DR. PRAMOD P. WANGIKAR
Associate Professor
Address:
Dept
of Chemical Engineering,
Indian
Powai,
Mumbai 400076
Phone: +91 22 2576 7232
Fax:
+91 22 2572 6895 OR +91
22 2572 3480
Email: pramodw{at}iitb.ac.ii
Academic Qualifications
Year Details of Degree
1995 Ph.D. in
Chemical and Biochemical Engineering
The
Thesis Topic: Tailoring Enzyme Function in Organic Media
Thesis Supervisor:
Prof. Jonathan S. Dordick
Ph.D. research included tailoring enzymes via
protein, solvent and catalyst engineering for biocatalytic applications under extreme
conditions such as in the presence of organic solvents, at high temperatures,
etc.
1991 Bachelor of Chemical Engineering (First Class with Distinction)
University Department of Chemical Technology,
Awards received
·
INAE Young Engineer Award, 2005.
·
G. R. Manudhane Excellence in Research Award, IIT
·
BOYSCAST fellowship (DST, Govt of India) to visit
·
DAE Young Scientist Award (Dept. of Atomic Energy, Govt. of
·
AICTE Career Award for Young Teachers (1998).
·
Fellowship from the National Institute of Health (
Current Research Activities:
A)
Bioinformatics: The wealth of biological data on genomics,
proteomics, structure, etc., has a vast amount of knowledge hidden in it. Our focus has been on deriving “new
biological knowledge” from this data by applying data-mining and statistical
tools. Our research can be further
classified in the following categories:
(i)
Application of computational geometry and data-mining tools in
structural biology: Pattern search in protein three dimensional structure database;
Pharmacophore discovery by geometric techniques.
(ii)
Uncovering of regulatory networks via simulation of dynamic gene
expression data.
(iii)
Apply systems science approach & integrate the biological data
available at different levels.
Development of virtual / in silico
cells.
B)
Physiologically Based
Pharmacokinetic Modeling: Physiologically based
pharmacokinetic (PBPK) models describe how foreign substances (e.g. drugs and
toxins) are processed in the body by absorption, distribution, metabolism, and
excretion (ADME). The tremendous growth of computational power and biological
knowledge create the context for innovative multi-scale modeling solutions that
can substantially improve guidance in toxicology and drug development. In our
modeling, we incorporate different scales ranging from the molecular level to
the fluid flow level to the physiological system level. Our research consists
of the following key sub-goals: (1) Molecular Level Models to predict
physicochemical and biochemical characteristics of drug molecules; (2) Fluid
Flow Models to account for variability due to blood perfusion in various
sub-populations. (3) System Level Models and Integration: We plan to model
whole-body physiological level phenomena and also account for the genetic
variability in different subpopulation types (e.g. SNPs affecting
transporters). The molecular level and fluid dynamics level information will be
integrated into the physiological level model using systems and feedback
control theory.
C)
Fermentation Modeling, monitoring
and control: Our current work is based on experimental and
theoretical analysis of rifamycin production using Amycolatopsis medittriane.
The work involves development of a kinetic model for growth, product
formation and substrate uptake. Model is
being developed for fermentation in a complex media that offers multiple
choices of carbon and nitrogen sources.
The model parameters are determined via a specially designed
experimental plan. Further, the model is
being applied in model based optimization, monitoring and control of the
fermentation process. This is with
academic as well as potential commercial interest in the production technology
for rifamycin. We have been applying
several novel optimization techniques for optimal productivity at the flask as
well as fermentor level. A similar
strategy is being applied to the fermentation of D-ribose using a transketolase
deficient strain of B. subtilis. The
modeling and optimization strategy being developed is general and can be
applied to any industrial fermentation process.
Professional Experience (in
reverse chronological order):
|
Sr. No |
Employer |
Position Held |
Duration |
|
1 |
Indian
|
Associate Professor |
March 2003-Present |
|
2 |
Indian
|
Assistant Professor |
December 1997 to March
2003 |
|
3 |
Indian
|
Assistant Professor |
July 1996 to December 1997 |
|
4 |
EnzyMed
Inc. ( |
Scientist |
May 1995 to July 1996 |
Current Strength of Research
Group (at IIT
·
M. Tech. Dissertation students: 2
·
M.Sc. senior project students: 2
·
B. Tech. Senior project students: 2
Contribution in new course
development: A new course / elective on
“Bioinformatics” was designed and offered to M.Tech. / Ph.D. students for the
first time in IIT Bombay in Spring 2001 semester. A similar course was offered as a six-day
“continuing education program” for the working professionals from industry and
academia in June 2001, which became extremely popular. The Continuing Education Program in
Bioinformatics has now been offered four times so far at IIT Bombay and has
been oversubscribed each time.
Research Experience at
EnzyMed Inc.,
Courses taught:
1. Bioinformatics (Graduate
level) www.che.iitb.ac.in/faculty/pw/cl662.htm
2. Modeling and simulation of
bioprocesses (Graduate level)
3. Biochemical engineering
(Graduate level)
4. Chemical Kinetics
(Undergraduate level, 3rd year)
5. Thermodynamics I (Undergraduate
level, 2nd year).
Research papers in Refereed
Journals.
1. Bapat, P. M., Padiyar, N. U., Dave, N. N., Dash, S., Bhartiya, S., Wangikar P. P. (2006) Model based optimization of substrate feeding recipe for Rifamycin fermentation. AICHE Journal, in press
2. Bapat, P. M., Das, D., Dave, N. N., Wangikar P. P. (2006) Phase shifts in the stoichiometry of rifamycin B fermentation and correlation with the trends in the parameters measured online. Journal of Biotechnology, in press DOI:10.1016/j.jbiotec.2006.06.014
3.
Joshi, S., Rana,
S., Wangikar, P. P., Durani, S. (2006)
Computational design of proteins stereochemically optimized in size, stability
and folding speed”, Biopolymers, in
press DOI: 10.1002/bip.20537
4.
Chandrasekaran, S., Bhartiya, S., Wangikar,
P.P. (2006) “Substrate specificity
of lipases in alkoxycarbonylation reaction: QSAR model development and
experimental validation”, Biotechnol. Bioeng., in press.
5.
Bapat, P. M., Sohoni, S. V., Moses, T. A., Wangikar
P. P. (2006) A cybernetic model to predict the effect of freely
available nitrogen substrate on rifamycin B production in complex media. Applied Microbiology and Biotechnology,
in press
6.
Bapat, P. M., Bhartiya, S., Venkatesh, K. V., Wangikar P. P. (2006) A structured kinetic model
to represent the utilization of multiple substrates in complex media during
rifamycin B fermentation. Biotechnol. Bioeng., ., 93,
779-790.
7.
Bapat, P. M., Nandy, S. K., Wangikar, P.
P., and K.V. Venkatesh (2006) “Quantification of metabolically
active biomass using Methylene Blue dye Reduction Test (MBRT): Measurement of
CFU in about 200 s” Journal of Microbiological Methods, 65, 107-116
8.
Tendulkar, A. V., Sohoni, M. A., Ogunnaike, B. and Wangikar, P. P. (2005) “A geometric
invariant-based framework for the analysis of protein conformational space” Bioinformatics,
21, 3622-3628
9.
Tendulkar, A. V., Joshi, A. A., Sohoni, M. A., and Wangikar, P.
P. (2004) “Clustering of Protein Structural Fragments Reveals
Modular Building Block Approach of Nature” J. Mol. Biol, 338, 611-629
10.
Bapat, P. M., Wangikar, P. P.
(2004) “Optimization of rifamycin B fermentation in shake flasks via a
machine-learning-based approach” Biotechnol.
Bioeng., 86, 201-208
11.
Das, P., Ganesh, A., and Wangikar, P. P.
(2004) “Influence of pretreatment for de-ashing of sugarcane bagasse on
pyrolysis products” Biomass Bioenergy, 445-457
12.
Tendulkar, A. V., Wangikar, P.P., Sohoni, M. A., Samant, V. V., Mone, C. Y. (2003)
“Parameterization and Classification of Protein Universe via Geometric
Techniques”. J. Mol. Biol, 334, 157-172.
13.
Wangikar, P.P., Tendulkar, A. V., Ramya, S.,
14.
Sureshkumar S. V., Phale P. S., Durani S., Wangikar,
P. P. (2003) “ A Combined Sequence
and Structure Analysis of the Fungal Laccase Family” Biotechnol. Bioeng.,
83, 386-394.
15.
Bapat, P. M., Kundu, S., Wangikar, P. P.
(2003) “An optimized method for Aspergillus
16.
Chandrasekaran, S., Wangikar, P.P. (2003) “Method for Lipase-Catalyzed Carbonate
Synthesis via One- and Two-Step Alkoxycarbonylation Reactions”, Biotechnol.
Prog., 19, 332-337.
17.
Bhunia , A., Durani, S., Wangikar, P. P.
(2001) “Horseradish Peroxidase Mediated Degradation of Dyes” Biotechnology and Bioengineering, 72, 562-567.
18.
Gandhi, N., Patil, N. S., Sawant, S., Joshi, J. B. Wangikar, P. P., Mukesh, D. (2001) “Lipase
Catalyzed Esterification” Catalysis
Reviews, 42 (4) 439-480.
19.
Wangikar, P. P., Michels, P.C., Clark, D.S. Dordick, J.S. (1997)
“Structure and Function of Subtilisin BPN’ Solubilized in Organic Solvents” J. Am. Chem. Soc., 119, 70-76
20.
Wangikar, P. P., Carmichael, D.,
21.
Wangikar, P. P., Rich, J.O., Clark, D.S., Dordick, J.S. (1995)
“Probing Enzymic
22.
Xu, Z. -F., Affleck, R.A., Wangikar, P. P.,
Suzawa, V.S., Dordick, J.S., Clark, D.S. (1994) “
23.
Wangikar, P. P., Graycar, T.P., Estell, D.A., Clark, D.S., Dordick,
J.S. (1993) “Protein and Solvent Engineering of Subtilisin BPN’ in Nearly Anhydrous Organic Media” J. Am. Chem. Soc. 115, 12231-12237.
24.
Dordick, J. S., Xu, Z-F, Wangikar, P. P.
(1992) “Enzyme Design for Non-aqueous Media” in Biocatalysis in
Non-conventional Media, eds. J. Tramper et al, Elsevier Science Publishers.
Full length papers in refereed conference
proceedings.
1.
Tendulkar, A.V., Ogunnaike, B. and Wangikar,
P. P. Gaussian Mixture Modeling of a-Helix subclasses: Structure and sequence variations. Accepted
in
2.
Xuan Tien Doan, Rajgopalan
Srinivasan, Bapat, P. M., Wangikar P. P. “Dynamic PCA for phase
identification of Rifamycin B fermentation in multi-substrate complex media”,
accepted in Advanced Control of Chemical Processes (ADCHEM)
List of
Sponsored projects undertaken:
|
Sr. No |
Sponsoring Agency (name of scheme, if any) |
Project Title |
Duration |
|
1 |
Council of Scientific and Industrial
Research: New Millenium Initiative in
Technology Leadership |
Development of Portable and versatile
Bioinformatics Software |
20-7-2002 to 20-7-2004 |
|
2 |
Ministry of Human Resources Development
(Thrust Areas Project) |
Development of Bio-Informatic Platform for
Organisation, Modelling and Stimulation of Gene Expression Data. |
17-5-2002 to 17-5-2005 |
|
3 |
Department of Science & Technology |
Application of Plant Peroxidases &
Laccases for removal of recalcitrant organic Chemicals and dyes from
Industrial Wastewater |
7-2-2000 to 7-10-2003 |
|
4 |
All |
CAREER AWARD for Young Teachers |
27-10-1998 to 27-10-2001 |
|
5 |
IRCC, IIT |
Development of Multiphase Bioreactors for
Contimuous Optical Resolution |
24-6-1998 to 24-6-2001 |
|
6 |
Board of Research in Nuclear Sciences (DAE
Young Scientist Award) |
Biocatalytic Synthesis of a Combinatorial
Library of Carbanates for drug discovery |
20-1-1998 to 20-1-2001 |
|
7 |
IRCC, IIT |
Seed Grant for Preliminary experiments to
complete the Proof of Principle Study |
2-4-1998 to 2-4-2001 |
Consultation Assignments
undertaken:
|
Sr. No |
Company Name |
Project
Title |
Start Date
to End date |
|
|
Ongoing
Projects |
|
|
|
1 |
Persistent
Systems Pvt Ltd. Pune |
To provide assistance in the area of
Bioinformatics |
5-2-2002 to
May 2003 |
|
2 |
Lupin Ltd., Tarapore |
Data-mining and pattern extraction from historic
fermentation data for development of soft-sensors. |
5-12-2002 to May 2003 |
|
|
Completed
Projects |
|
|
|
3 |
Orchid Chemicals & Pharm Ltd., Chennai |
Development of Biotechnology Activity |
20-4-2000 to 20-4-2001 |
|
4 |
Orchid Chemicals & Pharm Ltd., Chennai |
Development of new processes for production of
pharmaceuticals |
22-3-1999 to 22-3-2000 |
|
5 |
Ramakrishna Vidyut Ayurvedic Pharmacy |
Chemical Analysis of Mahabhringaraj Hair Oil |
1-1-2001 to 30-6-2001 |
|
6 |
Spectrum Ethers Ltd. |
Evaluation of Chemical Process |
19-8-1999 to 20-9-1999 |
Continuing Education
Programs (Workshops for working professionals) organized: http://www.che.iitb.ac.in/bioinformatics/shortcourse.htm
|
|
Topic of the workshop |
Duration |
Dates |
No. of participants |
|
1. |
Introduction to Statistical Design of Experiments. |
3 days |
April 25-27, 2005 |
15 |
|
2. |
Recent advances in fermentation and enzyme
technology |
3 days |
March 9-11, 2000 |
18 |
|
3. |
Recent advances in fermentation and enzyme
technology |
4 days |
Sept. 13-16,
2000 |
8 |
|
4. |
Bioinformatics |
6 days |
June
11-16, 2001 |
48 |
|
5. |
Bioinformatics (in-house course for Persistent
Systems Pvt. Ltd., Pune) |
2 days |
Oct 19-20.
2001 |
25 |
|
6. |
Bioinformatics |
6 days |
Nov. 26-
Dec. 1, 2001 |
50 |
|
7 |
Bioinformatics |
6 days |
May 6-11,
2002 |
35 |
|
8 |
Recent developments in fermentation and downstream
processing |
4 days |
Oct. 14-17, 2003 |
15 |
|
9 |
Bioinformatics |
6 days |
November 17-22, 2003 |
35 |