevagram

Research Publications (Bioinformatics)

J Infect Dis Ther 4:297. doi:10.4172/2332-0877.1000297 2. (2016)

Isoniazid with Multiple Mode of Action on Various Mycobacterial Enzymes Resulting in Drug Resistance

Jena L, Nayak T, Deshmukh S, Wankhade G, Waghmare P, Harinath BC

Abstract:

Isoniazid (INH), is one of the drugs shown to be effective and has been extensively used in TB control. Interestingly tuberculosis showed predominant drug resistance to isoniazid and thus lead to multi drug therapy in TB treatment. However, isoniazid is still advocated in latent TB and use as prophylactic in HIV infection and in children for prevention of TB. It is of interest that different studies revealing interaction of isoniazid with around 117 enzymes of mycobacteria influencing metabolic pathways by number of ways in addition to inhibiting mycolic acid synthesis and thus affecting growth of mycobacteria. The purpose of this review is to present the various mechanisms of action of isoniazid at different enzymes of MTB causing drug resistance..


Genomics Inform 2016;14(3):104-111 (2016)

Virtual Screening for Potential Inhibitors of NS3 Protein of Zika virus

Sahoo M, Jena L, Daf S, Kumar S

Abstract:

Zika virus (ZIKV) is a mosquito borne pathogen, belongs to Flaviviridae family having a positive-sense single-stranded RNA genome, currently known for causing large epidemics in Brazil. Its infection can cause microcephaly, a serious birth defect during pregnancy. The recent outbreak of ZIKV in February 2016 in Brazil realized it as a major health risk, demands an enhanced surveillance and a need to develop novel drugs against ZIKV. Amodiaquine, prochlorperazine, quinacrine, and berberine are few promising drugs approved by Food and Drug Administration against dengue virus which also belong to Flaviviridae family. In this study, we performed molecular docking analysis of these drugs against nonstructural 3 (NS3) protein of ZIKV. The protease activity of NS3 is necessary for viral replication and its prohibition could be considered as a strategy for treatment of ZIKV infection. Amongst these four drugs, berberine has shown highest binding affinity of –5.8 kcal/mol and it is binding around the active site region of the receptor. Based on the properties of berberine, more similar compounds were retrieved from ZINC database and a structure-based virtual screening was carried out by AutoDock Vina in PyRx 0.8. Best 10 novel drug-like compounds were identified and amongst them ZINC53047591 (2-(benzylsulfanyl)-3-cyclohexyl- 3H-spiro[benzo[h]quinazoline-5,1'-cyclopentan]-4(6H)-one) was found to interact with NS3 protein with binding energy of –7.1 kcal/mol and formed H-bonds with Ser135 and Asn152 amino acid residues. Observations made in this study may extend an assuring platform for developing anti-viral competitive inhibitors against ZIKV infection..


Genomics Inform 2016;14(3):96-103 (2016)

Identification of suitable natural inhibitor against Influenza A (H1N1) Neuraminidase protein by molecular docking.

Sahoo M, Jena L, Rath SN, Kumar S

Abstract:

The influenza A (H1N1) virus, also known as swine flu is a leading cause of morbidity and mortality since 2009. There is a need to explore novel anti-viral drugs for overcoming the epidemics. Traditionally, different plant extracts of garlic, ginger, kalmegh, ajwain, green tea, turmeric, menthe, tulsi, etc. have been used as hopeful source of prevention and treatment of human influenza. The H1N1 virus contains an important glycoprotein, known as neuraminidase (NA) that is mainly responsible for initiation of viral infection and is essential for the life cycle of H1N1. It is responsible for sialic acid cleavage from glycans of the infected cell. We employed amino acid sequence of H1N1 NA to predict the tertiary structure using Phyre2 server and validated using ProCheck, ProSA, ProQ, and ERRAT server. Further, the modelled structure was docked with thirteen natural compounds of plant origin using AutoDock4.2. Most of the natural compounds showed effective inhibitory activity against H1N1 NA in binding condition. This study also highlights interaction of these natural inhibitors with amino residues of NA protein. Furthermore, among 13 natural compounds, theaflavin, found in green tea, was observed to inhibit H1N1 NA proteins strongly supported by lowest docking energy. Hence, it may be of interest to consider theaflavin for further in vitro and in vivo evaluation.


J Pharmacogenomics Pharmacoproteomics 7: 159. doi:10.4172/2153-0645.1000159 (2016)

Genomics and Proteomics of Virulent, Avirulent and Drug Resistant Strains of Tuberculous Mycobacteria

Jena L, Wankhade G, Waghmare P, Harinath BC

Abstract:

Mycobacterium tuberculosis (MTB), the causal organism of the oldest infectious disease tuberculosis is the leading cause of morbidity and mortality worldwide. This pathogenic organism has been evolved into variety of strains with diverse genotype, phenotype and pathogenic properties such as MTB H37Rv and CDC1551 strains which are virulent, while MTB H37Ra is an avirulent strain and MTB KZN strain is resistant to different antituberculosis drugs. Due to the advancement in genome sequencing and molecular biology, whole genomes of different MTB strains have been completely sequenced. Genomic as well as proteomic comparison among the sequenced strains will help in understanding the differences between virulent, avirulent and resistant organisms. This article reviews the information available on completely sequenced MTB strains and presents the studies reported by researchers on genomic and proteomic comparison of various MTB strains.


Avicenna J Med Biochem. 2016 June; 4(1):e33958., DOI: 10.17795/ajmb-33958 (2016)

Identification of Unique Inhibitor against Oncogenic Proteins of High Risk Human Papillomavirus

Kumar S, Jena L, Sahoo M, Nayak T, Mohod K, Daf S, Varma AK

Abstract:

Background: Globally, the human papillomavirus (HPV) remains the foremost cause of cancer mortality among women. There is a need to identify natural anti-cancerous compounds that can fight against life-threatening infections by HPV. Various kinds of natural plant-originated compounds have been used in the traditional system of medicine for cancer therapy. Different studies have reported the effective inhibition of HPV infection enacted by certain natural compounds. Out of all the different HPV types, HPV-16 and 18 are the ones mainly associated with causing cervical cancer; furthermore, the E6 and E7 oncoproteins of these two high-risk HPV types typically interact with tumor protein 53 (p53) and retinoblastoma tumor suppressor proteins (pRb) of human host which consequent to cancer formation.
Objectives: The goal of this study is to identify unique plant-originated compounds to utilize in order to combat the high-risk human papillomavirus oncoproteins using docking measures.
Materials and Methods: Twelve natural compounds jaceosidin, withaferin A, curcumin, epigallocatechin-3-gallate (EGCG), artemisinin, gingerol, ursolic acid, ferulic acid, berberin, silymarin, resveratrol, and indol-3-carbinol were docked against E6 and E7 oncoproteins of high-risk HPV types 16 and 18 using a protein-ligand docking software called AutoDock4.2.
Results: Out of these 12 natural compounds, withaferin A was found to inhibit all four oncoproteins withminimumbinding energy.
Conclusions: These in silico findings indicate that withaferin A may be used as a common drug for cervical cancer caused by highrisk HPV types, perhaps by restoring the normal functions of tumor suppressor proteins.


EJBPS, 2016, Volume 3, Issue 5, 487-494. (2016)

Effect of G67R and G207E mutations on stability of Arylamine N-acetyltransferase in isoniazid resistance strains of Mycobacterium tuberculosis revealed by molecular dynamics simulation study

Jena L, Deshmukh S, Nayak T, Wankhade G, Harinath BC

Abstract:

Isoniazid (INH) is a front line drug used in the treatment of tuberculosis (TB) that remains a major cause of death worldwide. Isoniazid is a prodrug, requiring activation in the mycobacterial cell by the catalase / peroxidase activity of the KatG whereas arylamine N-acetyltransferase (NAT), a drug-metabolizing enzyme of MTB (Rv3566c) can acetylates isoniazid by transferring an acetyl group from acetyl coenzyme A to the terminal nitrogen of INH. Two mutations in NAT enzymes (G67R and G207E) were reported in clinical isolates of MTB associated with INH resistance. To study the effect of these mutations on NAT, molecular dynamics (MD) simulation analysis was performed for both wild type and two mutant models of NAT. Additionally, we performed docking of INH with the foresaid models of NAT enzyme followed by MD simulation of respective protein-ligand complexes. We have found that the binding site pocket was more stable in NAT_G67R mutant and the residues of this mutant model fluctuate less in both bound and unbound cases. In mutant models, the alteration of Gly to Arg (G67R) or Glu (G207E) provides extra electrostatic interaction with neighboring amino acids which supports the stability of the binding interfaces. Thus the stability of the mutant models observed by computational approach, might help in enhanced acetylation of INH and detoxification, resulting in isoniazid resistance in addition to the over expression of the enzyme when exposed to the drug.


Mycobact Dis 2016, 6: 202. doi: 10.4172/2161-1068.1000202 (2016)

Computational Approach in Understanding Mechanism of Action of Isoniazid and Drug Resistance

Jena L, Wankhade G, Waghmare P, Harinath BC

Abstract:

Most Multi Drug Resistance and Extremely Drug Resistance clinical strains of Mycobacterium tuberculosis are found to be resistant to the anti-tuberculousis drugs such as Isoniazid and Rifampicin. The mechanism of action and drug resistance due to Isoniazid has been the subject of extensive study. According to Tuberculosis drug resistance mutation database, 22 genes/proteins are associated with Isoniazid resistance such as katG, nat, inhA, ahpc, ndh, kasA etc. Mutation in the gene seems to affect the formation of Isoniazid to its active form or enhancing the catabolism thus making it ineffective. Studies in different laboratories have shown usefulness of computational approach in elucidating the mechanism of action of Isoniazid and development of drug resistance. Computational studies in our laboratory showed that a mutation in KatG (S315T/S315N) prevents free radical formation, thus the development of resistance to the drug. Further, we observed through molecular dynamics simulation approach that mutation (G67R/G207E) in NAT enzyme increases the stability and catalytic ability of the mutant enzyme, thus making the drug ineffective.


Biochem Mol Biol Educ. 2016 May 6;44(3):230-40 (2016)

Need assessment of enhancing the weightage of applied biochemistry in the undergraduate curriculum at MGIMS, Sevagram

Kumar S, Jena L, Vagha J

Abstract:

In order to review the need assessment of enhancing the weightage of Applied Biochemistry in the undergraduate curriculum at Mahatma Gandhi Institute of Medical Sciences (MGIMS), Sevagram, a validated questionnaire was sent to 453 participants which include 387 undergraduate students, 11 interns, 23 postgraduate students, and 32 faculty members. A web-based data collection and analysis tool was designed for online questionnaire distribution, data collection, and analysis. Response rate was 100%. Most of the respondents agreed that the subject Biochemistry has relevance in clinical practice (81.24%) and applied based learning of Biochemistry by medical undergraduates would help in overall improvement in the health standards/ patients care (83.44%). According to 65.12% respondents, most of the medical undergraduates read Biochemistry just for examination purpose only. Nearly half of the respondents agreed that minute details of biochemical reactions were not much useful in clinical practice (53.86%) and the vast majority of diagrammatic cycles memorized by the medical undergraduates had no relevance in clinical practice (51.21%), the decreased interest in learning the Applied Biochemistry was due to more amount of clinically irrelevant information taught to medical undergraduates (73.51%), there was a need to rethink for removing the diagrammatic biochemical cycles from curriculum for medical undergraduates (48.12%), the less learning of Applied Biochemistry or competencies would affect the clinical skills and knowledge of medical undergraduates (70.42%). The result of this study suggests that there is need for restructuring the Biochemistry curriculum with more clinical relevance.


International Journal of Mycobacteriology (4):276-283 (2015)

Study of mechanism of interaction of truncated isoniazid–nicotinamide adenine dinucleotide adduct against multiple enzymes of Mycobacterium tuberculosis by a computational approach

Lingaraja Jena, Shraddha Deshmukh, Pranita Waghmare, Satish Kumar, Bhaskar C. Harinath

Abstract:

Objective/Background: Isoniazid (INH) is one of the effective antituberculosis (TB) drugs used for TB treatment. However, most of the drug-resistant Mycobacterium tuberculosis (MTB) clinical strains are resistant to INH, a first-line antituberculous drug. Certain metabolic enzymes such as adenosylhomocysteinase (Rv3248c), universal stress protein (Rv2623), nicotinamide adenine dinucleotide (reduced)-dependent enoyl-acyl carrier protein reductase (Rv1484), oxidoreductase (Rv2971), dihydrofolate reductase (Rv2763c), pyrroline- 5-carboxylate dehydrogenase (Rv1187) have been identified to bind INH–nicotinamide adenine dinucleotide (INH–NAD) and INH–nicotinamide adenine dinucleotide phosphate adducts coupled to Sepharose resin. These enzymes are reported to be involved in many important biochemical processes of MTB, including cysteine and methionine metabolism, mycobacterial growth regulation, mycolic acid biosynthesis, detoxification of toxic metabolites, folate biosynthesis, etc. The truncated INH–nicotinamide adenine dinucleotide (oxidized) adduct, 4-isonicotinoylnicotinamide, isolated from urine samples of human TB patients treated with INH therapy is proposed to have antimycobacterial activity.
Methods: To understand the mechanism of interaction of the truncated INH–NAD adduct, binding energy studies were carried out on the aforementioned six enzymes with known three-dimensional structures using AutoDock4.2.
Results: In silico docking analysis of these MTB enzymes with the truncated INH–NAD adduct showed favorable binding interactions with docking energies ranging from 5.29 to 7.07 kcal/mol.
Conclusion: Thus, in silico docking study revealed that the INH–NAD adduct, which is generated in vivo after INH activation, may undergo spontaneous hydrolysis to form the truncated INH–NAD adduct and further binds and inhibits multiple enzymes of MTB, in addition to InhA, confirming that INH is an effective anti-TB drug acting at multiple enzymes. Further analysis of amino acid residues in the active site of INH–NAD-binding proteins showed the probable presence of catalytic triad in four enzymes possibly involved in INH binding to the enzyme.


International Journal of Mycobacteriology (4):354-355 (2015)

Efficacy and safety of isoniazid preventive therapy in light of increasing multi-drug resistance in tuberculosis

Lingaraja Jena, Bhaskar C. Harinath

Tuberculosis (TB) has emerged as a major warning to global public health as 33% of the world population is considered to be infected with Mycobacterium tuberculosis (MTB). Further, multi-drug-resistant strains of MTB in association with human immunodeficiency virus (HIV) have further created a worrying aspect to the TB problem. The current epidemics of extensively drug-resistant TB have also been an increasing threat in some regions around the world [1]. Most drug-resistant clinical strains of MTB, are resistant to isoniazid (INH), one of the most effective anti-TB drugs used for TB treatment [2]. Since existing TB control methods seem inadequate to prevent the rise in TB incidence among HIV-infected persons, the World Health Organization recommends INH preventive therapy (IPT) for HIV-infected persons as part of the core services [3].


Genomics Inform. 13(2):60-7 (2015)

In Silico Docking to Explicate Interface between Plant-Originated Inhibitors and E6 Oncogenic Protein of Highly Threatening Human Papillomavirus 18

Kumar S, Jena L, Sahoo M, Kakde M, Daf S, Varma AK

Abstract:

The leading cause of cancer mortality globally amongst the women is due to human papillomavirus (HPV) infection. There is need to explore anti-cancerous drugs against this life-threatening infection. Traditionally, different natural compounds such as withaferin A, artemisinin, ursolic acid, ferulic acid, (–)-epigallocatechin-3-gallate, berberin, resveratrol, jaceosidin, curcumin, gingerol, indol-3-carbinol, and silymarin have been used as hopeful source of cancer treatment. These natural inhibitors have been shown to block HPV infection by different researchers. In the present study, we explored these natural compounds against E6 oncoprotein of high risk HPV18, which is known to inactivate tumor suppressor p53 protein. E6, a high throughput protein model of HPV18, was predicted to anticipate the interaction mechanism of E6 oncoprotein with these natural inhibitors using structure-based drug designing approach. Docking analysis showed the interaction of these natural inhibitors with p53 binding site of E6 protein residues 108–117 (CQKPLNPAEK) and help reinstatement of normal p53 functioning. Further, docking analysis besides helping in silico validations of natural compounds also helped elucidating the molecular mechanism of inhibition of HPV oncoproteins.
Keywords: human papillomavirus 18, molecular docking, neoplasms, plant products


Interdiscip Sci Comput Life Sci. 7:1–7. (2015)

Virtual Screening for Potential Inhibitors of high-risk Human papillomavirus 16 E6 Protein

Satish Kumar, Lingaraja Jena, Kanchan Mohod, Sangeeta Daf, Ashok K Varma

Abstract:

Human papillomavirus (HPV), a life-threatening infection is the leading cause of cancer mortality among women worldwide and needs for designing anti-cancerous drugs. In the present study, we explored speci¯c novel inhibitors against E6 onco-protein of high risk HPV 16, known to inactivate tumor suppressor p53 protein. A homology model of HPV 16 E6 was built and validated using bioinformatics approach. A total of 5000 drug like compounds were downloaded from ZINC database based on the properties similar to the known inhibitor Jaceo- sidin (5, 7-Dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-6-methoxy-4H-chromen-4-one). Virtual-ligand-screenings approaches were applied to screen appropriate drug like compounds using molecular docking program Auto Dock Vina in PyRx 0.8 and 5 best novel drug-like compounds were identi¯ed as potential competitive inhibitors against HPV 16 E6 compared to Jaceosidin. Two amongst these 5 identi¯ed most potential inhibitors, N-[(5-methyl-1H- benzimidazol-2-yl)methyl]-4-oxo-3, 4-dihydrophthalazine-1-carboxamide and 6-[3-(3-°uoro-4-methyl-phenyl)-1, 2, 4-oxadiazol-5-yl]-1, 4-dihydroquinoxaline-2, 3-dione were found to interact with E6 with binding energy of ¡7:7 and ¡7:0 Kcal/mol respectively and form H-bonds with p53 binding site of E6 protein residues 113-122 (CQK- PLCPEEK). These two inhibitors may help restoration of p53 functioning. The Bioinformatics approach extends a promising platform for developing anti-cancerous competitive inhibitors targeting high-risk HPV 16.
Keywords: HPV 16, E6, Virtual Screening, Inhibitors, Cancer, p53


International Journal of Mycobacteriology 3(4):276-282 (2014)

Computational approach to understanding the mechanism of action of isoniazid, an anti-TB Drug

Lingaraja Jena, Pranita Waghmare, Supriya Kashikar, Satish Kumar, Bhaskar C. Harinath

Abstract:

Tuberculosis (TB) is an ancient disease caused by Mycobacterium tuberculosis (MTB), which remains a major cause for morbidity and mortality in several developing countries. Most drug-resistant MTB clinical strains are resistant to isoniazid (INH), a first-line anti-TB drug. Mutation in KatG, a catalase-peroxidase, of MTB is reported to be a major cause of INH resistance. Normally upon activation by KatG, INH is converted to an active intermediate which has antimycobacterial action in MTB. This INH intermediate in the presence of NADH forms INH-NAD adduct which inhibits inhA (2-trans-enoyl-acyl carrier protein reductase) of MTB, thus blocking the synthesis of mycolic acid, a major lipid of the mycobacterial cell wall. In this docking study, the high binding affinity of INH-NAD adduct towards InhA was observed in comparison with INH alone. In this study, two resistant mutants of KatG (S315T and S315N) were modeled using Modeller9v10 and docking analysis with INH was performed using AutoDock4.2 and the docking results of these mutants were compared with the wild type KatG. Docking results revealed the formation of a single hydrogen (H) bond between the secondary amine nitrogen (–NH) of INH with Thr or Asn residues in place of Serine at 315 position of KatG mutant strains respectively, whereas in the case of the wild type, there was no H-bond formation observed between INH and Ser315. The H-bond formation may prevent free radical formation by KatG in mutant strains thus the development of resistance to the drug. This in silico evidence may implicate the basis of INH resistance in KatG mutant strains.
Keywords: Isoniazid, KatG, InhA, Drug resistance, Mutation


Indian J Tuberc. 61(3):200-6 (2014)

Effect of single amino acid mutations on function of Mycobacterium tuberculosis H37Rv and H37Ra by computational approaches

Lingaraja Jena, Supriya Kashikar, Satish Kumar, Bhaskar C. Harinath.

Abstract:

BACKGROUND: Studies have been reported on genomic analysis to explain virulence of MTB H37Rv vs. MTB H37Ra strain. Proteomic comparison analysis at our centre has shown variability of 244 proteins in MTB H37Rv. A single amino acid mutation in protein sequence may cause alteration in protein structure and function that may account for virulence and drug resistance properties of pathogenic organisms.

AIM: To find the effect of single amino acid mutations on Mycobacterium tuberculosis H37Rv and H37Ra using computational approaches

METHODS: Proteins with single amino acid mutation were analysed by different mutation analysis systems such as SIFT, PolyPhen, PROVEAN and HOPE. Subsequently, structure comparison of proposed modelled structure of mutant proteins of MTB H37Ra with native proteins of MTB H37Rv was performed.

RESULTS: We observed that amongst 40 single amino acid mutated proteins of MTB H37Ra, five were found to be damaged by all the mutation analysis systems. Upon structure comparison, the RMSD values between the native and mutant type proteins were found to be significantly higher. All the five proteins showed important biological function in MTB H37Rv. Further, when these five proteins of MTB H37Ra were compared with corresponding proteins of other virulent strains of MTB (i.e. F11 and CDC 1551), similar observation was made.

CONCLUSION: The data suggests the important role of single amino acid mutation in five proteins in causing changes in the virulence and pathogenicity of clinical strains of MTB.


Int. J. Bioautomation.18(4):315-324 ( 2014)

Molecular Docking Explains Atomic Interaction between Plant-originated Ligands and Oncogenic E7 Protein of High Risk Human Papillomavirus Type 16

Satish Kumar, Lingaraja Jena, Sneha Galande, Sangeeta Daf, Ashok K Varma.

Abstract:

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.
Keywords: comparative modeling, DNA probes, genome, HPV, neoplasms, proteome.


Genomics Inform. 12(2):64-70 ( 2014)

Elucidating Molecular Interactions of Natural Inhibitors with HPV-16 E6 Oncoprotein through Docking Analysis

Satish Kumar, Lingaraja Jena, Sneha Galande, Sangeeta Daf, Kanchan Mohod, Ashok K Varma.

Abstract:

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The life-threatening infection caused by HPV demands the need for designing anticancerous drugs. In the recent years, different compounds from natural origins, such as carrageenan, curcumin, epigallocatechin gallate, indole-3-carbinol, jaceosidin, and withaferin, have been used as a hopeful source of anticancer therapy. These compounds have been shown to suppress HPV infection by different researchers. In the present study, we explored these natural inhibitors against E6 oncoprotein of high-risk HPV-16, which is known to inactivate the p53 tumor suppressor protein. A robust homology model of HPV-16 E6 was built to anticipate the interaction mechanism of E6 oncoprotein with natural inhibitory molecules using a structure-based drug designing approach. Docking analysis showed the interaction of these natural compounds with the p53-binding site of E6 protein residues 113-122 (CQKPLCPEEK) and helped the restoration of p53 functioning. Docking analysis, besides helping in silico validation of natural compounds, also helps understand molecular mechanisms of protein-ligand interactions.
Keywords: DNA probes HPV; molecular docking; neoplasms; plant products


Genomics Inform. 11(4):289-291 (2013)

hpvPDB: An Online Proteome Reserve for Human Papillomavirus

Kumar S, Jena L, Daf S, Mohod K, Goyal P, Varma AK

Abstract:

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.
Keywords: comparative modeling, DNA probes, genome, HPV, neoplasms, proteome.


International Journal of Mycobacteriology 2(4): 220 - 226 (2013)

Comparative proteomic analysis of Mycobacterium tuberculosis strain H37Rv versus H37Ra

Lingaraja Jena, Supriya Kashikar, Satish Kumar, Bhaskar C. Harinath

Background

Mycobacterium tuberculosis (MTB) H37Ra is an attenuated tubercle bacillus closely related to the virulent type strain MTB H37Rv. In spite of extensive study, variation in virulence between the MTB H37Rv and MTB H37Ra strains is still to be understood. The difference in protein expression or structure due to mutation may probably be an important factor for the virulence property of MTB H37Rv strain.

Methods

In this study, a whole proteome comparison between these two strains was carried out using bioinformatics approaches to elucidate differences in their protein sequences.

Results

On comparison of whole proteome using NCBI standalone BLAST program between these two strains, 3759 identical proteins in both the strains out of 4003 proteins were revealed in MTB H37Rv and 4034 proteins were revealed in MTB H37Ra; 244 proteins of MTB H37Rv and 260 proteins of MTB H37Ra were found to be non-identical. A total of 172 proteins were identified with mutations (Insertions/deletions/substitutions) in MTB H37Ra while 53 proteins of MTB H37Rv and 85 proteins of MTB H37Ra were found to be distinct. Among 244 non-identical proteins, 19 proteins were reported to have an important biological function; In this study, mutation was shown in these proteins of MTB H37Ra.

Conclusion

This study reports the protein differences with mutations between MTB H37Rv and H37Ra, which may help in better understanding the pathogenesis and virulence properties of MTB H37Rv.


Onl J Bioinform., 14 (3): 302-310, 2013

In silico inhibitors for human papillomavirus 16 E7 protein

Kumar S, Jena L, Mohod K, Daf S, Varma A.

Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. In silico inhibitors against E7 onco-protein of high risk HPV 16 which inactivates retinoblastoma tumor suppressor protein (pRB) is described. A homology model of HPV 16 E7 was built using Phyre 2 server followed by structural refinement and energy minimization by YASARA Energy Minimization Server. The refined model reliability was assessed through Procheck, ProSA and ProQ. A total of 5000 drug like compounds were downloaded from ZINC database based on the properties similar to the known inhibitor Jaceosidin (5,7-Dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-6-methoxy-4H-chromen-4-one). Virtual -ligand - screenings approaches were applied to screen the appropriate drug like compounds using molecular docking program Auto Dock Vina in PyRx 0.8 and 5 best novel drug-like compounds were identified as potential competitive inhibitors against E7 of HPV 16 compared to Jaceosidin, a known inhibitor.


International J Bioautomation, 2012;16(2):101-110.

In silico Structural Prediction of E6 and E7 Proteins of Human papillomavirus Strains by Comparative Modeling

Satish Kumar, Lingaraja Jena, Vidya W. Bhomale & Sangeeta Daf

More than 200 different types of Human papillomavirus (HPV) are identified, 40 transmit extensively through sexual contacts affecting the genital tract. HPV strains have been etiologically linked to vaginal, vulvar, penile, anal, oral and cervical cancer (99.7%) as a result of mutations leading to cell transformations due to interference of E6 and E7 oncoproteins with p53 and pRB tumor suppressor genes respectively, besides other cellular proteins. As structures of E6 and E7 proteins are not available, the simultaneous structural analysis of E6 and E7 proteins of 50 different HPV strains was carried out in detail for prediction and validation, using bioinformatics tools. E6 and E7 proteins sequences were retrieved in FASTA format from NCBI and their structures predicted by comparative modeling using modeller9v6 software. Further, most of the HPV strains showed good stereochemistry results in most favored regions when subjected to PROCHECK analysis and subsequently each protein was validated using ProSA-web tool. The work carried out on comparing and exploring the structural variations in these oncogenic proteins might help in genome based drugs and vaccines designing, beyond their limitations.


Bioinformation 8(24): 1240-1242 (2012)

MycoProtease-DB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases

Lingaraja Jena, Satish Kumar & Bhaskar Chinnaiah Harinath

MycoProtease-DB is an online MS SQL and CGI-PERL driven relational database that domiciles protease information of Mycobacterium tuberculosis (MTB) complex and Nontuberculous Mycobacteria (NTM), whose complete genome sequence is available. Our effort is to provide comprehensive information on proteases of 5 strains of Mycobacterium tuberculosis (H37Rv, H37Ra, CDC1551, F11 and KZN 1435), 3 strains of Mycobacterium bovis (AF2122/97, BCG Pasteur 1173P2 and BCG Tokyo 172) and 4 strains of NTM (Mycobacterium avium 104, Mycobacterium smegmatis MC2 155, Mycobacterium avium paratuberculosis K-10 and Nocardia farcinica IFM 10152) at gene, protein and structural level. MycoProtease-DB currently hosts 1324 proteases, which include 906 proteases from MTB complex with 237distinct proteases & 418 from NTM with 404 distinct proteases. Flexible database design and easy expandability & retrieval of information are the main features of MycoProtease-DB. All the data were validated with various online resources and published literatures for reliable serving as comprehensive resources of various Mycobacterial proteases.

Availability: The database is available for free at
                     http://www.bicjbtdrc-mgims.in/MycoProtease-DB/


 

Bioinformation 2011;6(3):131-133.

MTB-PCDB: Mycobacterium tuberculosis proteome comparison database.

Lingaraja Jena, Gauri Wankhade, Satish Kumar & Bhaskar Chinnaiah Harinath

The Mycobacterium tuberculosis Proteome Comparison Database (MTB-PCDB) is an online database providing integrated access to proteome sequence comparison data for five strains of Mycobacterium tuberculosis (H37Rv, H37Ra, CDC 1551, F11 and KZN 1435) sequenced completely so far. MTB-PCDB currently hosts 40252 protein sequence comparison data obtained through inter-strain proteome comparison of five different strains of MTB. 2373 proteins were found to be identical in all 5 strains using MTB H37Rv as reference strain. To enable wide use of this data, MTB-PCDB provides a set of tools for searching, browsing, analyzing and downloading the data. By bringing together, M. tuberculosis proteome comparison among virulent & avirulent strains and also drug susceptible & drug resistance strains MTB-PCDB provides a unique discovery platform for comparative proteomics among these strains which may give insights into the discovery & development of TB drugs, vaccines and biomarkers.

Availability: The database is available for free at
                     http://www.bicjbtdrc-mgims.in/MTB-PCDB/


Bioinformatics India. Oct-Dec 2005;3(4):36-46.

 FilaDB - Database software for information storage and retrieval on detection and management of filaria patients. Deshmukh P, Jumde J, Kumar S, Reddy MVR, Harinath BC.

Filariasis is prevalent in the developing tropical countries. The disease is reported to be responsible for 5 million DALYS (Disability Adjusted Life Years) lost annually, ranking third among the Tropical diseases after Malaria and Tuberculosis (WHO, 2002).  According to the recent estimates available, there are 412 million people exposed to the infection in India with 31 million people harboring microfilariae and another 20 million suffering from chronic manifestations. Long-term treatment with DEC followed by immunomonitoring, appears to be effective in successful management of filariasis. Extensive data relating to filaria detection and monitoring has been developed for the past few decades at JB Tropical Disease Research Centre. This was burdened with paper-based patient record of data organisation. An integrated computer-based database management system is perceived as an attractive solution to such information storage burden. FilaDB – a user-friendly database software has been developed at this Centre to provide an environment that is convenient and efficient for clinicians and medical researchers to use in retrieving and storing patient’s information, their status, diagnosis, monitoring and overall management. FilaDB is designed by using ASP as frontend and MySQL as a backend. This network based database software can be assessed by the end users on the LAN. It provides dynamic, easy and user-friendly multiple parameter search facility to access information for diagnosis of infection, immunomonitoring and management for development of evidence based medicine to individualize treatment.  As this is the patients’ information database software, security as well as confidentially of the data is also maintained.