Dr. Vikash Kumar Dubey
Assistant Professor, Department of Biotechnology,
Indian Institute of Technology Guwahati, Assam, India-781039
Phone: +91- 361-2582203, Fax: +91-361-2582249
E-mail: vdubey@iitg.ac.in
Research Interests:
a) Protein engineering and structure-function relationship of proteins. Basic research into issues of protein
stability, activity, folding and evolution, with applied research in the development of useful form of
therapeutically important proteins by improving their activity and stability.
b) Purification, characterization and structure determination of proteases and their commercial
exploitation.
c) Development of drug against Leishmaniasis by targeting parasite specific metabolic pathways
(trypanothione metabolism).
Academic Details
Ph.D (Molecular Biology): Banaras Hindu University, Varanasi, U.P, India (2003)
Topic of Ph.D thesis: “Protein Folding Problem: Folding intermediates in procerain from Calotropis
procera and cytochrome c552 from Hydrogenobacter thermophilus.”
Advisor: Prof. M.V. Jagannadham, Molecular Biology Unit, Institute of Medical Sciences,
Banaras Hindu University, Varanasi
M.Sc (Biochemistry): Banaras Hindu University, Varanasi, U.P, India (1999)
B.Sc (Chemistry): Banaras Hindu University, Varanasi, U.P, India (1997)
Professional Experience
September 2006- Present: Assistant Professor, Department of Biotechnology, Indian Institute of Technology
Guwahati
January 2004- September 2006: Post-Doctoral Research Associate, Florida State University, Tallahassee,
Florida, USA.
Advisor: Prof. Michael Blaber, Department of Biomedical Sciences, College of Medicine, Florida State
University, Tallahassee, FL 32306-4300, USA
September 2002-January 2003: Fellow of “Intituto Pasteur-Foundazione Cenci Biolognetti”,
Rome, Italy.
Advisor: Prof. Maurizio Brunori, Department of Biochemical Sciences, University of Rome, Italy.
January 2000-December 2001: Junior Research Fellow (CSIR-JRF)
January 2002-December 2003: Senior Research Fellow (CSIR-SRF)
Award and Honors
1
1. Editor-in-Chief: “Journal of Proteins and Proteomics”
http://www.serialspublications.com/journals1.asp?jid=364&dtype=1&jtype=1
2. Editorial Advisory board: Advances in Natural and Applied Sciences (www.aensi.org).
3. Editorial Advisory board: Advances in Medical and Dental Sciences (www.aensi.org).
4. Editor: “Biotechnology and Molecular Biology Reviews” (http://www.academicjournals.org/bmbr).
5. Editorial board member of “International Journal of
(http://www.ijmst.org-a.googlepages.com/journaleditorialboard).
Medical
Sciences
and
Technology”
6. Editorial board member of “International Journal of Life Sciences and Technology” (http://www.ijlst.orga.googlepages.com/journaleditorialboard).
7. Editor board member of International Journal of BioSciences and Technology http://www.ijbst.org;
International
Journal
of
Biological
Sciences
and
Technology
(http://sites.google.com/a/ijblst.org/journal/Home); International Journal of BioSciences,
Psychiatry and Technology (http://sites.google.com/a/ijbspt.org/journal/Home)
8. Editorial
Review
Board
member
(http://www.scientificjournals.org/index.php).
9.
of
Scientific
Journals
International
(SJI).
Reviewer for several journals like Biochemistry, Phytochemistry, International Journal of Biological
Macromolecules, Biotechnology and Molecular Biology Reviews etc.
10. Senior Research Fellowship, CSIR, Government of India
11. Training Fellowship from “Intituto Pasteur-Foundazione Cenci Biolognetti”, Rome, Italy
12. Junior Research Fellowship, CSIR, Government of India.
13. Qualified national
lectureship.
eligibility
test
(CSIR-NET),
for
research
fellowship
and
eligibility
for
Publications in international Journals
31. Nandini Sarkar, Abhay Narain Singh and Vikash Kumar Dubey*. Effect of curcumin on amyloidogenic
property of molten globule like intermediate state of 2,5-Diketo-D-Gluconate Reductase A. Biol Chem.
In Press . [*Corresponding author]
30. Syed Baquer Rizvi , Anil Kumar Shukla and Vikash Kumar Dubey*. A Simple method based on
multiple alignment and phylogeny to derive a correlation between the protein fold and sequence via
motif search. Interdisciplinary Sciences-- Computational Life Sciences, In Press.
29. Bishal Kumar Singh and Vikash Kumar Dubey*. In silico studies on tryparedoxin peroxidase of
Leishmania infantum: Structural aspects. Current Pharmaceutical Biotechnology. In Press
[*Corresponding author]
28. Nandini Sarkar Pramod Kumar Srivastava and Vikash Kumar Dubey*. Understanding the Language
of Vitamin C. Current Nutrition & Food Science, 2009, 5, 53-55. [*Corresponding author]
27. Bishal K. Singh, Nandini Sarkar, M.V. Jagannadham and Vikash K. Dubey*. Modeled Structure of
Trypanothione Reductase of Leismania infantum. Biochemistry and Molecular Biology Reports, 2008,
41, 444-447. [*Corresponding author]
26. Vikash K Dubey* and M.V Jagannadham. Roles for cavities in protein structure: New
insights. Current Proteomics, 2008, 5, 157-160 [*Corresponding author]
25. Ritu Tomar, Vikash Kumar Dubey,* and M.V. Jagannadham* Biophysical characterization
2
and folding studies of plant protease, Wrightin: identification folding intermediate under
different conditions. The Protein Journal, 2009, In press [*Co-corresponding author]
24. Monu Pande, N K Prasanna Kumari, Vikash Kumar Dubey*, Pinky Tripathi, and M.V.
Jagannadham*. Stability and Unfolding Studies on Alkaline Denatured State (Ip) of Pepsin.
Process Biochemistry, 2009, 44 (2009) 906–911 [*Co-corresponding author]
23. Ritu Tomar, Vikash Kumar Dubey, and M.V. Jagannadham* Effect of Alkyl Alcohols on partially
unfolded state of Proteinase K: differential stability of -helix and -sheet rich regions of the enzyme.
Biochimie, 2009, In press. DOI: 10.1016/j.biochi.2009.04.013
22. Jihun Lee, Vikash K Dubey, Liam M Longo, Michael Blaber. Logical OR Redundancy within the AsxPro-Asx-Gly Type I β-turn Motif. 2008, Journal of Molecular Biology, 377, 1251-1264.
21. Vikash K. Dubey*, Monu Pande, Bishal Kumar Singh and Medicherla V. Jagannadham. Realm of
Papain-Like Proteases: Applications of their Inhibitors. Afr. Journal of Biotechnology, 2007, 6, 10771086. [*Corresponding author]
20. Vikash K. Dubey*, Bishal K Singh, Nandini Sarkar, Monu Pande and M.V Jagannadham. Biophysical
characterization of Fibroblast Growth Factor homologous Factor-1b (FHF-1b): Sodium dodecyl sulfate
promotes two state folding. Protein & Peptide Letters, 2008, 15, 215-218 [*Corresponding author]
19. Vikash Kumar Dubey, Jihun Lee, Thayumana Somasundaram, Sachiko Blaber and Michael Blaber.
Spackling the crack: stabilizing human fibroblast growth factor-1 by targeting the N- and C-termini strand interactions. J. Mol. Biol., 2007, 371, 256-268.
18. Sreedevi Nallamsetty, Vikash K. Dubey, Monu Pande, P. K. Ambasht and M.V. Jagannadham.
Accumulation of partly folded states in the equilibrium unfolding of ervatamin A: Spectroscopic
description of the native, intermediate, and unfolded states. Biochimie, 2007, 89, 1416-24.
17. Monu Pande, Vikash Kumar Dubey, Vishal Sahu and M.V. Jagannadham. Conformational Plasticity
of Cryptolepain: Accumulation of Partially Unfolded States in Denaturants induced Equilibrium
Unfolding. Journal of Biotechnology, 2007, 131, 404-414.
16. Monu Pande, Vikash K. Dubey, and Medicherla V. Jagannadham. Crystallization and preliminary x–
ray analysis of cryptolepain: A novel glycosylated serine protease from Cryptolepis buchanani. Acta
Crystallographica, 2007, F63, 74-77
15. Jihun Lee, Vikash Kumar Dubey, Thayumanasamy Somasundaram and Michael Blaber. Conversion
of type I 4:6 to 3:5 -turn types in human acidic fibroblast growth factor: Effects upon structure, stability,
folding, and mitogenic function . Proteins: Structure Function Bioinformatics. 2006, 62, 686-697.
31. Monu Pande, Vikash K. Dubey, Subhash Chandra Yadav and Medicherla V. Jagannadham. A Novel
Serine Protease Cryptolepain, from Cryptolepis buchanani: Purification and Biochemical
Characterization. J Agric Food Chem. 2006, 27, 10141-10150.
13. Vikash Kumar Dubey, Monu Pande and M.V. Jagannadham. Snapshots of Protein Folding Problem:
Implications of Folding and Misfolding Studies. Protein & Peptide Letters, 2006, 13, 883- 888.
12. Vikash K. Dubey, Ashu Saha, M.V. Jagannadham and A.M. Kayastha. Effect of Organic solvent on
“molten globule” state of procerain: -sheet to -helix switchover in presence of TFE. Protein and
Peptide Lett. 2006, 13, 545-547.
11. Vikash K. Dubey, Jihun Lee, and Michael Blaber. Redesigning Symmetry-Related “Mini-Core”
Regions of FGF-1 to Increase Primary Structure Symmetry: Thermodynamic and Functional
Consequences of Structural Symmetry. Protein Science, 2005, 14, 2315-2323.
10. Carlo Travaglini-Allocatelli, Stefano Gianni, Vikash K. Dubey, Alessandro Borgia, Adele Di Matteo,
3
Daniele Bonivento, Francesca Cutruzzola, Kara L. Bren, Maurizio Brunori. An obligatory intermediate in
the folding pathway of cyctochrome C552 from Hydrogenobacter thermophilus. J. Biol Chem., 2005,
280, 25729-25734.
9.
Vikash Kumar Dubey and Michael Blaber. Redesigning symmetry-related “mini-core” regions of FGF1 to increase primary structure symmetry. 2005. Protein Science, 14 (Supp. 1), 175.
8.
Stephen R. Brych, Vikash K. Dubey, Ewa Bienkiewicz, Jihun Lee, Timothy M. Logan and Michael
Blaber. Symmetric primary and tertiary structure mutations within a symmetric superfold: A solution and
not a constraint to achieving a foldable polypeptide? J. Mol. Biol., 2004, 344, 769-780.
7.
Monica Sundd, Suman Kundu, Vikash Kumar Dubey and M.V. Jagannadham. Unfolding of ervatamin
C in the presence of organic solvents: Sequential unfolding of the protein in O-state. Journal of
Biochemistry and Molecular Biology, 2004, 37, 586-596.
6.
Vikash Kumar Dubey and M.V. Jagannadham. Differences in the unfolding of procerain induced by
pH, GuHCl, urea and temperature. Biochemistry, 2003, 42, 12287-12297.
5. Vikash Kumar Dubey and M.V. Jagannadham. Procerain, a stable cysteine protease from Calotropis
procera. Phytochemistry, 2003, 62, 1057-1071.
Other Publications in international Journals
4. Vikash Kumar Dubey. Structural Genomics on Membrane Proteins.
Biotechnology, 2009, 157 (1), 111.
Applied Biochemistry and
Publications In Indian Journals
3.
Bishal K. Singh, Nandini Sarkar and Vikash K. Dubey*. Modeled Structure of Trypanothione
synthetase of Leishmania infantum for development of novel therapeutics for leishmaniasis. Current
Trends in Biotechnology and Pharmacy. 2008, 2, 390-395. [*Corresponding author]
2.
Anil Kumar Shukla, Utpal Bora and Vikash Kumar Dubey*. Functional Adaptations in Fibroblast
Growth Factor (FGFs) Family. Journal of Proteins and Proteomics, In Press, [*Corresponding author]
1.
Naresh Kasoju, Shahin Sharif Ali, Vikash Kumar Dubey* and Utpal Bora*. Exploiting the potential of
Collagen as a Natural Biomaterial in Drug Delivery. Journal of Proteins and Proteomics, In Press, [*Cocorresponding author]
submitted
2. Nandini Sarkar, Anil K. Shukla and Vikash Kumar Dubey *. A Short Tale of Protein Misfolding,
Aggregation and Diseases. Current Medicinal Chemistry. [*Corresponding author]
.
Conference presentations/ proceedings
13. Abhay Narain Singh, Bishal Kumar Singh, and Vikash Kumar Dubey*. Drug designing against
leishmaniasis by targeting parasite specific trypanothione metabolic pathway. NE Conference of
Medical Microbiologysts-09. Guwahati Medical College Guwahati, April 24-26, 2009.
12. Nandini Sarkar, and Vikash Kumar Dubey*. Studies on 2,5 Diketo D Gluconate Reductase:
Identification of Amyloid forming folding intermediate under acidic condition. 77th Annual Meeting of
Society of Biological Chemists, India held at IIT Madras, Chennai December 18-20, 2008. [Received
B.S Narasinga Rao Best Poster presentation Award]
11. Bishal Kumar Singh, and Vikash Kumar Dubey*. Structure of Trypanothione Reductase of Leishmania
infantum: A therapeutic target for drug discovery. International conference on Biotechnology, Vellore
Institute of Technology, India. February 6-8, 2008.
10. Jihun Lee, Vikash Dubey, L. Longo and Michael Blaber A Logical OR Redundancy within the Asx-
4
Pro-Asx-Gly Type I -turn Motif. 22nd Annual Symposium of The Protein Society. July 19-23, 2008 at
the San Diego, California, USA. (Published in Protein Science, Vol 17, Suppl. 1, p232 2008)
9. Vikash Kumar Dubey, Jihun Lee, Thayumanasamy Somasundaram and Michael Blaber. Stability,
folding and functional consequences of imposed primary structure symmetry of FGF-1. Research Fair,
College of Medicine, Florida State University, Tallahassee, USA, Feb., 28, 2006
8. Jihun Lee, Vikash Kumar Dubey, and Michael Blaber. Effect of type I 3:5 G1 bulge -turn on protein
stability and folding kinetics. Research Fair, College of Medicine, Florida State University, Tallahassee,
USA, Feb., 28, 2006.
7. Vikash Kumar Dubey and Michael Blaber. Redesigning symmetry-related “mini-core” regions of FGF-1
to increase primary structure symmetry. 19th Annual Symposium of Protein Society. Boston, USA. July
29 - Aug. 3, 2005.
6. Vikash K. Dubey, Stephen R. Brych, Jihun Lee, and Michael Blaber. Protein symmetry, stability and
function, CALCON 2004 - the 59th Annual Calorimetry Conference,. Santa Fe, New Mexico, USA, June
27 - July 1, 2004.
5. Carlo Travaglini-Allocatelli, Stefano Gianni, M.G. Bigotti Alessandro Borgia, Vikash K. Dubey,
Francesca Cutruzzola and Maurizio Brunori.The folding landscape of cytochrome c family: tarps,
intermediate and pathways. European Molecular Biology Organization’s meeting on Protein folding and
misfolding at Rome, Italy, April 3-5, 2003
4. Vikash Kumar Dubey and M.V. Jagannadham. Equilibrium Unfolding of procerain: Sequential unfolding
in molten globule like state. European Molecular Biology Organization’s meeting on Protein folding and
misfolding at Rome, Italy, April 3-5, 2003.
3. Vikash Kumar Dubey and M.V. Jagannadham. Procerain, a stable cysteine protease from Calotropis
procera. International Symposium on Stabilization of Enzyme and Biosensors, Chennai, India.
November 24-29, 2001
2. Attended research scholar’s conference on “Frontier areas of science, engineering and technology
(VISION-2001)” at Department of physics, Banaras Hindu University, Varanasi, India, May 6, 2001.
1. Vikash Kumar Dubey and M.V. Jagannadham. Cleavage of one specific disulfide bond of Ervatamin C.
National Symposium on Biophysics, at Institute of Chemical Biology, Calcutta, India, January 15-17,
2001.
Patent filed*
3. Vikash Kumar Dubey and Michael Blaber. Mutant polypeptides of Fibroblast Growth Factor-1 (US
patent Application No. 11/983,217 dated November 7, 2007)
1. Vikash Kumar Dubey and Michael Blaber. Mutant polypeptides of Fibroblast Growth Factor-1 (US
patent Application No. 11/983,215 dated November 7, 2007)
1. Vikash Kumar Dubey and Michael Blaber. Mutant polypeptides of Fibroblast Growth Factor-1 (US
patent Application No. 11/983,206 dated November 7, 2007)
*Although the names are same, all three are separate patents. each application is about different mutant
forms and bear unique application numbers.
oooOooo
5
Scientific Contributions of Dr. Vikash Kumar Dubey
Proteases are one of the most important classes of enzyme and expressed throughout the animal
and plant kingdoms as well as in viruses and bacteria. The protease family has drawn special
attention for drug target for cure of several diseases such as osteoporosis, arthritis and cancer.
Dr. Dubey has purified a novel protease, procerain form a medicinal plan Calotropis procera and
studied extensively with respect to activity- stability and folding (Phytochemistry, 2003, 62, 10571071; Biochemistry, 2003, 42, 12287-12297)
Moreover, Dr. Dubey has likewise made cutting edge contributions to the general
knowledge of the scientific community regarding protein folding and the role of turn sequences in
the stabilization of proteins (Journal of Molecular Biology, 377, 1251-1264; Proteins: Structure
Function Bioinformatics. 2006, 62, 686-697). Equally important, his research proved to be of great
practical value in the treatment of cardiovascular diseases which are characterized by an
impaired supply of blood resulting from narrowed or blocked arteries. Cardiovascular diseases
are the leading cause of death world wide. Dr. Dubey provided stunning new insights in the
development of a stable mutant form of human acidic fibroblast growth factor (FGF-1) for
developing a new treatment for patients suffering from degenerative heart disease. Obstructed
blood vessels and blocked arteries have traditionally been treated through angioplasty—the
mechanical widening of a vessel—or with bypass surgery. However, many patients exhibit
numerous small blockages that defy treatment by one of these traditional means. Until now, such
patients have effectively had no hope for successful medical intervention. Their medical condition
is effectively a death sentence. Dr. Dubey, however, has made scientific advances that at last
offer hope to these patients. He has conducted research that is critical to designing a new and
alternative treatment whereby stable mutant from of FGF-1 could be injected into the affected
areas of these patients’ hearts (J. Mol. Biol., 2007, 371, 256-268; Protein Science, 2005, 14,
2315-2323. J. Mol. Biol., 2004, 344, 769-780.)
His current research is also focused on development of novel theraputics against
Leishmaniasis by targeting parasite specific metabolic pathways (trypanothione metabolism).
According to current World Health Organization (WHO) statistics there are 12 million people
currently affected by leishmaniasis in 88 countries on five continents - Africa, Asia, Europe, North
America and South America - with a total of 350 million people at risk. Two million new cases (1.5
million for Cutaneous leishmaniasis and 500,000 for visceral leishmaniasis) are considered to
occur annually. More than 90% of the visceral cases in the world are reported from Bangladesh,
Brazil, Sudan, and India. In India, the state of Bihar accounts for more than 90% of the total
cases. The research aims at discovering novel lead candidates from Indian medicinal plants for
the treatment of leishmaniasis that can be further developed in affordable drugs. Moreover,
6
structure function and folding studies of trypanothione reductase, a key enzyme of trypanothione
metabolism is also being investigated ( Biochemistry and Molecular Biology Reports, 2008, 41,
444-447; Current Trends in Biotechnology and Pharmacy. 2008, 2, 390-395).
7