Dr. Uttam Pal, PhD - S. N. Bose National Centre for Basic Sciences - Project Scientist

Dr. Uttam Pal

PhD

S. N. Bose National Centre for Basic Sciences

Project Scientist

Kolkata, West Bengal | India

Main Specialties: Chemistry

Additional Specialties: Computational Chemistry

ORCID logohttps://orcid.org/0000-0003-2110-4610


Top Author

Dr. Uttam Pal, PhD - S. N. Bose National Centre for Basic Sciences - Project Scientist

Dr. Uttam Pal

PhD

Introduction

I develop the computational models of small molecules and chemical processes using quantum or classical mechanics. I also study the biomolecules such as proteins and nucleic acids and their interactions with small molecules. How the drug molecules work, how do they cease to work and how we can develop new drugs are the areas I am exploring through my research.

Primary Affiliation: S. N. Bose National Centre for Basic Sciences - Kolkata, West Bengal , India

Specialties:

Additional Specialties:

Research Interests:


View Dr. Uttam Pal’s Resume / CV

Metrics

Number of Publications

76

Publications

Number of Profile Views

646

Profile Views

Number of Article Reads

244

Reads

Number of PubMed Central Citations

65

PubMed Central Citations

Education

Jan 2011 - Aug 2016
Jadavpur University
Ph.D.
Aug 2008 - Jul 2010
University of Calcutta
M.Sc.
Jul 2005 - Jul 2008
Presidency University
B.Sc.

Experience

Jun 2018
Saha Institute of Nuclear Physics
Research Assistant
Nov 2016
CSIR-Indian Institute of Chemical Biology
Project Assistant
Feb 2011 - Feb 2016
CSIR-Indian Institute of Chemical Biology
DST-INSPIRE (Innovation in Science Pursuit for Inspired Research) Fellow
Jan 2011 - Jan 2011
Indian Institute of Chemical Biology CSIR
Junior Research Fellow (Council of Scientific & Industrial Research)
Jan 2011 - Jan 2011
CSIR-Indian Institute of Chemical Biology
CSIR-Junior Research Fellow
May 2009 - Jul 2009
Saha Institute of Nuclear Physics
Summer Intern
May 2009 - Jul 2009
Saha Institute of Nuclear Physics
Summer Intern
Jul 2018
SN Bose National Centre for Basic Sciences
Project Scientist

Top co-authors

Nakul C Maiti
Nakul C Maiti

Case Western Reserve University

13
Nakul Chandra Maiti
Nakul Chandra Maiti

Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB)

7
Biswadip Banerji
Biswadip Banerji

CSIR-Indian Institute of Chemical Biology

7
Sumit Kumar Pramanik
Sumit Kumar Pramanik

CSIR-Indian Institute of Chemical Biology

5
Samita Basu
Samita Basu

Saha Institute of Nuclear Physics

4
Dulal Senapati
Dulal Senapati

Jackson State University

3
Moumita Chatterjee
Moumita Chatterjee

University of Delaware

3
Sudeshna Sen
Sudeshna Sen

CSIR-Indian Institute of Chemical Biology

3
Snehasikta Swarnakar
Snehasikta Swarnakar

Indian Institute of Chemical Biology

3
Anupam Roy
Anupam Roy

Institute of Physics

3

Publications

76Publications

244Reads

65PubMed Central Citations

DNA Damage and Apoptosis Induction in Cancer Cells by Chemically Engineered Thiolated Riboflavin Gold Nanoassembly.

ACS Appl Mater Interfaces 2018 Feb 27;10(5):4582-4589. Epub 2018 Jan 27.

Department of Chemistry, Government General Degree College, Singur, Hooghly, West Bengal 712409, India.

View Article
February 2018
18 Reads
6.72 Impact Factor

Structural Insight of Amyloidogenic Intermediates of Human Insulin.

ACS Omega 2018 Feb;3(2):2452-2462

Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India.

View Article
February 2018
4 Reads

Mesoporous silica for drug delivery: Interactions with model fluorescent lipid vesicles and live cells.

J Photochem Photobiol B 2018 Jan 1;178:19-26. Epub 2017 Nov 1.

Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India.

View Article
January 2018
4 Reads
2.96 Impact Factor

CCDC 1493320: Experimental Crystal Structure Determination

Other ; Related Article: Supriya Das, Uttam Pal, Moumita Chatterjee, Sumit Kumar Pramanik, Biswadip Banerji, and Nakul C. Maiti|2016|J.Phys.Chem.A|120|9829|doi:10.1021/acs.jpca.6b10017 ; Abstract ; An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

https://doi.org/10.5517/ccdc.csd.cc1m3xm8

View Article
January 2018
3 Reads

Constrained Photophysics of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one in the Bioenvironment of Serum Albumins: A Spectroscopic Endeavour Supported by Molecular Docking Analysis.

J Fluoresc 2017 Jul 22;27(4):1547-1558. Epub 2017 Apr 22.

Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India.

View Article
July 2017
6 Reads
1.93 Impact Factor

Tamarixetin 3-O-β-d-Glucopyranoside from Azadirachta indica Leaves: Gastroprotective Role through Inhibition of Matrix Metalloproteinase-9 Activity in Mice.

J Nat Prod 2017 05 11;80(5):1347-1353. Epub 2017 May 11.

Department of Natural Products, National Institute of Pharmaceutical Education and Research , Kolkata 700032, WB, India.

View Article
May 2017
11 Reads
3.80 Impact Factor

CCDC 1400035: Experimental Crystal Structure Determination

Other ; Related Article: Biswadip Banerji, Moumita Chatterjee, Uttam Pal, Nakul Chandra Maiti|2016|J.Phys.Chem.A|120|2330|doi:10.1021/acs.jpca.6b01078 ; Abstract ; An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

https://doi.org/10.5517/ccdc.csd.cc1hzvfr

View Article
January 2017
3 Reads

Envisaging Structural Insight of a Terminally Protected Proline Dipeptide by Raman Spectroscopy and Density Functional Theory Analyses.

J Phys Chem A 2016 Dec 6;120(49):9829-9840. Epub 2016 Dec 6.

Structural Biology & Bio-informatics Division and ‡Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology ; 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.

View Article
December 2016
8 Reads
2.69 Impact Factor

Orientation of tyrosine side chain in neurotoxic Aβ differs in two different secondary structures of the peptide.

R Soc Open Sci 2016 Oct 5;3(10):160112. Epub 2016 Oct 5.

Structural Biology and Bioinformatics Division , Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.c. Mullick Road, Kolkata 700032 , India.

View Article
October 2016
11 Reads

A Novel Spirooxindole Derivative Inhibits the Growth of Leishmania donovani Parasites both In Vitro and In Vivo by Targeting Type IB Topoisomerase.

Antimicrob Agents Chemother 2016 10 23;60(10):6281-93. Epub 2016 Sep 23.

Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India

View Article
October 2016
14 Reads
1 PubMed Central Citation(source)
4.48 Impact Factor

Silver-catalysed azide-alkyne cycloaddition (AgAAC): assessing the mechanism by density functional theory calculations.

R Soc Open Sci 2016 Sep 14;3(9):160090. Epub 2016 Sep 14.

Structural Biology and Bioinformatics Division , CSIR-Indian Institute of Chemical Biology; 4 , Raja S.C. Mullick Road, Kolkata , India.

View Article
September 2016
7 Reads

Conformational selection underpins recognition of multiple DNA sequences by proteins and consequent functional actions.

Phys Chem Chem Phys 2016 Aug 18;18(31):21618-28. Epub 2016 Jul 18.

Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India.

View Article
August 2016
16 Reads
4.49 Impact Factor

Binding interaction of a gamma-aminobutyric acid derivative with serum albumin: an insight by fluorescence and molecular modeling analysis.

Springerplus 2016 19;5(1):1121. Epub 2016 Jul 19.

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal India.

View Article
August 2016
17 Reads

Molecular Details of Acetate Binding to a New Diamine Receptor by NMR and FT-IR Analyses.

J Phys Chem A 2016 Apr 8;120(15):2330-41. Epub 2016 Apr 8.

Organic & Medicinal Chemistry Division and ‡Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , 4, Raja S.C. Mullick Road, Kolkata 700032, India.

View Article
April 2016
11 Reads
2.69 Impact Factor

STATISTICAL INSIGHT INTO THE BINDING REGIONS IN DISORDERED HUMAN PROTEOME

The human proteome contains a significant number of intrinsically disordered proteins (IDPs). They show unusual structural features that enable them to participate in diverse cellular functions and play significant roles in cell signaling and reorganization processes. In addition, the actions of IDPs, their functional cooperativity, conformational alterations and folding often accompany binding to a target macromolecule. Applying bioinformatics approaches and with the aid of statistical methodologies, we investigated the statistical parameters of binding regions (BRs) found in disordered human proteome. In this report, we detailed the bioinformatics analysis of binding regions found in the IDPs. Statistical models for the occurrence of BRs, their length distribution and percent occupancy in the parent proteins are shown. The frequency of BRs followed a Poisson distribution pattern with increasing expectancy with the degree of disorderedness. The length of the individual BRs also followed Poisson distribution with a mean of 6 residues, whereas, percentage of residues in BR showed a normal distribution pattern. We also explored the physicochemical properties such as the grand average of hydropathy (GRAVY) and the theoretical isoelectric points (pIs). The theoretical pIs of the BRs followed a bimodal distribution as in the parent proteins. However, the mean acidic/basic pIs were significantly lower/higher than that of the proteins, respectively. We further showed that the amino acid composition of BRs was enriched in hydrophobic residues such as Ala, Val, Ile, Leu and Phe compared to the average sequence content of the proteins. Sequences in a BR showed conformational adaptability mostly towards flexible coil structure and followed by helix, however, the ordered secondary structural conformation was significantly lower in BRs than the proteins. Combining and comparing these statistical information of BRs with other methods may be useful for high-throughput functional annotation of proteins, drug target identification and drug discovery linking protein disorder.

https://doaj.org/article/bec0fdc262df461b87689bacecbcbd4d

View Article
January 2016
3 Reads

ORIGIN OF PROTEIN AGGREGATION: IDENTIFICATION OF SOME CHARACTERISTIC TRAITS IN STRUCTURED AND INTRINSICALLY DISORDERED PROTEINS

Proteins containing amyloidogenic regions are prone to form aggregates and undergo amyloidosis. Literature shows that both the structured and disordered proteins might be amyloidogenic. However, the amyloidogenic proteins differ from their non-amyloidogenic counterpart in various physicochemical properties and, therefore, based on these properties they can be categorized. Our analysis also indicated that the sequence composition and the physicochemical properties such as isoelectric point (pI), hydrophobicity, aliphatic index (AI) and instability index (II) of amyloidogenic and non-amylidogenic proteins differed in large extent. However, unique to our finding is that such differences appeared to be exclusive for intrinsically disordered proteins. Structured amyloidogenic proteins were found to be more similar to their non-amyloidogenic counterparts except for their sequence composition and the distribution of their isoelectric points. In this report, we have shown from the sequence analysis that the distinction between amyloidogenic and non-amyloidogenic proteins is much wider in case of disordered proteins than the structured proteins. Our finding also suggests why structured proteins that are amyloidogenic require drastic change in the solution condition to undergo amyloid formation. The results have implication in developing better algorithms for the detection and differentiation of amyloidogenic proteins.

https://doaj.org/article/4c8b85448fbc47c6b1788067d93ebf5c

View Article
January 2016
3 Reads

Binding interaction of a novel fluorophore with serum albumins: steady state fluorescence perturbation and molecular modeling analysis.

Springerplus 2015 24;4:548. Epub 2015 Sep 24.

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal India.

View Article
October 2015
4 Reads
1 PubMed Central Citation(source)

Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins.

PLoS One 2014 3;9(3):e89781. Epub 2014 Mar 3.

Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India.

View Article
January 2015
5 Reads
5 PubMed Central Citations(source)
3.23 Impact Factor

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines.

J Phys Chem A 2014 Feb 30;118(6):1024-30. Epub 2014 Jan 30.

Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology , 4, Raja S.C. Mullick Road, Kolkata 700032, India.

View Article
February 2014
5 Reads
3 PubMed Central Citations(source)
2.69 Impact Factor

pKa determination of D-ribose by Raman spectroscopy.

J Phys Chem B 2014 Jan 17;118(4):909-14. Epub 2014 Jan 17.

Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Council of Scientific and Industrial Research , 4, Raja S.C. Mullick Road, Kolkata 700032, India.

View Article
January 2014
14 Reads
1 PubMed Central Citation(source)

2,2'-diphenyl-3,3'-diindolylmethane: a potent compound induces apoptosis in breast cancer cells by inhibiting EGFR pathway.

PLoS One 2013 28;8(3):e59798. Epub 2013 Mar 28.

Division of Cancer Biology and Inflammatory Disorder, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, West Bengal, India.

View Article
January 2014
4 Reads
9 PubMed Central Citations(source)
3.23 Impact Factor

pKa Determination of d-Ribose by Raman Spectroscopy

The Journal of Physical Chemistry B

View Article
January 2014
3 Reads

Potent anticancer activity of cystine-based dipeptides and their interaction with serum albumins.

Chem Cent J 2013 May 24;7(1):91. Epub 2013 May 24.

Department of Chemistry, CSIR-Indian Institute of Chemical Biology, 4, Raja S,C, Mullick Road, Kolkata 700032, India.

View Article
May 2013
8 Reads
3 PubMed Central Citations(source)
2.19 Impact Factor

Melatonin inhibits matrix metalloproteinase-9 activity by binding to its active site.

J Pineal Res 2013 May 17;54(4):398-405. Epub 2013 Jan 17.

Drug Development Diagnostics and Biotechnology Division, Department of Physiology, Indian Institute of Chemical Biology, Kolkata, India.

View Article
May 2013
14 Reads
13 PubMed Central Citations(source)
9.60 Impact Factor

CHAPERONE ACTION OF CYCLOPHILIN ON LYSOZYME AND ITS AGGREGATE

Various protein aggregates are formed in cellular systems when partially misfolded/folded states of proteins are trapped in a certain conformation. It eventually leads to the formation of larger and more stable aggregates. In the aggregated state proteins are functionally inactive and they are often enriched with antiparallel β-strands as compared to the native state. It has been established that a closely neaten molecular chaperone activity helps many proteins to preserve their cellular function by maintaining the protein conformation in their functional states. Thus the action of chaperone helps the cell to sustain various stresses that otherwise cause an extensive protein denaturation and aggregation. Recently, our laboratory demonstrated that AdK which has an inherent tendency to form inactive soluble aggregates could be disaggregated by cyclophilin derived from L. donovani (LdCyp) in an isomerase-independent fashion and resulted reactivation. Investigation is continuing to evaluate its action on amyloid aggregates formed by lysozyme. In addition the self and co-aggregation process of cyclophilin has been studied by fluorescence and TEM measurements. To our surprise, we observed the formation of elongated and fine fibrils when lysozyme was co-incubated with cyclophilin. Cyclophiln itself did not form any detectable aggregates under similar condition; however, it showed potential to disaggregate amorphous aggregate of lysozyme. Computational analysis was further performed to describe the aggregation and disaggregation of the proteins and their amyloidogenic behavior.

https://doaj.org/article/b8f255f33b594cc2aade0dc33ce50738

View Article
January 2013
3 Reads

Novel anti-inflammatory activity of epoxyazadiradione against macrophage migration inhibitory factor: inhibition of tautomerase and proinflammatory activities of macrophage migration inhibitory factor.

J Biol Chem 2012 Jul 29;287(29):24844-61. Epub 2012 May 29.

Division of Infectious Diseases and Immunology, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India.

View Article
July 2012
11 Reads
15 PubMed Central Citations(source)
4.57 Impact Factor

Nickel(II)-Schiff base complex recognizing domain II of bovine and human serum albumin: spectroscopic and docking studies.

Spectrochim Acta A Mol Biomol Spectrosc 2012 Jun 25;92:164-74. Epub 2012 Feb 25.

Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India.

View Article
June 2012
5 Reads
5 PubMed Central Citations(source)
2.35 Impact Factor

Interaction of Merocyanine 540 with serum albumins: photophysical and binding studies.

J Photochem Photobiol B 2012 Mar 29;108:23-33. Epub 2011 Dec 29.

Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India.

View Article
March 2012
4 Reads
3 PubMed Central Citations(source)
2.96 Impact Factor

Synthesis and bio-evaluation of human macrophage migration inhibitory factor inhibitor to develop anti-inflammatory agent.

Bioorg Med Chem 2011 Dec 24;19(24):7365-73. Epub 2011 Oct 24.

Department of Infectious Diseases and Immunology, Indian Institute of Chemical Biology, 4 Raja S C Mullick Road, Jadavpur, Kolkata 700 032, West Bengal, India.

View Article
December 2011
22 Reads
6 PubMed Central Citations(source)
2.79 Impact Factor

Top co-authors

Nakul C Maiti
Nakul C Maiti

Case Western Reserve University

13
Nakul Chandra Maiti
Nakul Chandra Maiti

Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB)

7
Biswadip Banerji
Biswadip Banerji

CSIR-Indian Institute of Chemical Biology

7
Sumit Kumar Pramanik
Sumit Kumar Pramanik

CSIR-Indian Institute of Chemical Biology

5
Samita Basu
Samita Basu

Saha Institute of Nuclear Physics

4
Dulal Senapati
Dulal Senapati

Jackson State University

3
Moumita Chatterjee
Moumita Chatterjee

University of Delaware

3
Sudeshna Sen
Sudeshna Sen

CSIR-Indian Institute of Chemical Biology

3
Snehasikta Swarnakar
Snehasikta Swarnakar

Indian Institute of Chemical Biology

3
Anupam Roy
Anupam Roy

Institute of Physics

3

Following

Snehasikta Swarnakar
Snehasikta Swarnakar

Indian Institute of Chemical Biology