@article { ISI:000287627200012, title = {Single nucleotide polymorphism in transcobalamin II (15V) induces structural changes in the protein as revealed by molecular modeling studies}, journal = {Biochemistry}, volume = {50}, number = {8}, year = {2011}, month = {MAR}, pages = {1396-1402}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Cobalamin is an essential micronutrient in mammals. Deficiencies of this micronutrient have been implicated as risk factors for various complex diseases. Cobalamin is transported to the cells by the transport protein transcobalamin II (TCII), and hence genetic variations (like single nucleotide polymorphisms) in TCII could be perceived to affect the binding of cobalamin to TCII, thereby modulating the intracellular concentrations of cobalamin. To understand whether three nonsynonymous mutations in TCII (I5V, P241R, and R381Q) alter the structure of the protein which could potentially affect cobalamin binding, we performed molecular dynamics simulation in silico. Superimposition of active sites of the four simulated models (wild type and three variants) with the human TCII crystal structure revealed that the distance between the N epsilon nitrogen atom of His-173 and the cobalt ion of cobalamin deviated considerably in the I5V model as compared to wild type and other variants. His-173 directly coordinates with the cobalt ion of cobalamin. Further, from our dynamic cross-correlation and principal component analysis it appears that in the I5V model the beta-domain moves apart from the alpha-domain creating a wide gap between the two domains. This might facilitate the initial binding of cobalamin in the I5V model as cobalamin enters the binding site through the gap between the two domains. These observations were not found in the other variants. We thus speculate that binding of cobalamin will be more facile in the I5V variant.

}, issn = {0006-2960}, doi = {10.1021/bi101095g}, author = {Silla, Yumnam and Chandamouli, Balasubramanian and Maiti, Souvik and Sengupta, Shantanu} } @article { ISI:000355317200045, title = {Selective inhibition of miR-21 by phage display screened peptide}, journal = {Nucleic Acids Research}, volume = {43}, number = {8}, year = {2015}, month = {APR}, pages = {4342-4352}, publisher = {OXFORD UNIV PRESS}, address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND}, abstract = {

miRNAs are nodal regulators of gene expression and deregulation of miRNAs is causally associated with different diseases, including cancer. Modulation of miRNA expression is thus of therapeutic importance. Small molecules are currently being explored for their potential to downregulate miRNAs. Peptides have shown to have better potency and selectivity toward their targets but their potential in targeting and modulating miRNAs remain unexplored. Herein, using phage display we found a very selective peptide against pre-miR-21. Interestingly, the peptide has the potential to downregulate miR-21, by binding to pre-miR-21 and hindering Dicer processing. It is selective towards miR-21 inside the cell. By antagonising miR-21 function, the peptide is able to increase the expression of its target proteins and thereby increase apoptosis and suppress cell proliferation, invasion and migration. This peptide can further be explored for its anti-cancer activity in vivo and may be even extended to clinical studies.

}, issn = {0305-1048}, doi = {10.1093/nar/gkv185}, author = {Bose, Debojit and Nahar, Smita and Rai, Manish Kumar and Ray, Arjun and Chakraborty, Kausik and Maiti, Souvik} } @article {43406, title = {Systematic evaluation of biophysical and functional characteristics of selenomethylene-locked nucleic acid-mediated inhibition of miR-21}, journal = {Biochemistry}, volume = {55}, year = {2016}, month = {DEC}, pages = {7023-7032}, abstract = {miRNAs constitute an important layer of gene regulation mediated by sequence-specific targeting of mRNAs. Aberrant expression of miRNAs contributes to a host of pathological states. Promoting cancer, miR-21 is upregulated in variety of cancers and promotes tumor progresion by suppressing a network of tumor suppressor genes. Here we describe a novel class of bicyclic RNA analogues, selenomethylene-locked nucleic acid (SeLNA), that display high affinity, improved metabolic stability, and increased potency for miR-21 inhibition. The thermal stability (T-m) for duplexes was increased significantly with incorporation of SeLNA monomers as compared to that of the unmodified DNA RNA hybrid. A comprehensive thermodynamic profile obtained by isothermal titration calorimetry revealed a favorable increase in the enthalpy of hybridization for SeLNA containing DNA and target RNA heteroduplexes. SeLNA modifications displayed remarkable binding affinity for miR-21 target RNA with a K-a of <= 1.05 x 10(8) M-1. We also observed enhanced serum stability for SeLNA RNA duplexes with a half-life of <= 36 h. These in vitro results were well correlated with the antisense activity in cancer cells imparting up to similar to 91\% inhibition of miR-21. The functional impact of SeLNA modifications on miR-21 inhibition was further gauged by investigating the migration and invasion characterisitics of cancer cells, which were drastically reduced to similar to 49 and similar to 55\%, respectively, with SeLNA having four such modifications. Our findings demonstrate SeLNA as a promising candidate for therapeutics for disease associated miRNAs.}, doi = {10.1021/acs.biochem.6b00895}, author = {Nahar, Smita and Singh, Amrita and Morihiro, Kunihiko and Moai, Yoshihiro and Kodama, Tetsuya and Obika, Satoshi and Maiti, Souvik} } @article {44188, title = {Superior HIV-1 TAR binders with conformationally constrained R52 arginine mimics in the Tat(48-57) peptide}, journal = {Chemmedchem}, volume = {13}, year = {2018}, month = {FEB }, pages = {220-226}, type = {Article}, abstract = {

We report a 100-fold increase in binding affinity of the Tat(48-57) peptide to HIV-1 transcriptional activator-responsive element (TAR) RNA by replacing Arg52, an essential and critical residue for Tat{\textquoteright}s specific binding, with (2S,4S)-4-guanidinoproline. The resulting Tat1M peptide is a far superior binder than Tat1M, a peptide containing another conformationally constrained arginine mimic, (2S,4S)-4-amino-N-(3-guanidinopropyl)proline, or even the control Tat peptide (CtrlTat) itself. Our observations are supported by circular dichroism (CD), isothermal titration calorimetry (ITC), gel electrophoresis and UV spectroscopy studies. Molecular dynamics simulations suggest increased interactions between the more compact Tat1M and TAR RNA, relative to CtrlTat. The CD signature of the RNA itself remains largely unchanged upon binding of the peptides. The Tat mimetics further have better cell uptake properties than the control Tat peptide, thus increasing their potential application as specific TAR-binding molecules.

}, keywords = {antiviral agents, arginine mimics, RNA, Tat peptide analogues, Tat-TAR binding}, issn = {1860-7179}, doi = {10.1002/cmdc.201700653}, author = {Bhosle, Govind S. and Kharche, Shalmali and Kumar, Santosh and Sengupta, Durba and Maiti, Souvik and Fernandes, Moneesha} }